Source: UNIVERSITY OF CALIFORNIA, DAVIS submitted to
IMPROVING BARLEY AND WHEAT GERMPLASM FOR CHANGING ENVIRONMENTS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
TERMINATED
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
0224328
Grant No.
2011-68002-30029
Project No.
CA-D-PLS-2125-CG
Proposal No.
2015-01656
Multistate No.
(N/A)
Program Code
A3121
Project Start Date
Feb 1, 2011
Project End Date
Jan 31, 2017
Grant Year
2015
Project Director
Dubcovsky, J.
Recipient Organization
UNIVERSITY OF CALIFORNIA, DAVIS
410 MRAK HALL
DAVIS,CA 95616-8671
Performing Department
Plant Sciences
Non Technical Summary
Climate change is causing increased abiotic and biotic stresses on barley and wheat. Examples of the impact of climate change are numerous and include: increasing CO2 concentration reduces the ability of wheat to assimilate nitrates, higher temperatures result in changes in geographic distribution of pathogens, and altered precipitation patterns increase the likelihood of short-term crop failures and long-term production declines. These constraints, compounded by increasing demand for food, and increasing costs for fertilizer, water and other inputs, require a national breeding strategy that capitalizes on innovations in plant breeding. This project brings together the barley and wheat communities to mitigate the impact of climate change on barley and wheat production. Wheat and barley public breeding programs face similar challenges and use similar technologies. A Triticeae CAP will strengthen the integration of these research, breeding and education communities and avoid unnecessary duplications. The Triticeae CAP will evaluate a broad group of barley and wheat germplasm for disease resistance, water and nitrogen use efficiency, and yield. This germplasm will include the National Small Grains Core Collections for barley and wheat and specialized mapping, association mapping, and nested association mapping populations. The same germplasm will be characterized with thousands of molecular markers to identify the gene variants controlling the different traits. Molecular markers will then be used to accelerate the deployment of the best gene variants into commercial barley and wheat varieties. Improvements in disease resistance and water and nitrogen use efficiency will help mitigate the impact of environmental changes associated with climate change on barley and wheat productivity. An expanded centralized marker and trait database coupled with extensive analysis tools will empower breeders to efficiently identify beneficial alleles and effectively exploit large volumes of data in applied plant breeding. This integrated research project will provide a problem-based learning environment to train a new generation of plant breeders and attract new students to agricultural sciences. A nationally-coordinated plant breeding education network will be used to share expertise in different plant breeding areas in the training of 29 PhDs in plant breeding. Educational programs featuring problem-based learning, collaborations with Minority Serving Institutions and social networking technology will be developed to expand the human capital needed to train and sustain the next generation of plant breeders and to attract new students to agricultural sciences.
Animal Health Component
(N/A)
Research Effort Categories
Basic
50%
Applied
50%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011549108010%
2011550108010%
2021549108010%
2021550108010%
2011549108110%
2011550108110%
2031549108010%
2031550108010%
2121549108010%
2121550108010%
Knowledge Area
202 - Plant Genetic Resources; 212 - Pathogens and Nematodes Affecting Plants; 203 - Plant Biological Efficiency and Abiotic Stresses Affecting Plants; 201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1549 - Wheat, general/other; 1550 - Barley;

Field Of Science
1080 - Genetics; 1081 - Breeding;
Goals / Objectives
Climate change increases the negative impact of abiotic and biotic stresses on crop production. These constraints, compounded by increasing demand for food, and increasing costs for fertilizer, water and other inputs, require a national plan for innovative plant breeding and education. This project will change the paradigm of how we utilize germplasm resources for barley and wheat improvement from a view centered on the characterization of accessions to one centered on the discovery and deployment of valuable alleles. This project brings together the barley and wheat communities leveraging and building on the successful USDA-funded barley and wheat Coordinated Agricultural Projects (CAPs) through synergy in numerous areas. The Triticeae CAP will strengthen the integration of these research, breeding and education communities and avoid unnecessary duplications. The overall goals of the project are to phenotype and genotype diverse barley and wheat germplasm pools to discover and deploy alleles that improve yield under biotic and abiotic stresses, and to use genetic markers to rapidly deploy favorable alleles and accelerate breeding cycles. This integrated research project will provide a problem-based learning environment to train a new generation of plant breeders and attract new students to agricultural sciences. The specific objectives of this project are: 1) Discover and deploy beneficial alleles from diverse wheat and barley germplasm. 2) Accelerate breeding through marker-assisted selection and genomic selection.3) Implement sequence-based genotyping methodologies to discover new allelic diversity. 4) Implement web-based tools to integrate marker-assisted selection and genomic selection strategies into breeding programs. 5) Develop and implement a Plant Breeding Education Network. The expected outcomes of this project include: i) A well characterized barley and wheat germplasm collection. ii) New nested association mapping populations. iii) Eight association mapping studies. iv) Identification of novel alleles for biotic and abiotic resistance. v) New technologies to genotype large numbers of accessions at reduced costs. vi) Genotypic and phenotypic information for a large number of breeding lines. vii) Development of genotyping by sequencing technologies for barley and wheat. viii) An expanded centralized marker and trait database that serves wheat and barley breeders. ix) New tools for the breeders to analyze marker and trait datasets. x) Marker-assisted selection and genomic selection approaches to reduce the length of breeding cycles, xi) New barley and wheat germplasm and varieties better adapted to changing environments, xii) 29 well trained Ph.D. student in plant breeding. xiii) More undergraduate students interested in plant breeding and agricultural sciences. xiv) A national network to train plant breeders. xv) New collaborations with Minority Serving Institutions. These outcomes will strengthen the national network of barley and wheat public breeding programs and ameliorate the negative impacts of climate change on US food security.
Project Methods
The methods used in this project are described by individual objectives Methods for objective 1. Discover and deploy beneficial alleles from diverse wheat and barley germplasm. Experienced barley and wheat breeders will provide standardized field-based evaluations of biotic and abiotic stress tolerance for the barley and wheat National Small Grain Core Collections, specialized genetic stocks and mapping, association mapping, and nested association mapping (NAM) populations. They will characterize this germplasm for yield, water and nitrogen use efficiency, and disease resistance. All germplasm will be genotyped at the USDA-ARS genotyping labs with high-throughput SNP platforms. The generated datasets will be used to identify valuable alleles that will be employed to mitigate negative impacts of climate change. Methods for objective 2. Accelerate breeding through marker-assisted selection and genomic selection. Markers linked to favorable alleles will be deployed in the public barley and wheat breeding programs using different SNP platforms. Forty-eight-SNP platforms will be used for marker-assisted selection, and 384- and 9,000-SNP platforms will be used to implement and evaluate genomic selection approaches. Methods for objective 3. Implement genotyping by sequencing (GBS) methodologies to discover new allelic diversity. We will test and implement two genome complexity-reduction methods: sequence capture using oligonucleotide baits and restriction digestion of genomic DNA. GBS polymorphisms will be added to SNP genetic maps in both wheat and barley. GBS will be also used to genotype the barley and wheat founders of the NAM populations as well as the wheat NAM populations. Multiplexing levels will be optimized to minimize costs while ensuring robust allele calls. Methods for objective 4: Implement web-based tools to integrate marker-assisted selection and genomic selection strategies into breeding programs. We will expand "The Hordeum Toolbox" to wheat and develop protocols for analyzing genotype, phenotype and pedigree data to integrate genomics information with plant improvement. The theoretical framework and the web-based tools will be developed to help breeders implement marker-assisted selection and genomic selection in breeding programs and to integrate data across programs. Methods for objective 5: Develop and implement a Plant Breeding Education Network. We will: 1) actively recruit students to agricultural sciences by building collaborations with minority serving institutions and providing curriculum support with a problem based learning approach and 2) create and implement a Plant Breeder Training Network, a collaborative learning community bringing together the public and private sector to train undergraduates and graduate students. This project will train 29 plant breeders and provide multiple opportunities for graduate and undergraduate students to participate in laboratory and field activities, workshops, and student symposia. Education and scientific advisory committees, professional educational evaluators, and an industry liaison committee will evaluate progress in the different objectives.

Progress 02/01/11 to 01/31/17

Outputs
Target Audience:The audiences targeted by this project include barley and wheat researchers, breeders (public and private), growers and members of the barley and wheat industry. The applied results of this project have been presented to wheat and barley researchers in scientific meetings and to wheat and barley growers and members of the wheat industry at field days, farm advisors meetings, and industry collaborators meetings. Results have been also made available through dedicated web pages. Our efforts directly reach the barley and wheat growers and industry by releasing improved varieties that cover roughly 8.5 million acres. This last number documents well the large audience reached by the TCAP project and the economic impact of this grant to the wheat industry and the US agriculture. The targeted audience is further expanded when public wheat and barley varieties are used by the milling, baking, malting, and brewing industries that contribute additional jobs and value to the economy. Private breeding companies are also part of the audience of this project since they routinely use public varieties in their crossing blocks, transferring part of this value to the private sector and further multiplying the economic benefits of the public breeding activities. The international wheat and barley research communities had access to the new association mapping and sequencing information through publications in peer-reviewed journals, presentations in national and international conferences, and sequences deposited in GenBank and T3. Since the last report, TCAP participants published 38 new peer reviewed scientific articles. Publications from the six years of the project have been cross-referenced 6,314 times (average 22 times per publication) documenting the impact of TCAP research. In addition, 17 new cultivars and 5 new germplasm were released during the sixth year of the project. All the genotypic and phenotypic data generated by the TCAP project are well organized and safely stored in the T3 database. This database works in close collaboration with GrainGenes. The T3 database is also providing the tools to retrieve and analyze this valuable information and has accelerated the time from data collection to data availability in a public form. The information of molecular markers for new disease resistance genes, nitrogen use efficiency genes and drought tolerance genes identified and mapped in this project reach a wide national and international audience of barley and wheat breeders. They incorporate these beneficial alleles into their own varieties, which limits applications of costly fungicides and reduces the need for N fertilization, increasing growers' profitability and benefiting the environment. To facilitate access to the new molecular markers for different traits, we incorporate detailed protocols to the publicly available MASWheat website (http://maswheat.ucdavis.edu/protocols/). In the education area the targeted audience included graduate and undergraduate students as well as students from Minority Serving Institutions (MSIs). The online communication tools developed by PBTN have reduced the isolation of students placed in smaller institutions and have increased collaboration among students. The PBTN tools are used by breeding programs and students around the globe and the platform has been adopted by other crop species in the USA. All graduated students (except one that took a year off to write) are working in industry or academia, documenting the demand for TCAP students. The online PBTN environment was used to deliver webinars and courses further expanding the audience of this project. Graduate students participated in a face-to-face workshop in collaboration with industry, and in a poster session at PAG. Undergraduate students were supported through online meetings. TCAP supported attendance of students at the National Association of Plant Breeders Meeting and to PAG. PBTN has provided an excellent communication tool for the project. Information about research and education was shared both internally and externally through TCAP seminar series, quarterly newsletters and meetings at PAG. Evaluation tools were refined; surveys and interviews were performed; and evaluation reports were created. Evaluation information was used to produce talks, posters and papers. This project brings together the barley and wheat communities into a Coordinated Agricultural Project to mitigate the impact of climate change on barley and wheat production by strengthening the integration of these communities and avoiding unnecessary duplications. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Education accomplishments TCAP The extensive resources invested by TCAP in student training, and the coordinated activities developed by the PBTN at a national level have resulted in a well-trained and well-integrated workforce. The online communication tools developed by PBTN have reduced the isolation of students placed in smaller institutions and have increased collaboration among students. The PBTN tools are used by breeding programs and students around the globe and the platform has been adopted by other crop species in the USA. A total of 56 graduate students completed their programs (10 MS and 46 PhD. Proposal target was 30). All graduated students (except one that took a year off to write) are working in industry or academia, documenting the demand for TCAP students (see also industry letters in Appendix 1). Ten additional graduate students that started later are expected to graduate by 2017 (96% expected graduation rate). Evaluation of the TCAP educational program by education experts has shown that TCAP students have a broader perspective of plant breeding than students outside the program. This group of students will provide the continuity and leadership required for sustainable plant breeding activities in the US. An economic impact analysis of the TCAP education program concluded that the future return to the plant breeding sector will be $1.11 to $2.50 for every $1 invested (using conservative assumptions). How have the results been disseminated to communities of interest?Results for this project have been diseminated through 287 scientific articles that have been crossreferenced 6314 times documenting their high impact. The applied results of this project have been presented to wheat and barley researchers in scientific meetings and to wheat and barley growers and members of the wheat industry at field days, farm advisors meetings, and industry collaborators meetings. Results have been also made available through dedicated web pages.Our efforts directly reach the barley and wheat growers and industry by releasing improved varieties that cover roughly 8.5 million acres. The international wheat and barley research communities had access to the new association mapping and sequencing information through publications in peer-reviewed journals, presentations in national and international conferences, and sequences deposited in GenBank and T3. To facilitate access to the new molecular markers for different traits, we incorporate detailed protocols to the publicly available MASWheat website . What do you plan to do during the next reporting period to accomplish the goals?A No Cost Extension for one year was completed in 2016. A new WheatCAP grant was prepared and submitted to USDA and was approved for funding. The TCAP will transition to the new grant WheatCAP with a similar team and the incorporation of several new young researchers.

Impacts
What was accomplished under these goals? Research accomplishments TCAP Genotyping: TCAP developed iSelect 9,000 SNP chips for barley and wheat and an iSelect 90,000 SNP chip for wheat. These SNP platforms were used to genotype the complete core collections of barley and wheat at the USDA National Small Grain Collection. The added value of this information is attracting breeders and researchers to utilize this germplasm in their programs. The same SNP platforms were used to genotype multiple association mapping panels and biparental populations in barley and wheat (spring and winter), which were the basis of several published GWAS and QTL mapping studies. Genotyping by sequencing (GBS) was tested and GBS bioinformatics pipelines were established. This technology generates thousands of polymorphic GBS tags and is being used to develop high-density maps of NAM populations. The low cost of GBS has also favored the implementation of genomic selection programs. TCAP enhanced the integration of USDA Genotyping laboratories and public breeding programs. The number of GBS markers increased dramatically to 636 million in wheat. In collaboration with Nimblegen, TCAP developed exon capture platforms for barley and wheat. The first wheat platform was based on low copy number regions and was used mainly for genetic diversity studies and SNP identification. The second platform, based on 286,799 exons from 82,511 genes, was used to identify SNPs in 12 parental lines of the NAM populations, and to identify ten million mutations in 2,700 tetraploid and hexaploid lines mutagenized with EMS from previously developed TILLING populations (King et al. 2015; Uauy et al. 2009). This last resource is providing loss-of-function mutations for most wheat genes (see answer to question 5 for a detailed description). Phenotyping: TCAP tested and implemented canopy spectral reflectance (CSR) protocols in the US barley and wheat public breeding programs. Breeders were able for the first time to see plants in the far red range! This technology was used to evaluate the National Small Grain Collection (NSGC) core collections of barley and wheat, and multiple AM and NAM populations. The water and N status of thousands of lines was evaluated using normalized indexes. These indexes were analyzed in GWAS populations and multiple QTL were identified. Several have been validated in the NAM populations. Lines with the best water and nitrogen use efficiency are being incorporated into the breeding programs' crossing blocks. Different allelic variants of the Grain Protein Content 1 (GPC-1) have been incorporated into wheat and barley commercial varieties. Some breeding programs are incorporating CSR indexes for indirect yield selection. All the phenotypic data is stored in T3. The Triticeae toolbox database (T3): extensive phenotypic and genotypic datasets were incorporated into T3. For wheat, T3 currently includes 164 million genotype data, 636 million GBS markers, 440,000 phenotypic data for 147 traits, 334 phenotype trials, and 13,720 line records. T3 has an intuitive interface, extensive tutorials and hyperlinks to other databases. T3 now uses two-dimensional "materialized view" tables to provide quicker access. T3 has implemented useful tools to query the genotypic and phenotypic data, to perform GWAS analysis, and to provide meta analyses of QTL data for all agronomic and morphological traits. Over the past year (Sept. 1, 2015 to Aug. 31, 2016) 5,955 unique visitors from within the United States used T3, representing a 16% increase from the previous year. T3 has also become an increasingly important source of information internationally. Over the past year, 6,251 unique non-United States visitors used T3. Major visit origination countries were Canada, United Kingdom, Germany, Australia, and China. This past year represented the first time that T3 received more international visits than domestic visits as international traffic increased by 52.0% over the previous year. Population development: An important legacy of TCAP is the development of publicly-available and fully genotyped AM panels, NAM populations, a wild barley introgression population, and several biparental populations. These genetic resources have been genotyped using the iSelect SNP chips, GBS and exon-capture, providing valuable tools for the rapid identification of associations between molecular markers and traits. Publications: Scientific knowledge was disseminated through 283 peer reviewed articles that were referred 5,674 times during the five years of the project. These included publications in Science, Nature, Nature Genetics, PNAS, Plant Cell, Genome Biology, etc. Varieties and Germplasm: TCAP coPIs released 82 commercial varieties and 98 improved germplasm. An economic study based on 2012 data estimated that $17.2 million per year were added to current barley and wheat varieties by CAP projects. A survey of the acreage of wheat and barley varieties planted in 2014 in the US showed that varieties released by the barley and wheat CAPs covered 8.5 million acres documenting the economic impact of this grant to the wheat industry and the US agriculture. WheatCAP and TCAP Awards: The WheatCAP program received the 2007 USDA-NRI "Discovery Award" for best research program and the 2011 U.S. Department of Agriculture (USDA) Secretary's Honor Award. The TCAP received the USDA-NIFA Partnership Award. Members of the TCAP group received the Wolf Prize in Agriculture (J. Dubcovsky), the Lifetime Achievement Award from the National Association of Plant Breeders (S. Baenziger), and the Plant Breeding Impact Award (B. Carver) for projects associated with the two CAP grants.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Baenziger, P. S., R. A. Graybosch, T. Regassa, R. N. Klein, G. R. Kruger, D. K. Santra, L. Xu, D. J. Rose, S. N. Wegulo, Y. Jin, J. Kolmer, G. L. Hein, M.-S. Chen, G. Bai, R. L. Bowden and J. Poland. 2016. Registration of NE05548 (Husker Genetics Brand Panhandle) Hard Red Winter Wheat. J. Plant Registrations. 10:276-282
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Bajgain, P., M.N. Rouse, and J.A. Anderson. 2016. Comparison between genotyping by sequencing and SNP-chip genotyping for QTL mapping in wheat. Crop Sci. 56: 117.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Bajgain, P., M.N. Rouse, T.J. Tsilo, G.K. Macharia, S. Bhavani, Y. Jin Y, and J.A. Anderson. 2016. Nested association mapping of stem rust Rrsistance in wheat using genotyping by sequencing. PLoS ONE 11(5): e0155760.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Bulli, P., J. Zhang, S. Chao, X. Chen, and M. Pumphrey. 2016. Genetic architecture of resistance to stripe rust in a global winter wheat germplasm collection. G3: doi: 10.1534/g3.116.028407
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Checovich, M. L., A. Galatro, J. Moriconi, M. Simontacchi, J. Dubcovsky, G. E. Santa-Mar�a. 2016. The stay-green phenotype of TaNAM-RNAi wheat plants is associated with maintenance of chloroplast structure and high enzymatic antioxidant activity. Plant Physiology and Biochemistry. 104: 257-265
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Chen, J., M. J. Guttieri, J. Zhang, D. Hole, E. Souza, and B. Goates. A novel QTL associated with dwarf bunt resistance in Idaho 444 winter wheat. Theor Appl Genet. 129:2313-2322.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Cruz, C.D., G.L. Peterson, W.W. Bockus, P. Kankanala, J. Dubcovsky, K.W. Jordan, E. Akhunov, F. Chumley, D.F. Baldelomar, and B. Valent. 2016. The 2NS translocation from Aegilops ventricosa confers resistance to the Triticum pathotype of Magnaporthe oryzae. Crop Science 56:9901000.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Froese, P.S., A.H. Carter (2016) Single nucleotide polymorphisms in the wheat genome associated with tolerance of acidic soils and aluminum toxicity. Crop Science 56:1662-1677
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Froese, P.S., T.D Murray, A.H Carter (2016) Quantitative Cephalosporium stripe disease resistance mapped in the wheat genome. Crop Science: 56:1586-1601
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Gao, L., J. Kielsmeirer-Cook, P. Bajgain, X. Zhang, S. Chao M.N. Rouse, and J.A. Anderson. 2015. Development of genotyping by sequencing (GBS) and array derived SNP markers for stem rust resistance gene Sr42. Mol. Breeding 35:207
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Gao, L., M.K. Turner, S. Chao, J. Kolmer, and J.A. Anderson. 2016. Genome wide association study of seedling and adult plant leaf rust resistance in elite spring wheat breeding lines. PLoS ONE 11: e0148671.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Gizaw S.A., K. Garland-Campbell K, A.H. Carter (2016) Use of spectral reflectance for indirect selection of yield potential and stability in Pacific Northwest winter wheat. Field Crops Research196:199-206.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Gizaw S.A., K. Garland-Campbell K, A.H. Carter (2016) Evaluation of agronomic traits and spectral reflectance in Pacific Northwest winter wheat under rain-fed and irrigated conditions. Field Crops Research 196:168-179.
  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Grogan, S.M. J. Anderson, P.S. Baenziger, K. Frels, M.J. Guttieri, S.D. Haley, K.-S. Kim, S. Liu, G.S. McMaster, M. Newell, P.V. Vara Prasad, S.D. Reid, K.J. Shroyer, G. Zhang, E. Akhunov, and P.F. Byrne. 2016. Phenotypic plasticity of winter wheat heading date and grain yield across the U.S. Great Plains. Crop Science 56:1-44.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Grogan, S.M., G. Brown-Guedira, S.D. Haley, G.S. McMaster, S.D. Reid, J. Smith, P.F. Byrne. 2016. Allelic variation in developmental genes and effects on winter wheat heading date in the U.S. Great Plains. PLOS ONE 11: e0152852
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Haas, M., Menke, J., Chao, S., Steffenson, B. J. 2016. Mapping quantitative trait loci conferring resistance to a widely virulent isolate of Cochliobolus sativus in wild barley accession PI 466423. Theor. Appl. Genet. 129:1831-1842.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Hoffstetter, A., A. Cabrera, and C. Sneller. 2016 Identifying quantitative trait loci for economic traits in an elite soft red winter wheat cultivar development population. Crop Sci. 56:547-558.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Hoffstetter, A.L., A. Cabrera, M. Huang, and C. Sneller. 2016. Optimizing training population data and validation of genomic selection for economic traits in soft winter wheat. G3 doi: 10.1534/g3.116.032532
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Huang, M., A. Cabrera, and C. Sneller. 2016. Genomic selection for wheat traits and trait stability. Theor. Appl. Genet. 129:1697-1710.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Leng, Y., R. Wang, S. Ali, M. Zhao, S. Zhong. 2016. Sources and genetics of spot blotch resistance to a new pathotype of Cochliobolus sativus in a USDA barley core collection. Plant Disease. 100: 1988-1993
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Li, K., J. Hegarty, C. Zhang, A. Wan, J. Wu, G.Brown-Guedira, X. Chen, M. Mu�oz-Amatria�n, D. Fu , and J. Dubcovsky. 2016. Fine mapping of barley locus Rps6 conferring resistance to wheat stripe rust. Theor Appl Genet. 129:845-859.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Mascher, M., V.J. Schunemann, U. Davidovich, A. Himmelbach, S. Hubner, T. Fahima, A. Korol, M. David, N. Marom, S. Riehl, M. Schreiber, S.H. Vohr, R.E. Green, I.K. Dawson, J. Russell, B. Kilian, G.J. Muehlbauer, R. Waugh, J. Krause, E. Weiss and N. Stein. 2016. Genomic evidence from 6000-year old grains sheds new light on barley domestication history. Nature Genetics 48:1089-1093
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Narayanan, S., P.V.V. Prasad, R. Welti. 2016. Wheat leaf lipids during heat stress: II. Lipid experiencing coordinated metabolism are detected by analysis of lipid co-occurrence. Plant Cell and Environment. 39:608-617.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Narayanan, S., P. Tamura, M. Roth, P.V.V. Prasad, R. Welti. 2016. Wheat leaf lipids during heat stress: I. High day and night temperatures results in major lipid alternations. Plant Cell and Environment. 39:787-803.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Naruoka, Y., K. Ando, P. Bulli, K. T. Muleta, S. Rynearson, and M.O. Pumphrey. 2016. Identification and validation of SNP markers linked to the stripe rust resistance gene Yr5 in wheat. Crop Science. 56: 3055-3065.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Nasseer, A. M., J. M. Martin, H.-Y. Heo, N. K. Blake, J. D. Sherman, M. Pumphrey, K. D. Kephart, S. P. Lanning, L. E. Talbert. 2016. Impact of a quantitative trait locus for tiller number on plasticity of agronomic traits in spring wheat. Crop Sci. 56:595-602.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Nice, L.M., B.J. Steffenson, G.L. Brown Guedira, E.D. Akhunov, T.J.Y. Kono, P.L. Morrell, R. Horsley, K.P. Smith and G.J. Muehlbauer. 2016. Development and genetic characterization of an advanced backcross  nested association mapping (AB-NAM) population of wild � cultivated barley. Genetics 203:1453-1467.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Nirmala, J., S. Chao, P. Olivera, B. Abeyo, M. Imtiaz, E. Akhunov, M.O. Pumphrey, Y. Jin and M.N. Rouse. 2016. Markers linked to wheat stem rust resistance gene Sr11 effective to Puccinia graminis f. sp. tritici race TKTTF. Phytopathology. 106:1352-1358.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Richards, J., Chao, S., Friesen, T.L., Brueggeman R. 2016. Fine mapping of the barley chromosome 6H net form net blotch susceptibility locus. G3. 6:1809-1818.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Russell, J., M. Mascher, I.K. Dawson, S. Kyriakidis, C. Calixto, F. Freund, M. Bayer, I. Milne, T. Marshall-Griffiths, S. Heinen, A. Hofstad, R. Sharma, A. Himmelbach, M. Knauft, M. van Zonneveld, J.W.S. Brown, K. Schmid, B. Kilian, G.J. Muehlbauer*, N. Stein and Robbie Waugh. 2016. Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. Nature Genetics 48:1024-1030
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Sch�nhofen, A., B. Hazard, X. Zhang, and J. Dubcovsky. 2016. Registration of common wheat germplasm with mutations in SBEII genes conferring increased grain amylose and resistant starch content. J. Crop Reg. 10:200-205.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Simmonds, J., P. Scott, J. Brinton, T.C. Mestre, M. Bush, A. Del Blanco, J. Dubcovsky, C. Uauy. 2016 A splice acceptor site mutation in TaGW2-A1 increases thousand grain weight in tetraploid and hexaploid wheat through wider and longer grains Theor Appl Genet. 129:10991112.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Turner, M.K, Y. Jin, M.N. Rouse, and J.A. Anderson. 2016. Stem rust resistance in Jagger winter wheat. Crop Sci. 56:17.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Varella, A. C., L. E. Talbert, M. L. Hofland, M. Buteler, , J. D. Sherman, N. K. Blake, H.Y. Heo, J. M. Martin, D. K. Weaver. 2016. Temporal patterns of pith expression and retraction in wheat stems and its effect on resistance to the wheat stem sawfly. Plant Breeding, 135:546-551.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Wang, R., Y. Leng, S. Shrestha, and S. Zhong. 2016. Coordinated and independent functions of velvet-complex genes in fungal development and virulence of the fungal cereal pathogen Cochliobolus sativus. Fungal Biology 120:948-960.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: 38. Wang, X., B. Yang, K. Li, Z. Kang, D. Cantu, J. Dubcovsky. Conserved Puccinia striiformis effector interacts with wheat NPR1 and reduces induction of Pathogenesis-Related genes in response to pathogens. Mol. Plant Microbe Int. http://dx.doi.org/10.1094/MPMI-10-16-0207-R.


Progress 02/01/15 to 01/31/16

Outputs
Target Audience:The audiences targeted by this project include barley and wheat researchers, breeders (public and private), growers and members of the barley and wheat industry. The applied results of this project have been presented to wheat and barley researchers in scientific meetings and to wheat and barley growers and members of the wheat industry at field days, farm advisors meetings, and industry collaborators meetings. Results have been also made available through dedicated web pages. Our efforts directly reach the barley and wheat growers and industry by releasing improved varieties. A survey of the acreage of wheat and barley varieties planted in 2014 in the US showed that varieties released by the barley and wheat CAPs covered 8.5 million acres. This last number documents well the large audience reached by the TCAP project and the economic impact of this grant to the wheat industry and the US agriculture. The targeted audience is further expanded when public wheat and barley varieties are used by the milling, baking, malting, and brewing industries that contribute additional jobs and value to the economy. Private breeding companies are also part of the audience of this project since they routinely use public varieties in their crossing blocks, transferring part of this value to the private sector and further multiplying the economic benefits of the public breeding activities. The international wheat and barley research communities had access to the new association mapping and sequencing information through publications in peer-reviewed journals, presentations in national and international conferences, and sequences deposited in GenBank and T3. Since the last report, TCAP participants published 71 new peer reviewed scientific articles. Publications from the first five years of the project have been cross-referenced 3,483 times documenting the impact of TCAP research. In addition, 16 new cultivars and 34 new germplasm were released during the fifth year of the project. All the genotypic and phenotypic data generated by the TCAP project are well organized and safely stored in the T3 database. This database works in close collaboration with GrainGenes. The T3 database is also providing the tools to retrieve and analyze this valuable information and has accelerated the time from data collection to data availability in a public form. The information of molecular markers for new disease resistance genes, nitrogen use efficiency genes and drought tolerance genes identified and mapped in this project reach a wide national and international audience of barley and wheat breeders. They incorporate these beneficial alleles into their own varieties, which limits applications of costly fungicides and reduces the need for N fertilization, increasing growers' profitability and benefiting the environment. To facilitate access to the new molecular markers for different traits, we incorporate detailed protocols to the publicly available MASWheat website (http://maswheat.ucdavis.edu/protocols/). In the education area the targeted audience included graduate and undergraduate students as well as students from Minority Serving Institutions (MSIs). Funding of MSIs continued and new funding sources to increase diversity were explored through a collaborative grant writing group during the fifth year of the project. A total of 148 graduate students participated in PBTN. A total of 108 graduate students were directly mentored by TCAP PIs, and of those, 71 were at least partially funded by TCAP, with five of those at MSIs. A total of 26 students already graduated and 11 more will graduate in 2015. We anticipate that 16 will graduate in 2016 and 3 in 2017. TCAP has trained 115 undergraduates, with 75 mentored by TCAP faculty and graduate students, and 40 by faculty from Minority Serving Institutions (MSIs). TCAP researchers have trained 29 postdocs. The online PBTN environment was used to deliver webinars and courses further expanding the audience of this project. Graduate students participated in a face-to-face workshop in collaboration with industry, and in a poster session at PAG. Undergraduate students were supported through online meetings. TCAP supported attendance of students at the National Association of Plant Breeders Meeting and to PAG. PBTN has provided an excellent communication tool for the project. Information about research and education was shared both internally and externally through TCAP seminar series, quarterly newsletters and meetings at PAG. Evaluation tools were refined; surveys and interviews were performed; and evaluation reports were created. Evaluation information was used to produce talks, posters and papers. This project brings together the barley and wheat communities into a Coordinated Agricultural Project to mitigate the impact of climate change on barley and wheat production by strengthening the integration of these communities and avoiding unnecessary duplications. Changes/Problems:The major change was the extension of the project for one year for thereasons presented in the section of plans for the 6th year. Thisrequest of a No Cost Extension has been approved by USDA-NIFA. The support of 25 graduate students that need one year to complete theirPhD programs wasone the driving forces for the request of a one-year NCE. One problem we are facing is the intensive recruitment by the private breeding sector that has absorbed some of our coPIs and postdocs faster than expected. Although this is a positive outcome for the training component of the project, it originated some delays in the project that will be completed during the one year no cost extension. We will continue our efforts to train the personnel required for the public and private breeding sector, since there seems to be a large need in this area. Changes implemented in previous years that will continue in 2015 Matt Rouse continues to replace Yue Jin as in Year 2 Don Obert budget and functions are covered by Mike Bonman's budget as in Year 2 Jesse Poland (KSU) is added in Year 3 key personnel without budget as in Year 2 Ed Souza moved to Bayer. He was an industry coordinator without funding, so there is no effect on budget. His function is now covered by David van Sanford, University of Kentucky. What opportunities for training and professional development has the project provided?Objective 5: Develop and implement a Plant Breeding Training Network (PBTN): The online PBTN environment was used to deliver webinars and courses. Graduate students participated in a face-to-face workshop in collaboration with industry, and in a poster session at PAG. Undergraduate students were supported through online meetings. TCAP supported attendance of students at the National Association of Plant Breeders Meeting and to PAG. PBTN has provided an excellent communication tool for the project. Funding of MSIs continued and new funding sources to increase diversity were explored through a collaborative grant writing group. Information about research and education was shared both internally and externally through TCAP seminar series, quarterly newsletters and meetings at PAG. Evaluation tools were refined; surveys and interviews were performed; and evaluation reports were created. Evaluation information was used to produce talks, posters and papers. A total of 148 graduate students participated in PBTN. A total of 108 graduate students were directly mentored by TCAP PIs, and of those, 71 were at least partially funded by TCAP, with five of those at minority serving institutions. Three graduate students left the program without completion and one interrupted to go to the army but plans to return. The remaining 68 have a degree distribution as follows - 58 PhD students, 9 Masters students and 1 unknown. The gender distribution of graduate students is 26 students were female, 38 male and 4 unreported. A total of 26 students already graduated and 11 more will graduate in 2015. We anticipate that 16 will graduate in 2016 and 3 in 2017. TCAP has trained 115 undergraduates, with 75 mentored by TCAP faculty and graduate students, and 40 by faculty from Minority Serving Institutions (MSIs). TCAP researchers have trained 29 postdocs. How have the results been disseminated to communities of interest?Since the last report, TCAP participants published71 papers in peer reviewed journals. The 2015 publications included high-impact scientific journals such as PNAS, Plant Cell, The Plant Journal, Genome Biology, Genetics, etc. Scientific results were disseminated through presentations in scientific meetings. Publications from the first five years of the project have been cross-referenced 3,483 times documenting the impact of TCAP research The results of the TCAP project were also disseminated as seeds of 16 improvedvarieties and 34improved germplasm.A survey of the acreage of wheat and barley varieties planted in 2014 in the US showed that varieties released by the barley and wheat CAPs covered 8.5 million acres reaching a very large audience, and documenting the economic impact of this grant to the wheat industry and the US agriculture. Varieties and germplasm were presented to growers and the barley and wheat industry in field days and industry meetings.Phenotyping and genotyping information was disseminated through the T3 database. Marker Assisted selection protocols were disseminated through MASwheat, (http://maswheat.ucdavis.edu/), andexpression data were disseminated through Wheat EXP (http://wheat.pw.usda.gov/GG3/node/237). What do you plan to do during the next reporting period to accomplish the goals?A No Cost Extension for one year was approved by USDA. The main reasons for this NCE request include (i) the delayed hiring of half of the graduate students, (ii) delays generated by personnel turnover, (iii) climatic events that destroyed a few field trials delaying population development, and (iv) the need of additional time to analyze and publish more integrated research results. The available funds provide opportunities to double the number of trained students with completed degrees, to increase the power of our association mapping studies and to validate and initiate deployment of the most valuable QTL discovered in the project. These different areas are described in more detail below. In the area of Education, the original TCAP committed to train 29 graduate students in Plant Breeding. We used the TCAP funding to leverage additional support from our institutions and industry, and the TCAP support was expanded to support 69 graduate students. By the time of this report 28 graduate students have successfully completed their MS and PhD programs and 12 more are expected to finish before the original end of the project (January 31, 2016). However, we still have 25 active graduate students that can greatly benefit from a one-year NCE. Twenty of them are expected to finish their degrees in 2016. Five will finish after the NCE, but we have already secured funds from our institutions to complete their studies. In some cases, PhD programs are requiring 5 years, which is not unusual for projects that require field experiments that can be performed only once a year and that are subject to unpredictable climatic conditions. In addition, it was not possible to hire all the students during the first year of the project. Roughly half of the students (52%) were hired after the first year of the grant, explaining the need for an additional year to finish their PhD programs. The support of these 25 graduate students wasone of the driving forces for the request of a one-year NCE. This additional year will allow us to expand the number of graduated students to 60, more than doubling the proposed target of the project. The NCE will also give as the opportunity to make a more thorough evaluation of the economic impact of the education and research activities. In addition to the graduate students, TCAP trained many technicians and postdocs that were in high demand by industry. One consequence of the successful training of these scientists and technicians was that many of them were hired by industry and academia before the completion of TCAP. In spite of these losses, the project managed to complete the proposed milestones, but some funds were not spent as planned. The replacement of some positions (for example in USDA laboratories) is sometimes highly regulated and cannot be accelerated. This was an important problem to the T3 database, since the individuals they train are in particularly high demand by industry. These funds have generated some opportunities that we plan to fully exploit during the NCE. The NCE year may be busier than usual for T3 as researchers conclude their projects and submit previously generated datasets. Likewise, researchers will continue to need to access past datasets from their own programs and other TCAP programs as data analysis reaches a peak before winding down. T3 will use the NCE year to develop the tools required to facilitate data preparation, upload, curation, and analysis and the integration of the new JBrowse tool that integrates breeding and genomics data. This project required the development of large and complex Nested Association Mapping Populations. Spring wheat populations were advanced as promised in the original project, and two years of field trials have been completed. However, processing of the harvested samples, measurement of seed quality traits on the population, data analysis and publication of the data will require one additional year. In addition, a second spring wheat NAM population of photoperiod insensitive lines was developed for California, where the photoperiod sensitive lines from the core population were not well adapted. This photoperiod insensitive NAM population requires a second year of field trials to increase the statistical power of the QTL analyses. As planned, the winter NAM populations took more time to develop, and will be completed by the end of 2015. In addition, a few field trials were lost to unusual climatic conditions, or lack of pathogens (e.g. three stem rust nurseries in Kenya). If the NCE is awarded, we will have the opportunity to complete the missing field trials, analyze the GBS data of the winter NAM populations, add field evaluation of the winter NAM population, analyze the data for the allele based wheat breeding program in soft winter wheat, and complete the NUE wheat validation studies. In barley, the NCE will be used to complete the high-throughput phenotyping of the barley 2-Row NAM populations and to explore more complex and expensive traits in subsets of the barley NAM populations. During the NCE we will perform additional allelic variation studies of the NSGC Barley Core for a major NUE QTL that was discovered through the TCAP. As we completed and published some of the planned AM projects (particularly in the disease resistance area), we found valuable QTL. The one-year NCE will allow us to validate these QTLs in biparental populations and initiate the introgression of the most significant QTL into commercial varieties. These activities will bring TCAP discoveries one step closer to the growers' fields. In the WUE and NUE association mapping panels evaluated so far, heritability was much lower than in the disease resistance panels, limiting the QTL detection to those with major effects. The one-year NCE will provide the opportunity to test the panels for one additional year, increasing the power of the statistical analyses. The reductions in the prices of marker technologies have resulted in some savings and carry-over funding in the genotyping labs, which can be efficiently used to genotype all the validation populations proposed for 2016, to initiate the deployment of the best QTL in breeding populations, and to broaden the application of genomic selection. The NCE will allow us to complete additional cycles of genomic selection, particularly in winter wheat and the wild barley introgression population, providing a more thorough evaluation of this powerful but complex technology. The genotyping laboratories have just started to implement GBS pipelines, and the NCE will provide the required time and resources to refine those pipelines and to start testing them in the breeding programs. The NCE will help us to improve the quality of the wheat haplotype map by genotyping additional winter wheat NAM populations using sequence-based approaches. In this additional year, we will develop automatic imputation of SNP sites characterized by sequence-based genotyping (whole exome capture and GBS) of a worldwide population of diverse wheat lines. This resource will be integrated into the T3 database and will increase the precision and power to map complex traits. In addition, it will improve the accuracy of phenotypic prediction in studies that utilized SNP arrays and GBS approach for genotyping.Many of the studies performed during the project involve the collaboration of breeders and students from multiple institutions, and therefore the data analysis and interpretation is frequently more complex than initially predicted. The one-year NCE will provide the opportunity to complete more thorough analyses of the data and develop better publications.?

Impacts
What was accomplished under these goals? Objective 1: Identification of new valuable alleles in diverse barley and wheat germplasm Disease resistance: In wheat, two global studies on stripe rust resistance were completed and published. Additional studies on stripe rust resistance mechanisms and utilization in breeding programs were published in 2015. Five new resistance genes effective against the virulent stem rust race Ug99 were published in 2015. Progress was also made in the identification or deployment of resistance genes against the wheat pathotype of rice blast, septoria tritici blotch, wheat curl mite resistance, Hessian fly and sawfly. In barley, comprehensive evaluations of the NSGC barley core collection have been completed for resistance to multiple isolates of the spot form net blotch pathogen, African (Ug99 race group) and North American races of the stem rust pathogen, a widely virulent isolate (ND4008) of the spot blotch pathogen, and the stripe rust pathogen. Water use efficiency (WUE) and heat stress:A spring wheat panel including 262 photoperiod insensitive lines was evaluated in multiple locations in the US and Mexico for WUE using canopy spectral reflectance (CSR) under terminal drought environments. GWAS revealed 19 QTL related to improved plant water status during the grain filling stage under water stress. These QTL were validated in independent NAM populations. Additional TCAP CSR studies evaluated the use of spectral data in the evaluation of yield under normal and water stress conditions. The effect of high temperatures during the day and during the night was investigated. In barley, WUE phenotyping activities were completed and all data was uploaded to T3. Nitrogen use efficiency (NUE):We characterized the transcriptome of loss-of-function mutations of the high grain protein content genesGPC1andGPC2in tetraploid wheat using RNA seq technology. In wheat, the favorableGpc-B1allele has been deployed in several commercial varieties, resulting in concrete improvements in NUE. Thehard and soft winter wheat panels have been genotyped and phenotyped for yield, yield stability, CSR and NUE at multiple locations under different N levels. Among the HWW, variation in CSR was significantly associated to NUE variation suggesting that CSR can be used to efficiently breed for NUE traits. In barley, all scheduled NUE field trials for the AM panels in low (70%) and normal (100%) nitrogen treatments have been completed and data have been uploaded to T3. Analysis of nine traits under the two nitrogen regimes identified 25 and 34 QTL for the two-rowed and six-rowed panels, respectively, with only one locus in common between the two. This major QTL associated with grain protein content located in the region of theGpc-H1locus on chromosome 6H appears to have four haplotypes segregating in the AM panels. Population development:The development of the 2,400 spring wheat NAM lines was completed in 2014, but the genotyping using the 90K iSelect array and GBS was completed in 2015. Some of these NAM populations were evaluated in the field in 2015, and the results are being used to validate the WUE QTL identified in the GWAS studies. The soft and hard winter wheat NAM populations were advanced to the F5generation. Multiple biparental populations have been established in WA and CA using the susceptible parent Avocet to validate the QTL identified in the stripe rust GWAS studies. In barley, the development of thesix- and two-rowed nested association mapping (NAM) populations is complete. The two-rowed NAM, comprised of 7,441 lines, was evaluated in Montana and Utah and the six-rowed NAM, comprised of 7,711 lines, was evaluated in Minnesota and North Dakota for heading date and plant height. The six-rowed NAM was also evaluated for bacterial leaf streak, powdery mildew, spike length, kernels per spike, and rachis internode length in one location. The number of productive tillers was measured in two locations, and grain protein content is being measured on 463 NAM lines. Genotyping by sequencing was completed for both NAMpopulationsand the data are beingcurated for use in association mapping. Objective 2: Accelerate breeding through marker technologies: Data and markers provided by the genotyping labs to the breeders were used to accelerate breeding cycles. Additional high-throughput marker assays have been developed for other valuable genes and have been shared with public and private breeders. Genome-wide marker data has been collected for thousands of lines that also have been evaluated for complex phenotypes. The combined analysis of the genotypic and phenotypic data has revealed many marker trait associations and has helped refine models for genomic selection. Barley and wheat genomic selection (GS) populations were genotyped and advancement of the planned cycles of GS is on target. Three different studies on GS theory and implementation were published this year. Linkage map construction is underway in collaboration with barley groups. GBS was also performed for 321 lines from the Wild Barley Diversity Collection, 576 RILs in two mapping populations, and 614 lines in the Barley iCore. Objective 3: Implement sequence-based genotyping methodologies:Development and use of pipelines aligning sequencing reads to the draft barley genome and the chromosome survey sequence of wheat have integrated the GBS SNP with the genome assemblies. GBS is now the main genotyping tool for the GS, AM and NAM populations. Genotyping by sequencing was done for more than 20,000 barley NAM and AM lines. We also used a second generation exome capture platform to re-sequence 286,800 exons from 81,000 genes in a tetraploid TILLING population. Each individual mutant showed an average of 2,500 mutations resulting in an overall mutation density of 30 mutations per kb. Nearly one million SNPs identified in NAM parental lines using exome capture and 320K Axiom arrays were projected to each of the 2,400 RILs to develop a high-resolution QTL mapping platform for wheat. The utility of a reference panel of 62 wheat accessions genotyped with exome capture forimputinghundreds of thousands markers in association mapping studies was confirmed. We have characterized diversity panel of wheat lines as well as the NAM population of spring wheat developing a first-generation haplotype map of hexaploid wheat. The SNP and GBS genotyping platforms have been used extensively to characterize the core wheat collection at the national Small Gran Collection and to establish the relationship between the different subspecies ofT. aestivum. Exome capture was performed for a barley panel of 267 geo-referenced two-rowed and six-rowed barley landraces and wild accessions. Objective 4. Implement web-based tools to integrate genotypic and phenotypic information.Phenotype and genotype data in the Triticeae Tool Box (T3) has been expanded. In September 2015, T3 included 18,068 lines (9,413 from barley and 8,655 from wheat) with phenotypic data (831,000 data points) and 25,682 lines (15,976 from barley and 9,706 from wheat) with genotypic data (221 million data points). The number of GBS markers increased dramatically in 2015 to 3.6 million in barley and 3.5 million in wheat. T3 is now expanding to take advantage of improved reference sequences for both wheat and barley. T3 remains the primary portal to all of the data generated over the past five years by TCAP?

Publications

  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Meints, B., B. Brouwer, B. Brown, A. Cuesta-Marcos, S. Jones, M. Kolding, S. Fisk, J. Marshall, K. Murphy, S. Petrie, K. Rhinhart, A. Ross, and P.M. Hayes. 2015. Registration of #STRKR barley germplasm. J. Plant Reg. 9:388392.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Meints, B., A. Cuesta-Marcos, A. Ross, S. Fisk, T. Kongraksawech, J.M. Marshall, K. Murphy, and P.M. Hayes. 2015. Developing winter food barley for the Pacific Northwest of the U.S. Crop Sci. 55: 1563-1573.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Mohammadi, M., A. Budde, R. Horsley, S. Ullrich, T. Blake, P. Hayes, D. Hole, D. Obert, B. Cooper, S. Chao, and K.P. Smith. 2015. A genome-wide association study of malting quality across eight U.S. barley breeding programs. Theor. Appl. Genet. 128:705-721.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Mu�oz-Amatria�n, M., S. Lonardi, M.C. Luo, K. Madishetty, J.T. Svensson, M.J. Moscou, S. Wanamaker, T. Jiang, A. Kleinhofs, G.J. Muehlbauer, R.P. Wise, N. Stein, Y. Ma, E. Rodriguez, D. Kudrna, P.R. Bhat, S. Chao, P. Condamine, S. Heinen, J. Resnik, R. Wing, H.W. Witt, M. Alpert, M. Beccuti, S. Bozdag, F. Cordero, H. Mirebrahim, R. Ounit, Y. Wu, F. You, J. Zheng, H. `imkov�, J. Dole~el, J. Grimwood, J. Schmutz, D. Duma, L. Altschmied, T. Blake, P. Bregitzer, L. Cooper, M. Dilbirligi, A. Falk, L. Feiz, A. Graner, P. Gustafson, P.M. Hayes, P. Lemaux, J. Mammadov, T.J. Close. 2015. Sequencing of 15,622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. The Plant Journal 84: 216-227.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Narayanan, S., P.V.V. Prasad, A.K. Fritz, D.L. Boyle, and B.S. Gill. 2015. Impact of high night-time and high daytime temperature stress on winter wheat. J Agron. Crop. Sci. 201:206-218.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Narayanan S, Tamura P, Roth M, Prasad PVV, Welti R. 2015. Wheat leaf lipids during heat stress: I. High day and night temperatures results in major lipid alternations. Plant Cell and Environment. DOI: 10.1111/pce.12649.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Narayanan S, Prasad PVV, Welti R. 2015. Wheat leaf lipids during heat stress: II. Lipid experiencing coordinated metabolism are detected by analysis of lipid co-occurrence. Plant Cell and Environment. DOI: 10.1111/pce.12648.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Naruoka Y, Garland-Campbell KA, and Carter AH (2015) Genome-wide association mapping for stripe rust (Puccinia striiformis f. sp. tritici) in US Pacific Northwest winter wheat (Triticum aestivum L.). Theor. Appl. Genet. 128:1083-1101
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Neupane, A., Tamang, P., Brueggeman, R.S., Friesen, T.L. 2015. Evaluation of a barley core collection for spot form net blotch reaction reveals distinct genotype specific pathogen virulence and host susceptibility. Phytopathology 105:509-517.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Pearce, S., F. Tabbita, D. Cantu, V. Buffalo, R. Avni, H. Vazquez-Gross, R. Zhao, C.J. Conley, A. Distelfeld, and J. Dubcovsky. 2015. Regulation of Zn and Fe transporters by the GPC1 gene during early wheat monocarpic senescence. BMC Plant Biol. 14:368
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Poets, A.M., Z. Fang, M.T. Clegg and P. L. Morrell. 2015. Barley landraces are characterized by geographically heterogeneous genomic origins. Genome Biology 16:173
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Poets, A.M., M. Mohammadi, K. Seth, H. Wang, T.J.Y. Kono, Z. Fang, G.J. Muehlbauer, K.P. Smith, and P.L. Morrell. The effects of both recent and long-term selection and genetic drift are readily evident in North American barley breeding populations. doi: http://dx.doi.org/10.1101/026625
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Pradhan GP, Prasad PVV. 2015. Evaluation of wheat chromosome translocation lines for high temperature stress tolerance at grain filling stage. PLoS One 10(2): e0116620.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Rife, T. W., S. Wu, R. Bowden and J. A. Poland. 2015. Spiked GBS: a unified, open platform for single marker genotyping and whole-genome profiling. BMC Genomics 16(1): 248.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Sherman, J.D., N. K. Blake, J. M. Martin, K. D. Kephart, D. K. Weaver, S. P. Lanning, H.-Y. Heo, M. Pumphrey, J. Chen, and L. E. Talbert. 2015. Impact of a major gene for stem solidness on agronomic performance of spring wheat near-isogenic lines. Crop Sci. 55: 514-520.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Sankaran S, L.R. Khot, and A.H. Carter. 2015. Field-based crop phenotyping: multispectral aerial imaging for evaluation of winter wheat emergence and spring stand. Computers and Electronics in Agriculture. 118:372379.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Tamang, P., Neupane A., Mamidi, S., Friesen, T., and Brueggeman R. 2015. Association mapping of seedling resistance to Spot Form Net Blotch in a worldwide collection of barley. Phytopathology. 105:500-8.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2015 Citation: Van Sanford, D. A., Anthony J., Clark, Gina L. Brown-Guedira, Christina Cowger, Yanhong Dong, and Byung-Kee Baik,. 2015. Registration of Pembroke 2014 Soft Red Winter Wheat. J. Plant Registrations. In press
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Varella, A. C., D. K. Weaver, J. D. Sherman, N. K. Blake, H-Y. Heo, J. Kalous, S. Chao, M. L. Hofland, J. M. Martin, K. D. Kephart, L. E. Talbert. 2015. Association analysis of stem solidness and wheat stem sawfly resistance in a panel of spring wheat germplasm from North America. Crop Sci. 55:2046-2055
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Wang, R., Y. Leng, S. Zhong. 2015. Functional characterization of the regulator gene VosA in the fungal cereal pathogen Cochliobolus sativus. Fungal Biology. doi:10.1016/j.funbio.2015.06.009
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Yaniv, E., D. Raats, Y. Ronin, A.B. Korol, A. Grama, H. Bariana, J. Dubcovsky, A.H. Schulman, T. Fahima. 2015. Evaluation of marker-assisted selection for the stripe rust resistance gene Yr15, introgressed from wild emmer wheat. Mol. Breed.. 35:43.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Zhong, S., Ali, S., Wang, R., Leng, Y., and Garvin, D. F. 2015. Brachypodium distachyon-Cochliobolus sativus pathosystem is a new model for studying plant-fungal interactions in cereal crops. Phytopathology 105: 482-489.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Akdemir, D., J.-L. Jannink. 2015. Locally epistatic genomic relationship matrices for genomic association and prediction and selection. Genetics 199:857-871.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Anderson, J.A., J.J. Wiersma, G.L. Linkert, S. Reynolds, J.A. Kolmer, Y. Jin, R. Dill-Macky, and G.A. Hareland. 2015. Registration of 'Rollag' Spring Wheat. J. Plant Registrations 9:201-207.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Bajgain, P., M.N. Rouse, S. Bhavani, and J.A. Anderson. 2015. QTL Mapping of Adult Plant Resistance to Ug99 Stem Rust in the Spring Wheat Population RB07/MN06113-8 Mol. Breeding 35:170-184
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Bajgain, P., M.N. Rouse, and J.A. Anderson. 2015. Comparison between genotyping by sequencing and SNP-chip genotyping for QTL mapping in wheat. 2015. Crop Sci. doi: 10.2135/cropsci2015.06.0389.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Bajgain, P., M.N. Rouse, P. Bulli, S. Bhavani, T. Gordon, R. Wanyera, P.N. Njau, W. Legesse, J.A. Anderson and M.O. Pumphrey. 2015. Association mapping of North American spring wheat breeding germplasm reveals loci conferring resistance to Ug99 and other African stem rust races. BMC Plant Biology. 15:249.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Babiker, E. M., T.C. Gordon, S. Chao, M. Newcomb, M.N. Rouse, Y. Jin, R. Wanyera, M. Acevedo, G. Brown-Guedira, S. Williamson, J. M. Bonman.2015. Mapping resistance to the Ug99 race group of the stem rust pathogen in a spring wheat landrace. Theor. Appl. Genet. 128:605-612.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Belcher,A.R. R.C. Graebner, A. Cuesta-Marcos, S. Fisk, T. Filichkin, K. P. Smith, V.C. Blake, and P.M. Hayes. 2015. Registration of the TCAP FAC-WIN6 barley panel for genome wide association studies. J. Plant Reg. 9:411-418.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Blake, N. K., J. M. Martin, H.-Y. Heo,K. D. Kephart, S. P. Lanning, L. E. Talbert. 2015. Registration of near-isogenic lines for photoperiod response in hard red spring wheat. J. Plant. Reg. 9:239-243.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Bonafede, M.D., G. Tranquilli, L.A. Pfl�ger, R.J. Pe�a, and J. Dubcovsky. 2015. Effect of allelic variation at the Glu-3/Gli-1 loci on breadmaking quality parameters in hexaploid wheat (T. aestivum L.). Journal of Cereal Science 62:143-150
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Bonman, J.M., E.M. Babiker, A. Cuesta-Marcos, K. Esvelt-Klos, G. Brown-Guedira, S. Chao, D. See, J. Chen, E. Akhunov, J. Zhang, H.E. Bockelman, and T.C. Gordon. 2015. Genetic diversity among wheat accessions from the USDA National Small Grains Collection. Crop Sci. 55:1243-1253.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Bowman, B., J. Chen, J. Zhang, J. Wheeler, Y. Wang, W. Zhao, S. Nayak, N. Heslot, H. Bockelman, and J.M. Bonman. 2015. Evaluating grain yield in spring wheat with canopy spectral reflectance. Crop Sci. 55:1881-1890.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Briggs J., S. Chen, W. Zhang, S. Nelson, J. Dubcovsky, M.N. Rouse. 2015. Mapping of SrTm4, a recessive stem rust resistance gene from diploid wheat effective to Ug99. Plant Diseases. 105: 1347-1354.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Cabrera, A., M. Guttieri, N. Smith, E. Souza, A. Sturbaum, D. Hua, C. Griffey, M. Barnett, P. Murphy, H. Ohm., J. Uphaus, M. Sorrells, E. Heffner, G. Brown-Guedira, D. Van Sanford and C. Sneller, C. 2015. Identification of milling and baking quality QTL in multiple soft wheat mapping populations. Theor. Appl. Genet. 128: 2227-2242.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2015 Citation: Carver, B.F., C.M. Smith, W-P. Chuang, R.M. Hunger, J.T. Edwards, L. Yan, G. Brown-Guedira, B.S. Gill, G. Bai, and R.L. Bowden. 2015. Registration of OK05312, a high yielding hard winter wheat donor of Cmc4 for wheat curl mite resistance. 2015. Journal of Plant Registrations In press
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Chapman, J., M. Mascher, A. Buluc, K. Barry, E. Georganas, A. Session, V. Strnadova, J. Jenkins, S. Sehgal, L. Oliker, J. Schmutz, K. Yelick, U. Scholz, R. Waugh, J. Poland, G. Muehlbauer, N. Stein and D. Rokhsar 2015. A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biology 16: 26.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2015 Citation: Chen, J. J. Wheeler, K. OBrien, W. Zhao, N. Klassen, J. Zhang, B. Bowman, Y. Wang, C. Jackson, J. M. Marshall, X.M. Chen. Registration of UI Platinum Hard White Spring Wheat. Journal of Plant Registration. In press.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Chen S., M.N. Rouse, W. Zhang, Y. Jin, E. Akhunov, Y. Wei, J. Dubcovsky. 2015. Fine mapping and characterization of Sr21, a temperature-sensitive diploid wheat resistance gene effective against the Puccinia graminis f. sp. tritici Ug99 race group. Theor Appl Genet. 128:645-656.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2015 Citation: Cruz, C.D., G.L. Peterson, W.W. Bockus, P. Kankanala, J. Dubcovsky, K.W. Jordan, E. Akhunov, F. Chumley, D.F. Baldelomar, and B. Valent. 2015. The 2NS translocation from Aegilops ventricosa confers resistance to the Triticum Pathotype of Magnaporthe oryzae. Crop Science In press.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Cuesta-Marcos, A., M. a Mu�oz-Amatria�n, T. Filichkin, I. Karsai, B. Trevaskis, S. Yasuda, P.M. Hayes, and K. Sato. 2015. The relationships between development and low temperature tolerance in barley near isogenic lines differing for flowering behavior. Plant Cell and Physiol. doi: 10.1093/pcp/pcv147.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: El-Feki, W.M., P.F. Byrne, S.D. Reid, and S.D. Haley. 2015. Registration of CO940610/Platte wheat doubled haploid mapping population. Journal of Plant Registrations 9:419423.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Fu J., R.L. Bowden, P.V. Vara Prasad & A.M.H. Ibrahim. 2015. Genetic variation for heat tolerance in primitive cultivated subspecies of Triticum turgidum L. Journal of Crop Improvement. 29:565-580.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Goodwin, S.B., J.R. Cavaletto, I.L. Hale, I. Thompson, S.S. Xu, T.B. Adhikari, J. Dubcovsky. 2015. A new map location of gene Stb3 for resistance to septoria tritici blotch in wheat. Crop Science 55:1-9.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Graebner, R.C., A. Cuesta-Marcos, S. Fisk, B.O. Brouwer, S.S. Jones, and P.M. Hayes. 2015. Registration of Alba barley. J. Plant Reg. 9:15.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Graebner, R.C., M. Wise, A. Cuesta-Marcos, M. Geniza, T. Blake, V. C. Blake, J. Butler, S. Chao, D. Hole, R. Horsley, P. Jaiswal, D. Obert, K. P. Smith, S. Ullrich, and P.M. Hayes. 2015. Quantitative trait loci associated with the tocochromanol (vitamin E) pathway in barley. PLOS One. 10: e0133767.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Currie, Y., M.S. Chen, R. Nickolov, G. Bai, L. Zhu. 2014. Impact of transient heat stress on polar lipid metabolism in seedlings of wheat near-isogenic lines contrasting in resistance to Hessian Fly (Cecidomyiidae) infestation. Arthropod-Plant Interactions 107:2196-2203
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Guo, J.-Y., K. Li, K. Wu, X. Wang, H. Lin, D. Cantu, C. Uauy, A. Dobon-Alonso, T. Midorikawa, K. Inoue, J. S�nchez, D. Fu, A. Blechl, E. Wallington, T. Fahima, M. Meeta, L. Epstein, and J. Dubcovsky. 2015. Wheat stripe rust resistance protein WKS1 reduces the ability of the thylakoid-associated ascorbate peroxidase to detoxify reactive oxygen species. Plant Cell. 27:1755-1770.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Guttieri, M. J., P.S. Baenziger, K. Frels, B. Carver, B. Arnall,, and B. Waters. Variation for grain mineral concentration in a diversity panel of current and historical Great Plains hard winter wheat germplasm. Crop Sci. 55: 1035-1052.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Guttieri, M.J., P. S. Baenziger, K. Frels, B. Carver, B. Arnall, S. Wang, E. Akhunov, and B.M. Waters. 2015. Prospects for selecting wheat with increased zinc and decreased cadmium concentration in grain. Crop Science 55: 1712-1728.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Heslot, N., J-L. Jannink, M.E. Sorrells. 2015. Perspectives for genomic selection applications and research in plants. Crop Sci. 55:112.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Hazard B., X. Zhang, M. Naemeh, M.K.Hamilton, B. Rust, H.E. Raybould, J.W. Newman, R. Marti, and J. Dubcovsky. 2015. Mutations in durum wheat SBEII genes conferring increased amylose and resistant starch affect grain yield components, semolina and pasta quality and fermentation responses in rats. Crop Sci. 55:28132825
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Hoffstetter, A., A. Cabrera, and C. Sneller. 2015 Identifying quantitative trait loci for economic traits in an elite soft red winter wheat cultivar development population. Crop Sci. doi: 10.2135/cropsci2015.06.0332.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Isidro, J., J-L Jannink, D. Akdemir, J. Poland, N. Heslot, and M. E. Sorrells. 2015. Training set optimization under population structure in genomic selection. Theor. Appl. Genet. 128:145-158.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Jordan, K.W., S. Wang, Y. Lun, L. Gardiner, R. MacLachlan, P. Hucl, K. Wiebe, D. Wong, K.L. Forrest, A.G. Sharpe, C.H.D. Sidebottom, N. Hall, C. Toomajian, T. Close, J. Dubcovsky, A. Akhunova, L. Talbert, U.K. Bansal, H.S. Bariana, M.J. Hayden, C. Pozniak, J.A. Jeddeloh, A. Hall, E. Akhunov, IWGS Consortium. 2015. A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes Genome Biology 16:48.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2015 Citation: Khot L, Sankaran S, Carter AH, Johnson DA, and Cummings TF (2015) UAS imaging-based decision tools for arid winter wheat and irrigated potato production management. International Journal of Remote Sensing. In press.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Kippes N., J.M. Debernardi, H. Vasquez-Gross, B.A. Akpinar, B.H., K. Kato, S. Chao, E. Akhunov and J. Dubcovsky. 2015. Identification of the VERNALIZATION 4 gene reveals the origin of spring growth habit in ancient wheats from South Asia. Proc. Natl. Acad. Sci. U.S.A. 112: E5401E5410.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Kumssa, T.T., P. S. Baenziger, M. N. Rouse, M. Guttieri, I. Dweikat, G. Brown-Guedira, S. Williamson, R. A. Graybosch, S. N. Wegulo, A. J. Lorenz, and J. Poland. 2015. Characterization of stem rust resistance in wheat cultivar Gage. Crop Sci. 55: 229-239.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: LeBoldus, J.M., Kinzer, K., Ya, Z., Yan, C., Friesen T. L., and Brueggeman, R. 2015. Genotype-by-sequencing of the plant pathogenic fungi Septoria musiva and Pyrenophora teres utilizing Ion Torrent sequence technology. Mol. Plant Pathol. 16:623-632.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Li, C., G. H. Bai, S. Chao and Z. Wang. 2015. A high-density SNP and SSR consensus map reveals segregation distortion regions in wheat. Biomed Research International http://dx.doi.org/10.1155/2015/830618.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Li, C., G. Bai, B.F. Carver, S. Chao and Z. Wang. 2015. Single nucleotide polymorphism markers linked to QTL for wheat yield traits. Euphytica DOI: 10.1007/s10681-015-1475-3
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Li, C., H. Lin, J. Dubcovsky. Factorial combinations of protein interactions generate a multiplicity of florigen activation complexes in wheat and barley. 2015. The Plant Journal. 84:70-82.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Li, G, Y. Wang, M. Chen, E. Edae, J. Poland, E. Akhunov, S. Chao, G. Bai, B.F. Carver, L. Yan 2015. Precisely mapping a major gene conferring resistance to Hessian fly in bread wheat using genotyping-by-sequencing. BMC Genomics. 16:108.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Kalous, J. R., J. M. Martin, J. D. Sherman, H. Y. Heo, N. K. Blake, S. P. Lanning, J. L. A. Eckhoff, S. Chao E. Akhunov, L. E. Talbert. 2015. Impact of the D genome and quantitative trait loci on quantitative traits in a spring durum by spring bread wheat cross. Theor. Appl. Genet. 128:1799-1811
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Lin, M., S. Cai, S. Wang, S. Liu, G. Zhang and G. Bai. 2015. Genotyping-by-sequencing (GBS) identified SNP tightly linked to QTL for pre-harvest sprouting resistance. Theor Appl Genet. 128:1385-1395.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Liu, M, M. Yu, G. Li, B.F. Carver, L. Yan. 2015. Genetic characterization and utilization of TaALMT1 in winter wheat. Molecular Breeding. 35:205.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Liu, L., M.D. Barnett, C.A. Griffey, S. Malla, W.S. Brooks, J.E. Seago, H. Butler, W.E. Thomason, E.G. Rucker, H.D. Behl, R.M. Pitman, D.W. Dunaway, M.E. Vaughn, J.T. Custis, B. Seabourn, R. Chen, M. Fountain, D. Marshall, R.A. Graybosch, L.A. Divis, L.E. Hansen, C. Cowger, S. Cambron, Y. Jin, B.R. Beahm, T.H. Hardiman, C.J. Lin, D.F. Mennel, and D.L. Mennel. 2015. Registration of LCS Wizard wheat. J. of Plant Registration. doi:10.3198/jpr2015.06.0035crc.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Liu, L., M. D. Barnett, C. A. Griffey, S. Malla, W. S. Brooks, J. E. Seago, W. E. Thomason, E. Rucher, H. D. Behl, R. M. Pitman, D. W. Dunaway, M. E. Vaughn, J. T. Custis, B. Seabourn, R. Chen, M. Fountain, D. Marshall, C. Cowger, S. Cambron, Y. Jin, B. R. Beahm, T. H. Hardiman, C. J. Lin, D. F. Mennel, and D. L. Mennel. 2015. Registration of Vision 45 wheat. J. of Plant Registration. 9:338344.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Liu, S., S.K. Sehgal, M. Lin, J. Li, H.N. Trick, B.S. Gill and G. Bai. 2015. Independent mis-splicing mutations in TaPHS1 causing loss of pre-harvest sprouting (PHS) resistance during wheat domestication. New Phytol. 208:928-35
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Maccaferri, M., J. Zhang, P. Bulli, Z. Abate, S. Chao, D. Cantu, E. Bossolini, X. Chen, M. Pumphrey, and J. Dubcovsky. 2015. A genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a worldwide collection of hexaploid spring wheat (Triticum aestivum L.). G3 5:449-465.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Mamo, B. E., and Steffenson, B. J. 2015. Genome-wide association mapping of Fusarium head blight resistance and agro-morphological traits in barley landraces from Ethiopia and Eritrea. Crop Sci. 55:14941512.


Progress 02/01/14 to 01/31/15

Outputs
Target Audience: The audiences targeted by the research component of this project include wheat and barley breeders (public and private), barley and wheat researchers, and barley and wheat industry and growers. The applied results of this project have been presented to wheat and barley growers at field days and farm advisors meetings. Our efforts directly reach the barley and wheat growers and industry by releasing improved varieties. Public wheat varieties accounted for 68% of the wheat ($ 11.5 billion) and 34% of the barley ($413 million) total production during 2012. The production value of public wheat and barley varieties is amplified multiple times through the milling, baking, malting, and brewing industries that contribute additional jobs and value to the economy. Private companies routinely use public varieties in their crossing blocks, transferring part of this value to the private sector and further multiplying the economic benefits of the public breeding activities. The international wheat and barley research communities had access to the new association mapping and sequencing information through publications in peer-reviewed journals, presentations in national and international conferences, and sequences deposited in GenBank. Since the last report, TCAP participants published 66 new peer reviewed scientific articles. Publications from the first three years of the project have been cross-referenced 1,839 times (~15 references per article) documenting the impact of TCAP research. In addition, 18 new cultivars (13 with PVP) and 32 new germplasm were released. Several of the disease resistance genes, nitrogen use efficiency genes and drought tolerance genes identified and mapped in this project are been incorporated into public and private wheat and barley varieties. These resistant varieties limit applications of costly fungicides and reduce the need for N fertilization, increasing growers’ profitability and benefiting the environment. To facilitate access to molecular markers for different traits, we incorporated multiple disease resistance protocols to the publicly available MASWheat website (http://maswheat.ucdavis.edu/protocols/). In the education area we targeted graduate and undergraduate students as well as students from Minority Serving Institutions (MSIs). A total of 136 graduate students participated in PBTN. Ninety-five graduate students were directly mentored by TCAP PIs, and of those, 54 were at least partially funded by TCAP, with two of those at MSIs (the remaining 41 participated in online classes). Eight students graduated. TCAP has trained 108 undergraduates, with 67 mentored by TCAP faculty and graduate students, and 41 by faculty from MSIs. TCAP has trained 25 postdocs and 27 visiting scientists. The online PBTN environment was used to deliver webinars and courses. Graduate students participated in a face-to-face workshop in collaboration with industry, and in a poster session at PAG. Eighteen TCAP students were supported to visit CIMMYT. Undergraduate students were supported through eleven online meetings. TCAP supported attendance of 98 students at the National Association of Plant Breeders Meeting, where 15 TCAP graduate students presented posters and participated in a professional support workshop. PBTN has provided an excellent communication tool for the project. Funding of MSIs continued and new funding sources to increase diversity were explored through a collaborative grant writing group. Information about research and education was shared both internally and externally through TCAP seminar series, quarterly newsletters and meetings at PAG. Evaluation tools were refined; surveys and interviews were performed; and evaluation reports were created. Evaluation information was used to produce talks, posters and papers. This project brings together the barley and wheat communities to mitigate the impact of climate change on barley and wheat production in a Triticeae Coordinated Agricultural Project (CAP) to strengthen the integration of these communities and avoid unnecessary duplications. Changes/Problems: Don Lee transferred his TCAP responsibilities and budget support to Deana M Namuth Covert, who moved in 2014 to Ohio State University. Funds have been transferred to OSU. Deanna will continue in TCAP with the same responsibilities. Tom Blake the barley breeder from Montana State University retired. The university offered the position to Dr. Jamie Sherman who is currently at MSU and is part of the TCAP project, facilitating the transition. One problem we are facing is the intensive recruitment by the private breeding sector that has absorbed some of our coPIs and postdocs. We will continue our efforts to train the personnel required for the public and private breeding sector, since there seems to be a large need in this area. Changes implemented in previous years that will continue in 2014 Matt Rouse continues to replace Yue Jin as in Year 2 Don Obert budget and functions are covered by Mike Bonman’s budget as in Year 2 Jesse Poland (KSU) is added in Year 3 key personnel without budget as in Year 2 Ed Souza moved to Bayer. He was an industry coordinator without funding, so there is no effect on budget. His function is now covered by David van Sanford, University of Kentucky. What opportunities for training and professional development has the project provided? Objective 5: Develop and implement a Plant Breeding Training Network (PBTN): A total of 136 graduate students participated in PBTN. Ninety-five graduate students were directly mentored by TCAP PIs, and of those, 54 were at least partially funded by TCAP, with two of those at minority serving institutions (the remaining 41 participated in online classes). Eight students graduated. TCAP has trained 108 undergraduates, with 67 mentored by TCAP faculty and graduate students, and 41 by faculty from minority serving institutions . TCAP has trained 25 postdocs and 27 visiting scientists. The online PBTN environment was used to deliver webinars and courses. Graduate students participated in a face-to-face workshop in collaboration with industry, and in a poster session at PAG. Eighteen TCAP students were supported to visit CIMMYT. Undergraduate students were supported through eleven online meetings. TCAP supported attendance of 98 students at the National Association of Plant Breeders Meeting, where 15 TCAP graduate students presented posters and participated in a professional support workshop. PBTN has provided an excellent communication tool for the project. TCAP PIs and students gave 35 stakeholder presentations increasing interest and awareness in plant breeding. Funding of MSIs continued and new funding sources to increase diversity were explored through a collaborative grant writing group. Information about research and education was shared both internally and externally through TCAP seminar series, quarterly newsletters and meetings at PAG. Evaluation tools were refined; surveys and interviews were performed; and evaluation reports were created. Evaluation information was used to produce talks, posters and papers. How have the results been disseminated to communities of interest? Publications and germplasm releases: Since the last report, TCAP participants published 66 new peer reviewed scientific articles. Publications from the first three years of the project have been cross-referenced 1,839 times (~15 references per article) documenting the impact of TCAP research. In addition, 18 new cultivars (13 with PVP) and 32 new germplasm were released. Improved varieties have been presented in field days. PIs attended industry and grower's meeting to showcase outputs of the TCAP project. PIs, postodcs and graduate students made presentations in scientific meetings What do you plan to do during the next reporting period to accomplish the goals? No major problems have been found, so we will continue with the original plan as outlined in the project proposal. We will continue the phenotyping of association mapping populations and will initiate the phenotyping of the spring NAM populations. We will use better genotyping platforms than the ones described in the proposal that will allow us to deliver more markers than originally promised. Additional funding was generated for MSI activities that will be expand DISEASE RESISTANCE: Barley diseases plans for 2015: Selected wild barley introgression line populations (in cv. Rasmusson background) segregating for disease reaction will be evaluated at the seedling or adult plant stage as appropriate at the respective institutions. Selected NAM populations segregating for disease reaction will be evaluated at the seedling or adult plant stage at the respective institutions. All data from these trials will be uploaded to T3 and analysis to identify favorable alleles will be conducted and manuscripts prepared. Wheat diseases plans for 2015: For the stripe rust studies we will initiate the validation of the 10 major QTL identified in the 1st set of the spring wheat NSGC. Sources of the different resistance alleles will be crossed with Avocet for validation and high-density mapping. For the NSGC 2nd spring set and the two winter sets we will complete the GWAS analysis and prepare the results for publication. We will also continue the GWAS and mapping studies for leaf and stem rust and publish the results. WATER USE EFFICIENCY: Barley: For a second year the winter LTT panel (n = 941+ checks) will be evaluated in OR, MN, ID, NE, OH, Spain, Canada, France, Germany, Hungary & Japan. A new location was added in Denmark. The accessions with the best LTT (n ~ 50 + checks) will be tested for LTT in controlled freeze tests. Wheat plan of work 2015 WUE: The major phenotyping objective for the spring wheat group in 2015 is to complete the second year of NAM evaluations. GWAS analysis of WUE, CSR and yield components will be completed and published. For the winter AM panel, we will collect phenotypic data for additional environments in 2015. These data will be combined with data from previous years for GWAS. NITROGEN USE EFFICIENCY: Barley: In the next year we will complete the GWAS analysis in all three barley AM panels and submit publications. Using haplotype information for the 6H QTL discovered in the SP6 panel, we will identify an informative set of lines for the six-row NAM population that contain the existing haplotypes at that locus. Wheat: Winter wheat validation trials (YQV, CSRV, NUEV, and YNVP): In 2015, the HRW validation trials will be evaluated in six locations and the SRW in nine locations. The ABB trials will be repeated in the 2014-15 season. NAMs by September of 2015. F5 plants will be genotyped with GBS. Accelerate breeding through marker-assisted selection and genomic selection. Two approaches will be employed to accelerate breeding cycles: marker-assisted selection and genomic selection. Marker-assisted selection in barley and wheat will be performed using prior marker-trait associations identified in biparental and AM populations. The testing of Genomic Selection strategies will continue in barley and winter wheat, where longer breeding cycles make GS more attractive. Barley In 2015, we will compare gains from random, phenotypic selection and GS in barley in three locations: MN, NE, OR. Wheat GS and ABB plan 2015: The HRW and SRW elite winter wheat panels will be genotyped with GBS. The allele-based breeding tests in 2015 will be of similar size as in 2014, but will consist of mostly new entries. GBS genotyping plans 2015: These GBS genotyped populations, AM panels and NAM populations will be used to identify favorable alleles for disease resistance, WUE and NUE. Implement sequence-based genotyping methodologies to discover new allelic diversity. This objective is focused on using exon capture and genotype-by-sequencing (GBS) technologies developed in the previous years of the grant to discover allelic variation in wheat and barley germplasm. The GBS data from the NAM populations will be used to construct sequence-based genetic maps of wheat and barley. Implement web-based tools to integrate marker-assisted selection and genomic selection strategies into breeding programs. The TCAP has developed The Triticeae Toolbox (T3) that stores all genotype and phenotype data from the project and provides easily queried data. The plans for 2015 include the development of new analyses tools: a) A training population design tool will be developed. b) A definition of core germplasm sets tool will also be developed. c) Multivariate analysis will also be developed. Planned integration with other networked genomics resources : a) Increased collaboration with GrainGenes. b) Integration with reference sequence resources: progress has been made in developing reference sequences for both barley and wheat. c) Application program interfaces to other breeding-related database systems. Planned features: a) Improved handling of GBS markers and big data. b) Experimental designs with field maps. c) Deposit of defined datasets. Education activities planned for 2015:a) Continue to create a T3 Tutorial. b) Rerun R course that was created in 2014. c) Rerun online course for plant breeding for drought tolerance. d) Online self-paced plant breeding strategies. e) Student organized TCAP seminar series. f) Group meeting at PAG. g) Conduct human capital workshop (Student presentations and Grant design) and Graduate student poster session. h) Support attendance of 50 students at the National Association of Plant Breeders (NAPB) meeting. i) Support Graduate Student travel.j) Support research collaborations with faculty and students at Minority Serving Institutions (MSIs). k) Attract diverse students to plant sciences grant l) Support undergraduate research internships at TCAP institutions.m) Support mentors of undergrads through entering mentoring program. n) Undergraduate online synchronous and asynchronous support and undergraduate research presentations. o) Pilot offering self-paced short courses with badging system p) Continue to explore long-term means of offering online courses. q) Pilot partnerships to expand TCAP/PBTN. r) PBTN maintenance and expansion. s) In depth interview of PIs, students and MSI faculty. t) Survey PIs, students and MSI faculty. u) Evaluation report. v) Advisory panel meeting. w) Dissemination of project knowledge.

Impacts
What was accomplished under these goals? Objective 1: Identification of new valuable alleles in diverse barley and wheat germplasm: Extensive phenotyping was performed in controlled environments and in field conditions for disease resistance, water use efficiency (WUE) and nitrogen use efficiency (NUE). Significant improvements were made in canopy spectral reflectance (CSR) protocols and analysis. Genotypic and phenotypic data sets from multiple environments were integrated into genome wide association studies (GWAS) that yielded valuable marker-trait associations for the different target traits. Disease resistance: The barley core collection and dedicated association mapping (AM) panels were evaluated for resistance to current races of major barley pathogens. Resistance alleles for stripe rust, stem rust, leaf scald, spot blotch, spot-form net blotch and cereal yellow dwarf virus were identified. Highly significant QTL for stripe rust resistance were identified by GWAS in the NSGC wheat core collections. GWAS were also performed for stem rust and leaf rust in both spring and winter wheat panels. Several GWAS studies were published. Resistance genes were also identified in biparental populations for resistance to stem rust race Ug99, leaf spot diseases, stem sawfly, Hessian fly, and orange wheat blossom midge. Many of these resistance genes have been incorporated into commercial varieties. Water use efficiency (WUE): Barley WUE phenotyping activities were completed and all data was uploaded to T3. Facultative barley varieties with improved low temperature tolerance (LTT) are being developed to take better advantage of winter precipitation. Using a large germplasm collection novel QTL were identified and known QTL were validated. The spring and winter wheat AM panels were evaluated in multiple locations in the US, Canada, and Mexico for WUE. GWAS identified several highly significant QTL for normalized water index NWI3 and related WUE traits, some consistent across locations. Valuable associations were detected in a tetraploid x hexaploid wheat population and in recombinant lines of the rye 1RS introgression. Studies of root characteristics and physiological traits associated with WUE and heat tolerance were completed and published in 2014. Nitrogen use efficiency (NUE): In barley, all scheduled NUE field trials for the AM panels (spring six-row, spring two-row, and winter six-row) in low (70%) and normal (100%) nitrogen treatments have been completed and data have been uploaded to T3. Preliminary association analyses of NUE-related traits and NUE indices in the spring six-row panel have identified a major QTL at the Gpc-1 locus and two other minor QTL. In wheat, the favorable Gpc-B1 allele has been deployed in several commercial varieties. This allele increases grain protein content resulting in concrete improvements in NUE. The hard and soft winter wheat panels have been genotyped and phenotyped for yield, yield stability, CSR and NUE at multiple locations under different N levels. Variation in NUE was detected among accessions. Population development: Development of the barley six- and two-row nested association mapping (NAM) populations was completed. A seed increase and preliminary trait evaluation of the six-row NAM was conducted in MN. The seed increase for the two-row NAM is being conducted in greenhouses in ND. The spring wheat NAM population was completed, the seed was increased and the first four sub-populations were phenotyped. The rest of the populations were planted for evaluation in 2015. The winter wheat NAM populations were advanced one generation as planned. Objective 2: Accelerate breeding through marker technologies: Two approaches have been followed to accelerate breeding cycles: marker-assisted selection (MAS) and genomic selection (GS). Using the 9K and 90K iSelect chips, AM panels and mapping populations were genotyped in a few months, greatly accelerating the pace of marker development and gene discovery. More than 7,000 barley and wheat lines were genotyped with these chips. In addition, high-throughput marker assays have been developed for valuable genes and have been shared with public and private breeders. Genotyping of the barley and wheat GS populations and advancement of the planned cycles of GS is on target. Preliminary results from the barley GS showed that two cycles of GS were equivalent to one cycle of phenotypic selection. Objective 3: Implement sequence-based genotyping methodologies: The two main technologies evaluated this year were exome capture and genotyping-by-sequencing (GBS). Barley and wheat exome capture assays were used for re-sequencing the parents of the NAM populations. A subset of 62 diverse wheat lines was genotyped by exome capture and GBS and 1.57 million SNPs were identified. These data revealed several selective sweeps that likely resulted from human-driven selection. These selective sweeps showed little overlap among genomes suggesting the importance of polyploidy in broadening adaptive variation. A second generation exon capture assay was used to re-sequence 1,000 tetraploid wheat TILLING mutant lines and to identify ~2,500,000 mutations. GBS pipelines have been developed and tested in barley and wheat and GBS has been adopted as the main genotyping tool for the GS, AM and NAM populations. Objective 4. Implement web-based tools to integrate genotypic and phenotypic information. Phenotype and genotype data in the Triticeae Tool Box (T3) has been greatly expanded. In November 2014, T3 included 17,600 lines with phenotypic data (768,000 data points) and 24,000 lines with genotypic data (131 million data points). The database now accommodates individual plot data and provides new analysis tools including the automatic calculation of indexes for CSR data. The ability of T3 to work with the Android Field Book was improved. Publications and germplasm releases: Since the last report, TCAP participants published 66 new peer reviewed scientific articles. Publications from the first three years of the project have been cross-referenced 1,839 times (~15 references per article) documenting the impact of TCAP research. In addition, 18 new cultivars (13 with PVP) and 32 new germplasm were released.

Publications

  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Avni R., R. Zhao, S. Pearce, Y. Jun, C. Uauy, F. Tabbita, T. Fahima, A. Slade, J. Dubcovsky, Assaf Distelfeld. 2014. Functional characterization of GPC-1 genes in hexaploid wheat. Planta. 239:313324.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Baenziger, P.S., R. A. Graybosch, T. Regassa, R. N. Klein, G. R. Kruger, D. K. Santra, L. Xu, D. J. Rose, S. N. Wegulo, Y. Jin, J. Kolmer, G. L. Hein, M.-S. Chen, G. Bai, R. L. Bowden and J. Poland. 2014. Registration of NE06545 (Husker Genetics Brand Freeman) Hard Red Winter Wheat. J. Plant Reg. 8:279-284
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Bernardo, A., G. Bai, J. Yu, F. Kolb, W. Bockus, Y. Dong. 2013. Registration of near-Isogenic winter wheat germplasm contrasting in Fhb1 for Fusarium head blight resistance. J. Plant Reg. 8:106-108.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Blake, N. K., R. N. Stougaard, B. Bohannon, D. K. Weaver, H.-Y. Heo, P. F. Lamb, D. Nash, D. M. Wichman, K. D. Kephart, J. H. Miller, G. V. P. Reddy, J. L. Eckhoff, W. E. Grey, S. P. Lanning, J. D. Sherman, and L. E. Talbert. 2014. Registration of Egan wheat. J. Plant Reg. 8:298-302.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Cai, J., G. Bai. 2014. Quantitative trait loci for Fusarium head blight resistance in Huangcandou x Jagger wheat population. Crop Sci. 54:2520-2528
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Carter, A.H., S.E. Cambron, H.W. Ohm, N. Bosque-P�rez, K.K. Kidwell. 2014. Identifying molecular markers associated with Hessian fly (Mayetiola destructor [Say]) resistance in the spring wheat (Triticum aestivum) cultivar Louise. Crop Sci. 54:1-11.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Carter, A.H., S.S. Jones, X.Cai, S.R. Lyon, K.A. Balow, G.B. Shelton, R.W. Higginbotham, X.M. Chen, D.A. Engle, B. Baik, S.O. Guy, T.D. Murray, C.F. Morris.2014. Registration of Puma wheat. J. Plant Reg. 8:273278.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Case, A.J., D.Z. Skinner, K.A. Garland-Campbell, A.H. Carter. 2014. Freezing tolerance-associated QTL in the Brundage x Coda wheat recombinant inbred line population. Crop Sci. 54:982-992
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Case, A.J., Y. Naruoka, X.M. Chen, K.A. Garland-Campbell, R.S. Zemetra, A.H. Carter. 2014. Mapping stripe rust resistance genes in a Brundage x Coda winter wheat population. PlosONE 9:e91758
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Chen, A., C. Li,, W. Hu, M. Lau, H. Lin, N.C. Rockwell, S.S. Martin, J.A. Jernstedt, J.C. Lagarias, and J. Dubcovsky. 2014. PHYTOCHROME C plays a major role in the acceleration of wheat flowering under long days. Proc. Natl. Acad. Sci. U.S.A. 111:10037-10044.
  • Type: Journal Articles Status: Accepted Year Published: 2015 Citation: Chen S., M.N. Rouse, W. Zhang, Y. Jin, E. Akhunov, Y. Wei, J. Dubcovsky. 2014. Fine mapping and characterization of Sr21, a temperature-sensitive diploid wheat resistance gene effective against the Puccinia graminis f. sp. tritici Ug99 race group. Theor. Appl. Genet. In press.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: del Blanco I.A., J. Hegarty, L. Gallagher, B. W. Falk, G. Brown-Guedira, E. Pellerin, J. Dubcovsky. 2014. Mapping of QTL for tolerance to Cereal Yellow Dwarf Virus in two-rowed spring barley. Crop Sci. 54:1468-1475
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Edae, E.A., P.F. Byrne, S.D. Haley, M.S. Lopes, and M.P. Reynolds. 2014. Genome wide association mapping of yield and yield components of spring wheat under contrasting moisture regimes. Theor. Appl. Genet. 127:791807.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Fang, Z., A.M. Gonzales, M.T. Clegg, K.P. Smith, G.J. Muehlbauer, B.J. Steffenson and P.L. Morrell. 2014. Two genomic regions contribute disproportionately to geographic differentiation in wild barley. G3 4:1193-20.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Goodwin, S.B., J.R. Cavaletto, I.L. Hale, I. Thompson, S.S. Xu, T.B. Adhikari, J. Dubcovsky. 2015. A new map location of gene Stb3 for resistance to septoria tritici blotch in wheat. Crop Sci. 55:19.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Graebner, R.C., A. Cuesta-Marcos, S. Fisk, B.O. Brouwer, S.S. Jones, and P.M. Hayes. 2014. Registration of Alba barley. J. Plant Reg. doi:10.3198/jpr2014.04.0027crc.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Guedira M., P. Maloney, M. Xiong, S. Petersen, J. P. Murphy, D. Marshall, J. Johnson, S. Harrison, G. Brown-Guedira. 2014. Vernalization duration requirement in soft winter wheat is associated with variation at the Vrn-B1 locus. Crop Sci. 54:1960-1971.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Gurung, S. S. Mamidi, J.M. Bonman, M. Xiong, G. Brown-Guedira, T. Adhikari. 2014. Genome-wide association study reveals novel quantitative trait loci associated with resistance to multiple leaf spot diseases of spring wheat. PLoS One. 9:e108179.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Forrest, K.L., V. Pujol, P. Bulli, M. Pumphrey, C. Wellings, S. Herrera-Foessel, J. Huerta-Espino, R. Singh, E.L. Lagudah, M. Hayden and W. Spielmeyer. 2014. Development of a SNP marker assay for adult plant resistance gene Lr67 of wheat using a genotyping by sequencing approach. Molecular Breeding. 34: 2109-2118.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Haley, S.D., J.J. Johnson, F.B. Peairs, J.A. Stromberger, E.E. Hudson, S.A. Seifert, R.A. Kottke, V.A. Valdez, J.J. Nachtman, J.B. Rudolph, G. Bai, X. Chen, R.L. Bowden, Y. Jin, J.A. Kolmer, M.-S. Chen, and B.W. Seabourn. 2014. Registration of 'Cowboy' wheat. J. Plant Reg. 8:169-172
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Haley, S.D., J.J. Johnson, F.B. Peairs, J.A. Stromberger, E.E. Hudson, S.A. Seifert, R.A. Kottke, V.A. Valdez, J.B. Rudolph, G. Bai, X. Chen, R.L. Bowden, Y. Jin, J.A. Kolmer, M.-S. Chen, and B.W. Seabourn. 2014. Registration of 'Antero' wheat. J. Plant Reg. 8:165-168.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Hazard B., X. Zhang, M. Naemehand J. Dubcovsky. 2014. Registration of Durum Wheat germplasm lines with combined mutations in SBEIIa and SBEIIb genes conferring increased amylose and resistant starch. J. Plant Reg. 8:334338.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Henry I.M., U. Nagalakshmi, M.C. Lieberman, K.J. Ngo, K.V. Krasileva, H. Vasquez-Gross, A. Akunova, E. Akhunov, J. Dubcovsky, T. H. Tai, L. Comai. 2014. Efficient genome-wide detection and cataloging of EMS-induced mutations using next-generation sequencing and exome capture. Plant Cell 26:13821397
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Heslot, N., D. Akdemir, M.E. Sorrells, J-L. Jannink. 2014. Integrating environmental covariates and crop modeling into the genomic selection framework to predict genotype by environment interactions. Theor. Appl. Genet. 127:463-480.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Heslot, N., J-L. Jannink, M.E. Sorrells. 2014. Perspectives for genomic selection applications and research in plants. Crop Sci. doi:10.2135/cropsci2014.03.0249
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Howell, T. I. Hale, D. L. Jankuloski, M. Bonafede, M. Gilbert, J. Dubcovsky. 2014 Mapping a region within the 1RS.1BL translocation in common wheat affecting grain yield and canopy water status. Theor. Appl. Genet. 127: 2695-2709
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Hulbert S.H., M.O. Pumphrey. 2014. A time for more booms and fewer busts? Unraveling cerealrust interactions. Mol. Plant-Microbe Interact.. 27:207-214
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Hussien, A., E. Tavakol, D.S. Horner, M. Mu�oz-Amatria�n, G.J. Muehlbauer and L. Rossini. 2014. Genetics of tillering in rice and barley. The Plant Genome 7:1-20
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Isidro, J., J-L Jannink, D. Akdemir, J. Poland, N. Heslot, and M. E. Sorrells. 2014. Training set optimization under population structure in genomic selection. Theor. Appl. Genet. doi 10.1007/s00122-014-2418-4.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Jin, F., G. Bai, D. Zhang, Y. Dong, L. Ma, W. Bockus, F. Dowell. 2014. Fusarium-damaged kernels and deoxynivalenol in Fusarium-infected U.S. winter wheat. Phytopathology 104:472-478.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Kippes N., J. Zhu, A. Chen. L.S. Vanzetti, A. Lukaszewski, H. Nishida, K. Kato, J. Dvorak, J. Dubcovsky (2013) Fine mapping and epistatic interactions of the vernalization gene VRN-D4 in hexaploid wheat. Mol. Genet. Genomics 289: 4762.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Kumssa, T.T., P. S. Baenziger, M. N. Rouse, M. Guttieri, I. Dweikat, G. Brown-Guedira, S. Williamson, R. A. Graybosch, S. N. Wegulo, A. J. Lorenz, and J. Poland. Characterization of stem rust resistance in wheat cultivar Gage. Crop Sci. doi:10.2135/cropsci2014.05.0348.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: LeBoldus, J.M., Kinzer, K., Ya, Z., Yan, C., Friesen T. L., and Brueggeman, R. 2014.Genotype-by-sequencing of the plant pathogenic fungi Septoria musiva and Pyrenophora teres utilizing Ion Torrent sequence technology. Mol. Plant Pathol. DOI: 10.1111/mpp.12214
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Liu. S., X. Yang, D. Zhang, G. Bai, S. Chao, W. Bockus. 2014. Genome?wide association analysis identified SNPs closely linked to a gene resistant to Soil?borne wheat mosaic virus. Theor. Appl. Genet. 127:1039-1047
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Liu, Z., D. Holmes, J.D. Faris, S. Chao, R.S. Brueggeman, M.C. Edwards, T.L. Friesen. 2014. Necrotrophic effector-triggered susceptibility (NETS) underlies the barley-Pyrenophora teres f. teres interaction specific to chromosome 6H. Mol. Plant Pathol. doi:10.1111/mpp.12172
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Lv B., R. Nitcher, X. Han, S. Wang, F. Ni, K. Li, S. Pearce, J. Wu, J. Dubcovsky, D. Fu. 2014. Characterization of FLOWERING LOCUS T1 (FT1) gene in Brachypodium and wheat. PLoS ONE 9:e94171
  • Type: Journal Articles Status: Accepted Year Published: 2015 Citation: Maccaferri, M. , J. Zhang, P. Bulli, Z. Abate, S. Chao, D. Cantu, E. Bossolini, X. Chen, M. Pumphrey, and J. Dubcovsky. 2015. A genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a worldwide collection of hexaploid spring wheat (Triticum aestivum L.). G3. In press
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Mohammadi, M., J. B. Endelman, S. Nair, S. Chao, S. S. Jones, G. J. Muehlbauer, S. E. Ullrich, B. Baik, M. L.Wise, and K. P. Smith. 2014. Association mapping of grain hardness, polyphenol oxidase, total phenolics, amylose content, and ?-glucan in US barley breeding germplasm. Mol. Breeding doi: 10.1007/s11032-014-0112-5.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Mu�oz-Amatria�n, M., A. Cuesta-Marcos, J.B. Endelman, J. Comadran, M. Bonman, H. Bockelman, S. Chao, J. Russell, R. Waugh, P.M. Hayes and G.J. Muehlbauer. 2014. Genetic diversity and population structure in a worldwide barley collection of landraces and cultivars and its potential for genome-wide association studies. PLoS One 9: e94688.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Mu�oz-Amatria�n, M., A. Cuestos-Marcos, P.M. Hayes and G.J. Muehlbauer. 2014. Barley genetic variation: implications for crop improvement. Brief. Funct. Genomics 13:341-350.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Narayanan, S., P.V.V. Prasad. 2014. Characterization of a spring wheat association mapping panel for root traits. Agron. J. 106: 1593-1604
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Narayanan, S., A. Mohan, K.S. Gill, P. V. V. Prasad. 2014. Variability of root traits in spring wheat germplasm. PLoS One. 9:e100317.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Narayanan, S., P.V.V. Prasad, A.K. Fritz, D.L. Boyle, and B.S. Gill. 2014. Impact of high night-time and high daytime temperature stress on winter wheat. J Agron. Crop. Sci. DOI: 10.1111/jac.12101
  • Type: Journal Articles Status: Accepted Year Published: 2015 Citation: 44. Neupane, A., Tamang, P., Brueggeman, R.S., Friesen, T.L. 2014. Evaluation of a barley core collection for spot form net blotch reaction reveals distinct genotype specific pathogen virulence and host susceptibility. Phytopathology
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Nitcher, R., S. Pearce, G. Tranquilli, X. Zhang, J. Dubcovsky. 2014. Effect of the Hope FT-B1 allele on wheat heading time and yield components. J. Heredity 105:666-675.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Pauli, D., G.J. Muehlbauer, K. Smith, B. Cooper, D. Hole, D. Obert, S. Ullrich and T. Blake. 2014. Association mapping of agronomic QTL in U.S. spring barley breeding germplasm. The Plant Genome. doi: 10.3835/plantgenome2013.11.0037.
  • Type: Journal Articles Status: Accepted Year Published: 2015 Citation: Pearce, S., F. Tabbita, D. Cantu, V. Buffalo, R. Avni, H. Vazquez-Gross, R. Zhao, C.J. Conley, A. Distelfeld, and J. Dubcovsky. 2015. Regulation of Zn and Fe transporters by the GPC1 gene during early wheat monocarpic senescence. BMC Plant Biol.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Prasad, P.V.V., and M. Djanaguiraman. 2014. Response of floret fertility and individual grain weight of wheat to high temperature stress: sensitive stages and thresholds for temperature and duration. Funct. Plant Biol. 41:12611269.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Rouse, M. N., L. E. Talbert, D. Singh, and J. D. Sherman. 2014. Complementary epistasis involving Sr12 explains adult plant resistance to stem rust in Thatcher wheat (Triticum aestivum L.). Theor. Appl. Genet. 127-1549-1559
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Sela H, Ezrati S, Yehuda PB, Manisterski J, Akhunov E, Dvorak J, Breiman A, Korol A. 2014. Linkage disequilibrium and association analysis of stripe rust resistance in wild emmer wheat (Triticum turgidum ssp. dicoccoides) population in Israel. Theor. Appl. Genet. 127:2453-63.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Sherman, J. D., J. M. Martin, N. K. Blake, S. P. Lanning and L. E. Talbert. 2014. Genetic basis of agronomic differences between a modern and a historical spring wheat cultivar. Crop Sci. 54:1-13.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Sherman, J., D. Nash, S. P. Lanning, J. M. Martin, N. K. Blake, C. F. Morris, and L. E. Talbert. 2014. Genetics of end-use quality differences between a modern and historical spring wheat. Crop Sci. 54:1972-1980.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Shjerve, R.A., J.D. Faris, R.S. Brueggeman, C. Yan, Y. Zhu, V. Koladia, T.L. Friesen 2014. Evaluation of a Pyrenophora teres f. teres mapping population reveals multiple independent interactions with the barley 6H chromosome region. Fungal Genet. Biol. 70:104-112.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Talbert, L. E, J. D. Sherman, M. L. Hofland, S. P. Lanning, N. K. Blake, R. Grabbe, P. F. Lamb, J. M. Martin, and D. K. Weaver. 2014. Resistance to Cephus cinctus Norton, the wheat stem sawfly, in a recombinant inbred line population of wheat derived from two resistance sources. Plant Breeding, 133:427-432.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Tamang, P., Neupane A., Mamidi, S., Friesen, T., and Brueggeman R. 2014. Association mapping of seedling resistance to Spot Form Net Blotch in a worldwide collection of barley. Phytopathology
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: The International Wheat Genome Sequencing Consortium (IWGSC, including G. Muehlbauer and E. Akhunov). 2014. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 18: 1251788
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Tsilo, T.J., J.A. Kolmer, and J.A. Anderson. 2014. Molecular mapping and improvement of leaf rust resistance in wheat breeding lines. Phytopathol. 104:865-870.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Wang S., Wong D., Forrest K., Allen A., Chao S., Huang B., Maccaferri M., Salvi S., Milner S., Cattivelli L., Mastrangelo A., Whan A., Stephen S., Barker G., Wieseke R., Plieske J., IWGSC., Lillemo M., Mather D., Appels R., Dolferus R., Brown-Guedira G., Korol A., Akhunova A., Feuillet C., Salse J., Morgante M., Pozniak C., Luo M.-C., Dvorak J., Morell M., Dubcovsky J., Ganal M., Tuberosa R., Lawley C., Mikoulitch I., Cavanagh C., Edwards K., Hayden M., Akhunov E. (2014) Characterization of polyploid wheat genomic diversity using a high-density 90,000 SNP array. Plant Biotechnol. J. 12:787-796.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Wang, X., X. Wang, L. Deng, H. Chang, J. Dubcovsky, H. Feng, Q. Han, L. Huang, Z. Kang. 2014. Wheat TaNPSN SNARE homologues are involved in vesicle-mediated resistance to stripe rust (Puccinia striiformis f. sp. tritici). J. Exp. Bot. doi:10.1093/jxb/eru241.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Williams, K.R. and M.E. Sorrells. 2014. Three dimensional seed size and shape QTL in hexaploid wheat (Triticum aestivum L.) populations. Crop Sci. 54:98-110.
  • Type: Journal Articles Status: Accepted Year Published: 2014 Citation: Yaniv, E., D. Raats, Y. Ronin, A.B. Korol, A. Grama, H. Bariana, J. Dubcovsky, A.H. Schulman, T. Fahima. Evaluation of marker-assisted selection for the stripe rust resistance gene Yr15, introgressed from wild emmer wheat. Mol. Breed.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Zhu J., S. Pearce, A. Burke, D.R. See, D.Z. Skinner, J. Dubcovsky, K. Garland-Campbell. 2013. Copy number variation at VRN-A1 and central FR-A2 loci are associated with frost tolerance in hexaploid wheat. Theor. Appl. Genet. 127:11831197.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Zhang, J., J. Chen, B.C. Bowman, K. OBrien, J.M. Marshall, and J.M. Bonman. 2014. Association mapping of Hagberg falling number in Hard White Spring Wheat. Crop Sci. 54:12431252.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Zhou, H., B.J. Steffenson, G. Muehlbauer, R. Wanyera, P. Njau and S. Ndeda. 2014. Association mapping of stem rust race TTKSK resistance in US barley breeding germplasm. Theor. Appl. Genet. 127:1293-1304.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Zhang D., R.L. Bowden, J. Yu, B. F. Carver, G. Bai. 2014. Association analysis of stem rust resistance in U.S. winter wheat. PLoS One 9:e103747
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Zhong, S., Ali, S., Wang, R., Leng, Y., and Garvin, D. F. 2014. Brachypodium distachyon-Cochliobolus sativus pathosystem is a new model for studying plant-fungal interactions in cereal crops. Phytopathology doi.org/10.1094/PHYTO-08-14-0214-R


Progress 02/01/13 to 01/31/14

Outputs
Target Audience: This project brings together the barley and wheat communities to mitigate the impact of climate change on barley and wheat production in a Triticeae Coordinated Agricultural Project (CAP) to strengthen the integration of these communities and avoid unnecessary duplications. The audiences targeted by the research component of this project include wheat and barley breeders (public and private), barley and wheat researchers, and barley and wheat industry and growers. Presentations to wheat growers explaining the direct applications of this research have been made in field days and farm advisors meetings throughout the country. Our efforts reach directly the barley and wheat growers and industry by releasing improved varieties. Public wheat varieties account for 68% of the wheat ($ 11.5 billion) and 34% of the barley ($413 million) total production during the last year. The $12-billion production value of public wheat and barley varieties is amplified multiple times through the milling, baking, malting, and brewing industries that contribute additional jobs and value to the economy. Private companies routinely use public varieties in their crossing blocks, transferring part of this value to the private sector and further multiplying the economic benefits of the public breeding activities. The international wheat research community had access to the new association mapping and sequencing information through publications in peer reviewed journals, several presentations in national and international conferences, and sequences deposited in GenBank. Since the last report, TCAP participants generated 51 new peer reviewed publications. In addition, 20 new cultivars and 16 new germplasm were released and 13 new mapping populations were developed. Several of the rust resistance genes identified and mapped in this project have been incorporated into public and private wheat varieties. These resistant varieties limited applications of costly fungicides, increasing growers’ profitability and benefiting the environment. To facilitate access to molecular markers for different traits we incorporated multiple disease resistance protocol to the publicly available through the MASWheat website http://maswheat.ucdavis.edu/protocols/. In the education area we targeted graduate and undergraduate students as well as students from Minoriy Serving Institutions. A total of 117 graduate students have participated in the plant breeding training network. Eighty-one are directly mentored by a TCAP PI while 42 students are at least partially funded by TCAP with two of those at minority serving institutions. Eighty-seven undergraduates have participated in the TCAP, with 49 of them being mentored by TCAP faculty and graduate students, 36 by faculty from Minority Serving Institutions (MSI) and 2 not-directly affiliated with TCAP. Six MSI students spent time at TCAP institutions in 2013. TCAP has trained a total of 20 Post-Doc’s and 25 visiting scientists. During 2013 we performed a survey to identify the current positions of people trained during the BarleyCAP, wheatCAP and TCAP projects. We identified 57 individuals that currently hold positions in companies located in the US, including of the breeding and seed companies. Forty are currently working in academic institutions in the US and 18 are working in other countries (public or private). This data confirms that the CAP projects have contributed significantly to the training of the personnel currently hired by the private sector in the seed industry. Changes/Problems: One problem we are facing is the intensive recruitment by the private breeding sector that has absorbed some of our coPIs and postdocs. We have replaced the departing personnel as described below and meet our proposed milestones. We will continue our efforts to train the personnel required for the public and private breeding sector, since there seems to be a large need in this area. Don Lee was replaced as PI for NE educational part by Deana Namuth who was also working int he project and is familiar with the activities performed by Don Lee. The education team decided to move some of the funding previously allocated to the development of online education materials to direct support for undergraduate and MSI students. Robert Muller was previously listed in key personnel as the person advising Clay Sneller with the implementation of Canopy Spectral Reflectance (with no dedicated budget). Since the TCAP group has already optimized the CSR equipment in the second year of the project, the role of the advisory personnel in CSR is no longer critical. Dr. Clay Sneller at The Ohio State University will still receive advice from Wade Thomison (VA) and Steve Baenziger (NE) that have expertise in this area. Changes implemented in 2012 that will continue in 2013. Matt Rouse continues to replace Yue Jin as in Year 2 Don Obert budget and functions are covered by Mike Bonman’s budget as in Year 2 Jesse Poland (KSU) is added in Year 3 key personnel without budget as in Year 2 Ed Souza is not included in Year 3 as in Year 2 (Industry coordinator without funding, no effect on budget). His function is now covered by David van Sanford, University of Kentucky. What opportunities for training and professional development has the project provided? Education: A total of 117 graduate students (Appendix H3) have participated in the plant breeding training network. Eighty-one are directly mentored by a TCAP PI while 42 students are at least partially funded by TCAP with two of those at minority serving institutions (36 are unaffiliated with TCAP, Appendix H4). Eighty-seven undergraduates have participated in the TCAP, with 49 of them being mentored by TCAP faculty and graduate students, 36 by faculty from Minority Serving Institutions (MSI) and 2 not-directly affiliated with TCAP. Six MSI students spent time at TCAP institutions in 2013. TCAP has trained a total of 20 Post-Doc’s and 25 visiting scientists. Plant Breeding Training Network (PBTN): The online environment was used to deliver and archive the courses Theory and Application of Association Analysis and Entering Mentoring. Two face-to-face graduate student workshops were presented in collaboration with industry, and a graduate student poster session was supported at PAG. A business plan was submitted to Ag*Idea to insure sustainability of course offerings. Undergraduate students have been supported through nine online meetings. Three educational lesson tools were completed and utilized in undergraduate classes. A short film “Stewards of the Ground” was created describing grower support for plant breeding. The PBTN has been used as a communication tool for project management. Linkages with the eXtension Plant Breeding and Genomics CoP were expanded. Increasing interest and awareness in plant breeding: TCAP PIs gave presentations at MSIs. Six MSI students participated in research at TCAP institutions in 2013. Funding and number of MSI institutions was expanded. Films were created and used in undergraduate classrooms. Information about research and education was shared both internally and externally through thirteen meetings of the TCAP seminar series, quarterly newsletters and meetings at PAG. Evaluation tools were refined. How have the results been disseminated to communities of interest? Since the last report, TCAP participants generated 51 new peer reviewed publications. In addition, 20 new cultivars and 16 new germplasm were released and 13 new mapping populations were developed. Improved varieties have been presented in field days. PIs attended industry and grower's meeting to showcase outputs of the TCAP project. PIs, postodcs and graduate students made presentations in scientific meetings What do you plan to do during the next reporting period to accomplish the goals? No major problems have been found, so we will continue with the original plan as outlined in the project proposal. We will continue the phenotyping of association mapping populations and will initiate the phenotyping of the spring NAM populations. We will use better genotyping platforms than the ones described in the proposal that will allow us to deliver 30x more markers than originally promised. Additional funding was genereated for MSI activities that will be expand Accelerate breeding through marker-assisted selection and genomic selection. Two approaches will be employed to accelerate breeding cycles: marker-assisted selection and genomic selection. Marker-assisted selection in barley and wheat will be performed using prior marker-trait associations identified in biparental and AM populations. Genomic selection is underway in barley and is being evaluated in the winter wheat program, where longer breeding cycles make GS more attractive. Implement sequence-based genotyping methodologies to discover new allelic diversity This objective is focused on using exon capture and genotype-by-sequencing (GBS) technologies developed in the previous years of the grant to discover allelic variation in wheat and barley germplasm. These technologies will be compared with the available iSelect SNP genotyping platforms. Implement web-based tools to integrate marker-assisted selection and genomic selection strategies into breeding programs. The TCAP has developed The Triticeae Toolbox (T3) that stores all genotype and phenotype data from the project and provides easily queried data. Activities: Various activities will be conducted to improve T3 In 2014. We will continue to hold regular User Group meetings and plan implementation features requested by users. Recent feature requests now in the queue for implementation include (1) Genetic map selection. T3 stores information on an increasing number of genetic maps necessitating the ability for users to select specific ones. (2) Adding new marker types, in particular DArT markers. (3) Enable generalized (rather than fixed) line properties. Properties are categorical descriptors of lines invariant to environment. Generalized properties make T3 flexible and extendible. (4) Comparison of line performance across trials. TCAP trials are often designed to contrast relevant climate change environments (e.g., dry versus irrigated; low versus normal N). Users will be able to design and visualize functions of line performance change in such trial pairs. (5) Improved CSR storage, retrieval, and analysis. Templates for CSR data, interfaces for uploading, and CSR index analysis will be developed. Novel full-spectrum CSR analyses will be implemented and tested. (6) A second (now annual) workshop will be organized with other interested database groups. (7) More tools for plot-level data will be developed. In particular, we want T3 to provide some support of experimental designs so that users can download randomized field layout files from T3. These files will be in formats compatible with tablet-based data collection apps. (8) T3 now contains two forms of high-dimensional data: marker and canopy spectral reflectance data. We plan to develop and test methods to analyze these data jointly to improve prediction power.

Impacts
What was accomplished under these goals? Genotyping: SNP Genotyping: A 92,000 SNP iSelect wheat chip was developed and used to genotype association mapping (AM) and nested association mapping (NAM) populations and to develop new maps. In barley, we evaluated genotyping-by-sequencing of multiplex amplicons, which includes multiplex PCR of bar-coded samples and pooling for sequencing. Genotyping of the barley and wheat AM, NAM, elite breeding germplasm, and genomic selection populations is on target. Exon capture: The Nimblegen exome capture assays targeting 110 Mb of sequence in the wheat genome and 90 Mb of sequence in the barley genome were used for re-sequencing 72 barley and 71 wheat accessions serving as parents of NAM populations. Transcriptome data from diploid tetraploid and hexaploid wheat was used to develop a 2nd generation exon-capture assay. Genotyping by sequencing (GBS): A wheat reference map integrating 2740 gene-associated single-nucleotide polymorphisms from the wheat iSelect assay, 1351 diversity array technology, 118 simple sequence repeat/sequence-tagged sites, and 416,856 genotyping-by-sequencing markers was developed. The hard red winter wheat association mapping panel was genotyped using both GBS and the 92K iSelect genotyping array. The Triticeae toolbox database (T3): Phenotype and genotype data in T3 has been greatly expanded and new breeding programs are contributing to T3. A total of 15,000 lines with phenotypic data (540,000 data points) and 22,000 lines with genotypic data (111 million data points) have been entered in T3. CSR data have been uploaded and tools to calculate and visualize WUE and NUE indexes have been developed. Phenotyping: Significant improvements were made in canopy spectral reflectance (CSR) protocols. CSR was used in 2013 to evaluate WUE and NUE association panels and the National Small Grain Collection (NSGC) core collections. The best drought resistant lines from the NSGC screen from 2011 and 2012 have been incorporated into the wheat breeding programs. Water use efficiency (WUE): In barley, two association mapping populations were evaluated for WUE at four locations. The facultative/winter panel was tested for low temperature tolerance at three locations. Two other panels were tested at a third location. Significant effects for chromosomal regions/genes involved in plant growth, development, and stress tolerance were identified. In wheat, 600 winter accessions from the NSGC were characterized for WUE and NUE. The spring wheat AM panel was evaluated for WUE in 9 locations and the winter AM panel in four locations. Seven additional specialized wheat mapping populations were phenotyped for root characteristics and physiological traits associated with WUE and agronomic performance. Nitrogen use efficiency (NUE): In barley, all scheduled NUE field trials (spring six-row, spring two-row, and winter six-row association mapping panels) in low (70%) nitrogen and normal (100%) nitrogen treatments have been completed. Trial data from 2012 has been uploaded to T3 and 2013 data is being curated. Preliminary analyses of NUE-related traits and NUE indices indicate that there is significant variation in the six-row panels for conducting association mapping. In wheat, the hard and soft winter wheat panels were evaluated at different N levels at two locations each. All the wheat AM panels were genotyped with the iSelect 92,000 SNP wheat chip. Disease resistance: The core barley National Small Grain Collection (NSGC) and dedicated AM panels were evaluated for resistance to current races of major barley pathogens. Resistance alleles for stripe rust, stem rust, leaf scald, spot blotch, spot-form net blotch, and the Cereal Yellow Dwarf Virus have been identified and resistant germplasm was developed. In wheat, the NSGC core collection was screened for leaf rust, stem rust, and stripe rust. More than 60 seedling and adult plant resistance loci have been identified and are being validated. A resistance gene that confers near immunity to race Ug99, Sr35, was cloned. Improved markers were developed for several rust resistance genes including adult plant resistance loci Lr67, Sr13, Sr21and Yr48, providing breeders with a broader set of resistance genes to deploy in their breeding programs. Population development: The spring wheat Nested Association Mapping (NAM) population was completed and the barley and winter wheat NAM populations were advanced as planned.

Publications

  • Type: Journal Articles Status: Awaiting Publication Year Published: 2013 Citation: Akdemir, D., and J.-L. Jannink. 2013. Ensemble learning with trees and rules: supervised, semi-supervised, unsupervised. Intelligent Data Analysis.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Akdemir, D., and J.-L. Jannink. 2013. Locally epistatic genomic relationship matrices for genomic association, prediction and selection. Joint Statistical Meetings (JSM) Proceedings. http://arxiv.org/pdf/1302.3463v6.pdf
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Bakhsh, A. N. Mengistu, P. S. Baenziger, I. Dweikat, S. N. Wegulo, D. Rose, G. Bai, and K.M. Eskridge. 2013. Effect of Fusarium head blight (FHB) resistance gene Fhb1 on agrnomic and end-use quality traits of hard red witner wheat. Crop Sci. 53:793-801.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Beecher B. S., A. H. Carter, D. R. See. 2012. Genetic mapping of new seed-expressed polyphenol oxidase genes in wheat (Triticum aestivum L.). Theor. Appl. Genet. 124:1463-1473
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Bernardo, A.N., R.L. Bowden, M.N. Rouse, M.S. Newcomb, D.S. Marshall, G-H., Bai. 2013. Validation of molecular markers for new stem rust resistance genes in U.S. hard winter wheat. Crop Sci. doi: 10.2135/cropsci2012.07.0446
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Blake, N. K., D. Clark, S. P. Lanning, G. R. Carlson, P. F. Lamb, D. Nash, D. M. Wichman, K. D. Kephart, R. N. Stougaard, J. Miller, J. L. Eckhoff, F. Menalled, E. Davis, and L. E. Talbert. 2013. Registration of WB9879CLP hard red spring wheat. J. Plant Reg. 7:205-208
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Cantu, D., V. Segovia D. MacLean, R. Bayles, X. Chen, S. Kamoun, J. Dubcovsky, D. G.O. Saunders, C. Uauy C. 2013. Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors. BMC Genomics. 14:270.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Carter A. H., S. S. Jones, S. R. Lyon, K. A. Balow, G. B. Shelton, R. W. Higginbotham, X. M. Chen, D. A. Engle, B. Baik, S. O. Guy, T. D. Murray, C. F. Morris. 2013. Registration of Otto wheat. J. Plant Reg. 7:195-200.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Carter A. H., K. Garland-Campbell, C. F. Morris, K. K. Kidwell. 2012. Chromosomes 3B and 4D are associated with several milling and baking quality traits in a soft white wheat (Triticum aestivum L.) population. Theor. Appl. Genet. 124:1079-1096.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Cavanagh C., S. Chao, S. Wang, B.E. Huang, S. Stephen, S. Kiani, K. Forreste, C. Saintenac, G. Brown-Guedira, A. Akhunova, D. See, G. Bai, M. Pumphrey, L. Tomar, D. Wong, S. Kong, M. Reynolds, M. Lopez da Silva, H. Bockelman, L.E. Talbert, J.A. Anderson, S. Dreisigacker, P.S. Baenziger, A.H. Carter, V. Korzun, P.L. Morrell, J. Dubcovsky, M. Morell, M. Sorrells, M. Hayden, and E. Akhunov. 2013. Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars.Proc. Natl. Acad. Sci. U.S.A. 110:8057-8062.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Chai, Y., Nirmala, J., Kleinhofs, A., and Steffenson, B. 2012. Failure of RPG1 protein to degrade in high-copy Rpg1 transgenic barley lines results in susceptibility to stem rust. Physiol. Molec. Plant Pathol. 80:10-18.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Chen, A. and J. Dubcovsky. The wheat gene VERNALIZATION1 is required for the down-regulation of the VRN2 flowering repressor in the leaves and for timely flowering in spring. PLoS Genetics. 8:e1003134
  • Type: Journal Articles Status: Accepted Year Published: 2013 Citation: Chen, J., J. Wheeler, J. Clayton, W. Zhao, K. OBrien, C. Jackson, J. M. Marshall, B.D. Brown, K. Campbell, X.M. Chen, R. Zemetra, and E.J. Souza. 2013. Registration of UI Stone Wheat. J. Plant Registration 7:321-326.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2013 Citation: Chen, J., Hu, G., Ch. Chu, and Y. Wu. 2013. STS markers developed from drought tolerance candidate genes and mapped in two mapping populations and one set of nulli-tetrasomic lines of common wheat (Triticum aestivum). Cereal Communication In press.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2013 Citation: Chutimanitsakun, Y, A. Cuesta-Marcos, S. Chao, A. Corey, T. Filichkin, S. Fisk, M. Kolding, B. Meints, Y. Ong, J.I. Rey, A.S. Ross, and P.M. Hayes. 2013. Application of marker-assisted selection and genome wide association scanning to the development of winter food barley germplasm resources. Mol. Breeding. In press.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Condon, B. J., Leng, Y., Wu, D., Bushley, K. E., Ohm, R. A., Otillar, R., Martin, J., Schackwitz, W., Grimwood, J., MohdZainudin, N., Xue, C., Wang, R., Tu, Z. J., Steffenson, B. J., Salamov, A., Sun, H., Lowry, S., LaButti, K., Han, J., Copeland, A., Lindquist, E., Lucas, S., Barry, K., Schmutz, J., Baker, S., Grigoriev, I. V., Zhong, S., and Turgeon, B. G.. 2013. Comparative genome structure, secondary metabolite and effector coding capacity across Cochliobolus pathogens. PLoS Genetics 9: e1003233
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Dai, J., G-H Bai, D-D Zhang, D-L Hong. 2013. Validation of quantitative trait loci for aluminum tolerance in Chinese wheat landrace FSW. Euphytica 192:171179.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2013 Citation: El-basyoni, I., P.S. Baenziger , I. Dweikat I., D. Wang , K. M. Eskridge and M. Saadalla . 2013. Using DArT markers to monitor genetic diversity throughout selection: A case Study in Nebraskas winter wheat breeding nurseries. Crop Science. In press
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2013 Citation: Fang Z, A. Eule-Nashoba, C. Powers, T.Y. Kono, S. Takuno, P.L. Morrell, and K.P. Smith. 2013. Comparative analyses identify the contributions of exotic donors to disease resistance in a barley experimental population. G3: Genes Genomes Genetics. In press
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Guttieri, M.J, R.J. Stein, B.M. Waters. 2013. Nutrient partitioning and grain yield of TaNAM-RNAi wheat under abiotic stress. Plant and Soil. DOI 10.1007/s11104-013-1713-1
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Hale I., X. Zhang, D. Fu, and J. Dubcovsky. 2013. Registration of wheat lines carrying the partial stripe rust resistance gene Yr36 without the Gpc-B1 high grain protein content allele. J. Plant Reg. 7:108-112.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2013 Citation: Kono, T.Y., K. Seth, J.A. Poland, and P.L. Morrell. 2013. SNPMeta: SNP annotation and SNP metadata collection without a reference genome. Molecular Ecology Resources In press
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Krasileva, K.V., V. Buffalo, P. Bailey, S. Pearce, S. Ayling, F. Tabbita, M. Soria, S. Wang, IWGS consortium , E. Akhunov, C. Uauy, J. Dubcovsky. 2013. Separating homeologs by phasing in the tetraploid wheat transcriptome. Genome Biology 14:R66 doi:10.1186/gb-2013-14-6-r66
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2013 Citation: Lei, L., X. Zhu, S, Wang, M. Zhu, B.F. Carver, L. Yan. 2013. TaMFT-A1 is associated with seed germination sensitive to temperature in winter wheat. PLoS One. In press.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2013 Citation: Hunger, R.M., J.T. Edwards, R.L. Bowden, L. Yan, P. Rayas-Duarte, G. Bai, G.W. Horn, J.A. Kolmer, K.L. Giles, M-S. Chen, Y. Jin, R.D. Osburn, M.B. Bayles, B.W. Seabourn, A.R. Klatt, and B.F. Carver. 2013. Billings wheat combines early maturity, disease resistance, and desirable grain quality for the southern Great Plains of the USA. J. Plant Reg. In press
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: International Barley Sequencing Consortium, K.F. Mayer, R. Waugh, J.W. Brown, A. Schulman, P. Langridge, M. Platzer, G.B. Fincher, G.J. Muehlbauer, K. Sato, T.J. Close, R.P. Wise and N. Stein. 2012. A physical, genetic and functional sequence assembly of the barley genome. Nature 491:711-716.
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Jia, Y., and J.-L. Jannink. 2012. Multiple trait genomic selection methods increase genetic value prediction accuracy. Genetics 192: 15131522.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Jin, F., D-D Zhang, W. Bochus, P.S. Baenziger, B.F. Carver, G-H Bai. 2013. Fusarium head blight resistance in U.S. winter wheat cultivars and elite breeding lines. Crop Sci. doi: 10.2135/cropsci2012.09.0531.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Liu, Z-L R.L. Bowden, G-H Bai. 2013. Molecular markers for leaf rust resistance gene Lr42 in wheat. Crop Sci. doi: 10.2135/cropsci2012.09.0532
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Liu, Sh., C.A. Griffey, M.D. Hall, A. L. McKendry, J. Chen, W.S. Brooks, G. Brown?Guedira, D. Van Sanford, D.G. Schmale. Molecular characterization of field resistance to Fusarium head blight in two US soft red winter wheat cultivars. Theor Appl Genet DOI 10.1007/s00122-013-2149-y
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Lu, S., M.C. Edwards, and T.L. Friesen, 2012. Genetic variation of single nucleotide polymorphisms identified at the mating type locus correlates with form-specific disease phenotype in the barley net blotch fungus Pyrenophora teres. Eur. J. Plant Pathol. 135:49-65.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Luckert, D., Toubia-Rahme, H., Steffenson, B. J., Choo, T.-M., and Molnar, S. J. 2012. Novel Septoria speckled leaf blotch resistance loci in a barley doubled-haploid population. Phytopathology 102:683-691.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Mascher, M., T.A. Richmond, D.J. Gerhardt, A. Himmelbach, L. Clissold, D. Sampath, S. Ayling, B. Steuernagel, M. Pfeifer, M. D'Ascenzo, E.D. Akhunov, P.E. Hedley, A.M. Gonzales, P.L. Morrell, B. Kilian, F.R. Blattner, U. Scholz, K.F.X. Mayer, A.J. Flavell, G.J. Muehlbauer, R. Waugh, J.A. Jeddeloh, and N. Stein. 2013. Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond. The Plant J. DOI: 10.1111/tpj.12294
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2013 Citation: Morrell, P.L., A.M. Gonzales, K.K.T. Meyer, and M.T. Clegg. 2013. Resequencing data indicate a modest effect of domestication on diversity in barley: a cultigen with multiple origins. J Hered. In press
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Mu�oz?Amatria�n, M., S.R Eichten, T. Wicker, T.A. Richmond, M. Mascher, B. Steuernagel, U. Scholz, R. Ariyadasa, M. Spannagl, T. Nussbaumer, K.F.X. Mayer, S. Taudien, M. Platzer, J.A. Jeddeloh, N.M. Springer, G.J. Muehlbauer, N. Stein. 2013. Distribution, functional impact and origin mechanisms of copy number variation in the barley genome. Genome Biology 14:R58.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Neelam K., G. Brown-Guedira, L. Haung. 2013. Development and validation of a breeder-friendly KASPar marker for wheat leaf rust resistance locus Lr21. Molecular Breeding 31:233-237
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Nitcher R., A. Distelfeld, C.T. Tan, L. Yan, J. Dubcovsky. 2013. Increased copy number at the FT-H1 locus is associated with accelerated flowering time in barley. General Genomics and Genetics.288:261-275
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Saintenac, C., W. Zhang, A. Salcedo, M. Rousse, H. Trick, E. Akhunov, and J. Dubcovsky. 2013. Identification of wheat gene Sr35 that confers resistance to Ug99 stem rust race group. Science 341:783-786
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Sherman, J. D., S. P. Lanning, D. See, and L. E. Talbert. 2013. Registration of near-isogenic spring wheat lines with all combinations of homozygous R-locus genotypes. J. Plant Reg. 7:242-244
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Pearce, S., J. Zhu, �. Boldizs�r, A. V�g�jfalvi, A. Burke, K. Garland-Campbell, G. Galiba, and J. Dubcovsky.2013. Large deletions in the CBF gene cluster at the Fr-B2 locus are associated with reduced frost tolerance in wheat. Theor. Appl. Genet. DOI 10.1007/s00122-013-2165-y
  • Type: Journal Articles Status: Published Year Published: 2012 Citation: Poland JA, Rife TW (2012) Genotyping-by-Sequencing for Plant Breeding and Genetics. Plant Gen 5: 92-102.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Saintenac C., Z. Zhang, S. Wang, E. Akhunov. 2013. Sequence-based mapping of polyploid wheat genome. G3 Bethesda. 3:1105-1114
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Talbert, L. E., P. Hofer, D. Nash, J. M. Martin, S. P. Lanning, J. Sherman, and M. J. Giroux. 2013. Hard white vs. hard red wheats: taste tests and milling and baking properties. Cereal Chem. 90:249-255
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Tan, C.T., B.F. Carver, M. Chen, Y. Gu, L. Yan. 2013. Genetic association of OPR and LOX genes with resistance to Hessian fly in hexaploid wheat. BMC Genomics 14:369.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Wang, J. Richards, T. Gross, A. Druka, A. Kleinhofs, B. Steffenson, M. Acevedo and R. Brueggeman (2013) The rpg4-mediated resistance to wheat stem rust (Puccinia graminis) in barley (Hordeum vulgare) requires Rpg5, a second NBS-LRR gene and an actin depolymerization factor. Mol. Plant Microbe Interact. 26:407-18.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Williamson, V.M., T. Varghese, F. Howard and J. Dubcovsky. 2013. A translocation from Aegilops ventricosa transferred to common wheat carries a resistance gene against root-knot nematodes. Crop Sci. 53: 14121418
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Zhou, Z., and Steffenson, B. 2013. Genome-wide association mapping reveals genetic architecture of durable spot blotch resistance in US barley breeding germplasm. Mol. Breed. 32:139-154.
  • Type: Journal Articles Status: Published Year Published: 2013 Citation: Zhou, H., and Steffenson, B. J. 2013. Association mapping of Septoria speckled leaf blotch resistance in U.S. barley breeding germplasm. Phytopathology 103:600-609.


Progress 02/01/12 to 01/31/13

Outputs
OUTPUTS: The TCAP project established nationally coordinated high-throughput phenotyping and genotyping platforms, innovative marker-based breeding strategies, and an integrated plant breeding education network to mitigate the negative effects of climate change on wheat and barley production. The TCAP project completed the proposed milestones for the second year. In the area of genotyping, we improved the iSelect 9,000 SNP barley chip and played a key role in the development of a new iSelect 90,000 SNP wheat chip. We mapped 7,517 SNPs integrated them into a consensus map, and identified regions of the wheat genome subjected to selection. The Nimblegen whole exome capture assays targeting 110 Mb of sequence in the wheat genome and 90 Mb of sequence in the barley genome have been designed and used to genotype selected wheat and barley NAM parental lines (300,000 SNPs identified). Genotyping by sequencing was expanded into new mapping populations generating tens of thousands of polymorphic GBS tags and high density maps (~20,000 markers each). During the second year of the project we improved the canopy spectral reflectance (CSR) protocols and used this technology to evaluate the NSGC core collections of barley and wheat genotyped in year one. In the area of water use efficiency (WUE) four barley association mapping panels were evaluated in six locations and two wheat panels were evaluated in eight locations for CSR and other physiological traits. Eight additional specialized mapping populations have been phenotyped for root characteristics, physiological traits associated to WUE, heat stress, and agronomic performance. In the area of nitrogen use efficiency, three barley and two wheat association mapping panels were evaluated under different nitrogen levels. In the area of disease resistance, the barley and wheat NSGC core collections were evaluated for resistance to stripe rust, stem rust and leaf rust. The barley collection was also evaluated for spot blotch and for spot form net blotch. Multiple disease resistance loci were identified by association mapping. A multi-parent wild barley introgression population was developed and genotyped and phenotyped. Nested association mapping populations for barley and wheat were advanced two generations. The genotypic and phenotypic data was incorporated into the Triticeae toolbox database (T3) that now uses two-dimensional "materialized view" tables to access genotype data, providing quicker access and more compact storage. In the area of education, 69 graduate students, 38 undergraduate students and 16 students from Minority Serving Institutions (MSI) participated in TCAP activities. Undergraduate students have been supported in their development through three online meetings with industry representatives and TCAP PIs. The online environment was used to deliver and archive four courses and sixteen seminars. Other communication tools include the quarterly newsletters and 3 films. During the second year TCAP participants generated 35 peer reviewed publications and released ten new improved varieties and germplasm. PARTICIPANTS: Individuals trained in this project: A total of 69 graduate students participated in the PBTN and 38 were directly supported by TCAP funding. Thirty-eight undergraduate students were mentored by graduate students and faculty and 16 students from Minority Serving Institutions participated in TCAP activities. Undergraduate students have been supported in their development through three online meetings with industry representatives and TCAP PIs. The online environment was used to deliver and archive 4 courses and 16 seminars. Other communication tools include the quarterly newsletters and films "Holding the future in the palm of your hand", "Seeds of Hope", and "Everything is local: Fighting the Wheat Stem Sawfly" with related handouts. The Education team and evaluators had established successful collaborations with representatives from Minority Serving Institutions (MSI) and completed the funding and evaluation of the first year activities. Most of the projects were renewed for a second year of funding. Collaborations: The T-CAP has catalyzed multiple interactions among breeding programs, genotyping labs and barley and wheat researchers that would have not been possible without the T-CAP support. The T-CAP supported International consortia for barley and wheat SNP development and gene capture. Collaborations with breeding database teams around the world were established. We contributed transcriptome data of tetraploid wheat to the International Wheat Sequencing Consortium. The T-CAP has promoted collaboration among the US breeding and genotyping programs accelerating the development of improved wheat and barley varieties. T-CAP initiated research collaborations with eight minority serving institutions (see above). T-CAP members S. Baenziger, D. Namuth-Covert, and J. Sherman with private plant breeders and industry professional are forming a consortium to provide online course sharing for plant breeding students. T-CAP is fostering collaborations by providing an online meeting environment. TARGET AUDIENCES: The audiences targeted by this project include wheat breeders, wheat researchers and plant breeding students. To facilitate access to new molecular markers we developed detailed protocols that have been made publicly available through the T-CAP web site. The new iSelect Illumina platforms have provided tens of thousands of markers for thousands of US cultivars and breeding lines generating changes in the way these lines are being used for breeding (e.g. selection of parental lines for crosses). Most breeders are now using more molecular markers for their breeding programs and some are starting to implement genomic selection strategies. The international wheat research community had access to the new mapping and sequencing information through publications in peer reviewed journals, several presentations in national and international conferences, and sequences deposited in GenBank. Presentations to wheat growers explaining the direct applications of this research have been made in field days and farm advisors meetings across the country. Several of the disease resistance genes identified and mapped in our laboratory have been incorporated into public and private wheat and barley breeding programs, limiting applications of costly fungicides, increasing growers' profitability and benefiting the environment. Plant breeding students and professionals are a target audience. TCAP has provided seminar and courses in state of the art techniques both for students and plant breeding professionals. TCAP is increasing awareness of plant breeding as a career and attracting more students to the field. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
The TCAP project has integrated the barley and wheat research and breeding activities across the country into a single collaborative community. This integration has facilitated the implementation of common high-throughput genotyping and phenotyping platforms and the integration of all the information in a centralized database. These new tools were used to characterize the complete germplasm core collections for barley and wheat and to discover new gene variants for improved water and nitrogen use efficiency and for disease resistance. Marker-assisted selection and genomic selection strategies are being implemented in the public barley and wheat breeding programs to deploy these valuable genes into commercial varieties and to accelerate breeding cycles. The TCAP is revitalizing training in plant breeding in the US. Sixty-nine graduate students and 54 undergraduate students are getting hands-on training in plant breeding and have now access to the best teachers and scientists in plant breeding and related disciplines through the Plant Breeding Training Network (PBTN). This online environment and the large student cohort have reduced the isolation of plant breeding students and better prepare them for the collaborative enterprise of plant breeding. Plant breeders from industry and other countries are making use of the materials we are creating. The collaborations with faculty at minority serving institutions have established a bridge that has been already used by MSI students to reach TCAP barley and wheat breeding programs. The T-CAP has delivered: a) 10 new wheat and barley varieties, b) 35 peer reviewed publications, c) 9,000 and 90,000 SNP iSELECT Illumina chips for wheat, d) improved metadata for the 9,000 SNP chip for barley, d) Gene capture platforms for wheat and barley, e) High density barley and wheat genetic maps integrating SNPs and genotyping by sequencing, f) Genotyped core germplasm collections for barley and wheat, g) An integrated genotyping-phenotyping database (T3), h) Association mapping and nested association mapping populations for water use efficiency, nitrogen use efficiency and disease resistance genes, i) A plant breeding training network that provides access to 69 graduate and 54 undergraduate students across the US to the best teachers and scientists j) Three workshops, six seminars, four online courses and three educational films.

Publications

  • 9.- Haley, S.D., Johnson, J., Peairs, F., Stromberger, J., Hudson, E., Seifert, S., Kottke, R., Valdez, V., Rudolph, J., Bai, G., Chen, X., Bowden, R.L., Jin, Y., Kolmer, J.A., Chen, M., Seabourn, B.W. 2012. Registration of 'Byrd' wheat. Journal of Plant Registrations. 6:302-305.
  • 10.- Haley, S.D., Johnson, J., Westra, P., Peairs, F., Stromberger, J., Hudson, E., Seifert, S., Kottke, R., Valdez, V., Rudolph, J., Bai, G., Chen, X., Bowden, R.L., Jin, Y., Kolmer, J.A., Chen, M., Seabourn, B.W. 2012. Registration of 'Brawl CL Plus' wheat. Journal of Plant Registrations. 6:306-310.
  • 11.- Haley, S.D., Johnson, J., Peairs, F., Stromberger, J., Hudson, E., Seifert, S., Kottke, R., Valdez, V., Rudolph, J., Martin, T.J., Bai, G., Chen, X., Bowden, R.L., Jin, Y., Kolmer, J.A., Chen, M., Seabourn, B.W. 2012. Registration of 'Denali' wheat. Journal of Plant Registrations. 6:311-314.
  • 1.- Anderson, J.A., J.J. Wiersma, G.L. Linkert, J.A. Kolmer, Y. Jin, R. Dill-Macky, J.V. Wiersma, G.A. Hareland, and R. H. Busch. 2012. Registration of 'Tom' Wheat. J. Plant Registrations. 6: 2: 180-185
  • 2.- Anderson, J.A., J.J. Wiersma, G.L. Linkert, J.A. Kolmer, Y. Jin, R. Dill-Macky, J.V. Wiersma, G.A. Hareland, and R. H. Busch. 2012. Registration of 'Sabin' Wheat. J. Plant Registrations. 6: 2: 174-179
  • 3.- Baenziger, P.S., R. A. Graybosch, t. Regassa, L.A. Nelson, R. N. Klein, D. K. Santra, D.D. Baltensperger, L. Xu, S. N. Wegulo, Y. Jin, J. Kolmer, Ming-shun Chen, and Guihua Bai. 2012. Registration of 'NE01481' hard red winter wheat. J. Plant Reg. 6:49-53.
  • 4.- Baenziger, P.S., R. A. Graybosch, T. Regassa, L.A. Nelson, R. N. Klein, D. K. Santra, D.D. Baltensperger, J. M. Krall, S. N. Wegulo, Y. Jin, J. Kolmer, Ming-shun Chen, and Guihua Bai. 2012. Registration of 'NI04421' hard red winter wheat. J. Plant Reg. 6:54-59.
  • 5.- Bernardo A. N., H. Ma, D. Zhang, and G. Bai. 2012. Single Nucleotide Polymorphism in wheat chromosome region harboring Fhb1 for Fusarium Head Blight resistance. Mol Breed. 29:477-488.
  • 6.-Blake, V.C., J.G. Kling, P.M. Hayes, J.-L. Jannink, S.R. Jillella, J. Lee, D.E. Matthews, S. Chao, T.J. Close, G.J. Muehlbauer, K.P. Smith, R.P. Wise and J.A. Dickerson. 2012. The Hordeum Toolbox - The barley coordinated agricultural project genotype and phenotype resource. The Plant Genome 5:81-91.
  • 7.- Chen, J. L. ; C. G. Chu; E. J. Souza; M. J. Guttieri; X.M. Chen; S. Xu; D. Hole; R. Zemetra. 2012. Genome-wide identification of QTL conferring high-temperature adult-plant (HTAP) resistance to stripe rust (Puccinia striiformis f. sp. tritici) in wheat. Mol. Breeding 3:791-800.
  • 8.- Edwards, J.T., R.M. Hunger, E.L. Smith, G.W. Horn, M.-S. Chen, L. Yan, G. Bai, R.L. Bowden, A.R. Klatt, P. Rayas-Duarte, R.A. Osburn, J.A. Kolmer, Y. Jin, D.R. Porter, K.L. Giles, B.W. Seabourn, M.B. Bayles, and B.F. Carver. 2012. 'Duster' wheat: A durable, dual-purpose cultivar adapted to the southern Great Plains of the USA. J. Plant Reg. 6:1-12.
  • 12.- Hazard B., X. Zhang, P. Colasuonno, C. Uauy, D.M. Beckles, and J. Dubcovsky. 2012. Induced mutations in the Starch Branching Enzyme II (SBEII) genes increase amylose and resistant starch content in pasta wheat. Crop Sci. 52: 1754-1766.
  • 17.- Liu, Z.-H., Zhong, S., Edwards, M.C., and Friesen, T.L. 2012. Virulence profile and genetic structure of a North Dakota population of Pyrenophora teres f. teres, the causal agent of net form net blotch of barley. Phytopath. 102:539-546.
  • 18.- Lorenz, A.J., K.P. Smith, and J.-L. Jannink. 2012. Potential and optimization of genomic selection for Fusarium head blight resistance in six-row barley. Crop Sci. Vol. 52 No. 4, p. 1609-1621.
  • 19.- Mengistu, N., P. S. Baenziger, K. M. Eskridge, I. Dweikat, S. N. Wegulo, K. S. Gill, and A. Mujeeb-Kazi. 2012. Validation of QTL for grain yield-related traits on wheat chromosome 3A using recombinant inbred chromosome lines. Crop Sci.: 52:1622-1632.
  • 20.- Morrell, P.L., Buckler, E.S., Ross-Ibarra, J. 2012. Crop genomes: advances and applications. Nat. Rev. Genet. 13:85-96
  • 21.- Naruoka, Y., J. D. Sherman, S. P. Lanning, N. K. Blake, J. M. Martin, and L. E. Talbert. 2012. Genetic analysis of long green leaf duration in spring wheat. Crop Sci. 52: 1: 99-109.
  • 22.- Pradhan G.P., P.V.V. Prasad, A.K. Fritz, M.B. Kirkham, and B.S. Gill. 2012. Response of Aegilops species to drought stress during reproductive stages of development. Functional Plant Biology. 39:51-59.
  • 23.- Pradhan G.P., P.V.V. Prasad, A.K. Fritz, M.B. Kirkham, and B.S. Gill. 2012. Effect of drought and high temperature stress on synthetic hexaploid wheat. Functional Plant Biology. 39:190-198.
  • 24.- Pradhan G.P., P.V.V. Prasad, A.K. Fritz, M.B. Kirkham, and B.S. Gill. 2012. High temperature tolerance in Aegilops species and its potential transfer to wheat. Crop Sci. 52: 292-304.
  • 25.- Poland J.A., P.J. Brown, M.E. Sorrells, and J.-L. Jannink. 2012. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PloS ONE 7:e32253.
  • 26.- Yu, L-X, A. Morgounov, R. Wanyera, M. Keser, S. Kumar Singh, and M.E. Sorrells. 2012. Identification of Ug99 stem rust resistance loci in winter wheat germplasm using genome-wide association analysis. Theor. Appl. Genet. 125:495-502.
  • 13.- Heslot, N., H.-P. Yang, M.E. Sorrells, and J-L. Jannink. 2012. Genomic selection in plant breeding: A comparison of models. Crop Sci. 52:146-160.
  • 14.- Lanning, S. P., P. Hucl, M. Pumphrey, A. H. Carter, P. F. Lamb, G. R. Carlson, D. M. Wichman, K. D. Kephart, D. Spaner, J. M. Martin and L. E. Talbert. 2012. Agronomic performance of spring wheat as related to planting date and photoperiod response. Crop Sci. 52:1633-1639.
  • 15.- Lanning, S. P., J. M. Martin, R. N. Stougaard, F. R. Guillen-Portal, N. K. Blake, J. D. Sherman, A. M. Robbins, K. D. Kephart, P. Lamb, G. R. Carlson, M. Pumphrey, and L. E. Talbert. 2012. Evaluation of near-isogenic lines for three height-reducing genes in hard red spring wheat. Crop Sci. 52:1145-1152.
  • 16.- Leng, Y. and S. Zhong. 2012, Sfp-type 4'-phosphopantetheinyl transferase is required for lysine synthesis, tolerance to oxidative stress and virulence in the plant pathogenic fungus Cochliobolus sativus. Mol. Plant Path. 13: 375-387.
  • 27.- Zhang X.H., H.Y. Pan and G.H. Bai. 2012. Quantitative trait loci for fusarium head blight resistance in U.S. hard winter wheat cultivar 'Heyne'. Crop Sci. 52:1187-1194.
  • 28.- Zhou, H., Muehlbauer, G., and Steffenson, B. 2012. Population structure and linkage disequilibrium in elite barley breeding germplasm from the United States. J. Zhejiang Univ. Sci. B (Biomed & Biotechnol.) 13:438-451.
  • 29.- Chai, Y., Nirmala, J., Kleinhofs, A., and Steffenson, B. 2012. Failure of RPG1 protein to degrade in high-copy Rpg1 transgenic barley lines results in susceptibility to stem rust. Physiol. Molec. Plant Pathol. 80:10-18.
  • 30.- Luckert, D., Toubia-Rahme, H., Steffenson, B. J., Choo, T.-M., and Molnar, S. J. 2012. Novel Septoria speckled leaf blotch resistance loci in a barley doubled-haploid population. Phytopathology 102:683-691.
  • 31.- Kulwal, P., G. Ishikawa, D. Benscher, Z. Feng, L-X Yu, A. Jadhav, S. Mehetre, and M. E. Sorrells. 2012. Association mapping for pre-harvest sprouting resistance in white winter wheat. Theor Appl Genet. 125:793-805.
  • 32.- Kumar S., S.K. Sehgal, U. Kumar, P.V.V. Prasad, A.K. Joshi, B.S. Gill. 2012. Genomic characterization of drought tolerance-related traits in spring wheat. Euphytica 186:265-276.
  • 33.- Rutkoski, J., J. Benson, Y. Jia, G. Brown-Guedira, J.-L. Jannink, and M.E. Sorrells. 2012. Evaluation of genomic prediction methods for Fusarium head blight resistance in wheat. The Plant Genome. 5:51-61.
  • 34.- Tao Li, Guihua Bai, Shuangye Wu and Shiliang Gu. 2012. Quantitative trait loci for resistance to fusarium head blight in a Chinese wheat landrace Huangfangzhu. Euphytica 185:93-102.
  • 35.- Zhang X.H., H.Y. Pan and G.H. Bai. 2012. Quantitative trait loci responsible for fusarium head blight resistance in Chinese wheat landrace Baishanyuehuang. Theor. Appl. Genet. 125:495-502.


Progress 02/01/11 to 01/31/12

Outputs
OUTPUTS: Genotyping: We used Illumina genotyping platforms including 9000 SNP markers for genotyping the NSGC barley core collection (2,446 accessions), the wheat core collection (4,416 accessions) and a set of 5,520 wheat breeding lines and mapping populations (>100 million datapoints). More than 3,000 polymorphic SNPs have been integrated into both wheat and barley consensus genetic maps. Taken together, this extensive SNP information provides a detailed description of the genetic composition of the wheat and barley germplasm and is being used to identify associations between SNP markers and useful agronomic traits. A successful pilot study for exon capture in wheat was completed with a 3.5 Mb capture array. The results were published in Genome Biology. Larger capture designs have been developed in barley (~60Mb) and wheat (~100Mb) as part of two international consortia. We also tested a genotyping by sequencing approach for genotyping two mapping populations in wheat and barley. In the wheat population we mapped over 27,000 SNP markers and 150,000 tags as dominant markers. We have trained several different genomic selection (GS) models in barley for agronomic, disease, and grain quality traits and published the results in Crop Science. For a winter barley GS experiments we completed 64 crosses using forty-seven facultative parents. Phenotypes to train the GS model include freezing tests and winter survival in St. Paul, MN and are currently available for a total of 209 lines. Genomic breeding values will be used to select parents for the next round of crossing. The T3 database was established and the SNP and phenotypic data generated during the first year of the project are being entered into T3. We have currently entered 50.6 million genotypic data points and 100,105 phenotypic data points for multiple traits. A user group has been formed and has defined templates and pipelines to upload data to T3. Phenotyping: To standardize the water and N use efficiency phenotyping using Canopy Spectral Reflectance (CSR), a CSR workshop was completed (40 participants). The first drought experiments confirmed the usefulness of CSR to detect differences in drought tolerance among wheat cultivars and isogenic lines. Agronomic and physiological traits and high-throughput canopy spectral reflectance indices were evaluated in 540 accessions from the wheat NSGC core collection. QTL associated with water and nitrogen use efficiency are being identified. One thousand lines of the wheat NSGC core collections were evaluated for stripe rust, leaf rust and stem rust. New genes for resistance to stripe rust have been identified and published. A thousand barley lines were also evaluated for resistance to spot blotch. Screening of ~1000 lines from the barley NSGC core for the spot form of net blotch was completed and data is being analyzed. Resistant lines are being incorporated into breeding programs. The research activities resulted in 28 manuscripts accepted for publication in peer reviewed journals, numerous presentations in scientific meetings and the release of 14 new varieties and 12 improved germplasm. PARTICIPANTS: Individuals trained in this project: A total of 94 four students and plant breeding professionals have participated in T-CAP training first year activities. Twenty three PhD students have initiated their training programs on T-CAP research projects (eleven above year one target by leveraging funds). The Plant Breeding Training Network has been launched and is being used by undergraduates, graduate students and PIs. Over 30 graduate students have been meeting regularly to help test the PBTN, and have begun to build community and share ideas. A graduate level course for 21 students has been offered online. Four other graduate students are participating in the project through evaluation or film production. Fourteen undergraduates have begun work with TCAP researchers and met online with a representative from Pioneer. The Education team and evaluators had a successful meeting with representatives from Minority Serving Institutions (MSI) to establish collaborations. MSI recommendations made through a focus group were implemented in the creation of a request for proposals (RFP). The RFP was distributed to about 80 MSIs and we received 12 proposals that were evaluated and 8 were awarded (total awards $80,000). MSI and TCAP faculty are building collaborative relationships and seven students at MSIs have begun work. The education team organized a successful launching meeting in San Diego, an online meeting with the advisory panel, a Canopy Spectral Reflectance training in Denver, developed educational and evaluation tools and published two newsletters. The education team also hosted a talk for breeding for climate change at the National Association for Plant Breeders and supported attendance of over 70 students from around the country. Collaborations: The T-CAP has catalyzed multiple interactions among breeding programs, genotyping labs and barley and wheat researchers that would have not been possible without the T-CAP support. The T-CAP has promoted collaboration among the US breeding and genotyping programs accelerating the development of improved wheat and barley varieties. The T-CAP has also provided the necessary support to engage in large International collaborations such as the development of the barley 9000 SNP platform, the barley and wheat gene capture Nimblegen platforms, the construction of high-density SNP consensus maps and the initiation of compatible databases among large projects in CIMMYT, Europe, Australia, Canada and the US. T-CAP initiated research collaborations with eight minority serving institutions (see above). T-CAP members S. Baenziger, D. Namuth-Covert, and J. Sherman with private plant breeders and industry professional are forming a consortium to provide online course sharing for plant breeding students. T-CAP is providing support to identify and overcome barriers in course sharing as well as material support by providing an online meeting environment. TARGET AUDIENCES: The audiences targeted by this project include wheat breeders and wheat researchers. To facilitate access to new resistance genes we developed molecular markers for the stripe rust resistance genes Yr48 and QYr.ucw-3BS. New molecular markers for different rust resistance genes have been made publicly available through the MASWheat website http://maswheat.ucdavis.edu/protocols/.. The international wheat research community had access to the new mapping and sequencing information through publications in peer reviewed journals, several presentations in national and international conferences, and sequences deposited in GenBank. Presentations to wheat growers explaining the direct applications of this research have been made in field days and farm advisors meetings in California Several of the stripe rust resistance genes identified and mapped in our laboratory have been incorporated into public and private wheat varieties in California using marker assisted selection. These varieties covered more than 70,000 acres in 2011, limiting applications of costly fungicides, increasing growers' profitability and benefiting the environment. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
The T-CAP helped US wheat and barley breeders to accelerate the release of 14 new varieties, 12 new improved germplasm and two mapping populations and to characterize tens of thousands of breeding lines by using molecular markers. The project also initiated the testing of genomic selection methods in barley and wheat to accelerate the rate of improvement for targeted traits. The project has published molecular markers for several resistance genes (rusts, soil-borne wheat mosaic virus, fusarium head blight, tan spot) and agronomic traits (number of productive tillers, drought tolerance). These markers facilitate the engineering of varieties with multiple favorable traits. The deployment of resistant varieties reduces the use of pesticides, minimizing their negative impact on the environment and on production costs. In the quality area, studies were published for markers for grain protein content, flour color, milling yield, endosperm texture, dough-mixing strength, and bread-making properties. The incorporation of genes with favorable effects on quality contributed to increased value of the barley and wheat crops and the competitiveness of the US growers. Several of these favorable alleles have been already incorporated into commercial public varieties. One of the major accomplishments of the T-CAP during its first year has been the completion of the genotyping of the core barley and wheat collections from the NSGC with a 9000 SNP platform. These data provide a comprehensive characterization of the genetic diversity of the US wheat and barley germplasm collections, a platform for association mapping studies, and the opportunity to select parental lines for developing nested association mapping populations. The phenotypic characterization of the core collections for disease resistance, water use efficiency and nitrogen use efficiency was initiated and the year one datasets are being analyzed for associations between genotypic and phenotypic traits. These associations are the basis for the identification of valuable alleles that will then be used by the breeding programs to add value to their lines. The T-CAP was instrumental in attracting new PhD students to plant breeding. In addition, the organization of a centralized training network has provided students in different parts of the country access to experts in the different scientific disciplines that support plant breeding. The T-CAP educational web site was also used to deliver educational and outreach materials. In summary, the T-CAP has generated an integrated network of public wheat breeding programs, and promoted collaboration among the US barley and wheat breeding and genotyping programs accelerating the development of improved varieties for the different cereal growing regions of the US. It has also empowered the US breeding programs to engage in large international efforts aimed to accelerate the improvement of these two important crops.

Publications

  • Chen, J., Ch. Chu, E.J. Souza, M.J. Guttieri, X. Chen, S. Xu, D. Hole, and R. Zemetra. 2011. Whole genome-wide mapping for high-temperature adult-plant resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a hard red winter wheat germplasm IDO444. Molecular Breeding (DOI 10.1007/s11032-011-9590-x).
  • Li, P., J. Chen, P. Wu, J. Zhang, Ch. Chu, D. See, G. Brown-Guedira, R. Zemetra, and E. Souza. 2011. QTL analysis for the effect of RhtB1 dwarfing gene on coleoptiles length, seedling root length and numbers of bread wheat (Triticum aestivum L.). Crop Sci. 51: 2561-2568.
  • Zhang, D., G. Bai, R. M. Hunger, W. W. Bockus, J. Yu, B. F. Carver, and G. Brown-Guedira. 2011. Association study of resistance to Soilborne Wheat Mosaic Virus (SBWMV) in U.S. winter wheat. Phytopathology 101:1322-1329.
  • Bernardo A. N., H. Ma, D. Zhang, and G. Bai. 2011. Single Nucleotide Polymorphism in Wheat Chromosome Region Harboring Fhb1 for Fusarium Head Blight Resistance. Mol Breed. DOI 10.1007/s11032-011-9565-y.
  • Tsilo, T., G.A. Hareland, S. Chao, and J.A. Anderson. 2011. Genetic mapping and QTL analysis of flour color and milling yield related traits using recombinant inbred lines in hard red spring wheat. Crop Sci. 51:237-246.
  • Tsilo, T.J., G.L. Linkert, G,A. Hareland, and J.A. Anderson. 2011. Registration of the MN98550-5/MN99394-1 wheat recombinant inbred mapping population. J. Plant Registrations 5: 257-260.
  • Tsilo, T.J., S. Simsek, J.-B. Ohm, G.A. Hareland, S. Chao, and J.A. Anderson. 2011. Quantitative trait loci influencing endosperm texture, dough-mixing strength, and bread-making properties of the hard red spring wheat breeding lines. Genome 54: 460-470.
  • Saintenac, C., D. Jiang, E. Akhunov. 2011. Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome. Genome Biology, 12:R88.
  • Naruoka, Y., L. E. Talbert, S. P. Lanning, N. K. Blake, J. M. Martin and J. D. Sherman. 2011. Genetics of productive tiller number and its relationship to economic traits in spring wheat. Theor. Appl. Genet. 123:1043-1053.
  • Kalous, J. R., J. M. Martin, J. D. Sherman, N. K. Blake, S. P. Lanning and L. E. Talbert. 2011. Phenotypic variation and patterns of linkage disequilibrium associated with introduced genes in spring wheat. Crop Sci. 51: 2466-2478.
  • Blake, N.K., S.P. Lanning, J. E. Berg, P. L. Bruckner, J. D. Sherman and L.E. Talbert. 2011. Registration of spring and winter habit wheat lines derived from elite cultivars of the alternate growth habit. J. Plant Reg. 5:418-421.
  • Heslot, N., H.-P. Yang, M.E. Sorrells, and J-L. Jannink. 2011. Genomic selection in plant breeding: A comparison of models. Crop Science. Accepted with minor revisions.
  • Naruoka, Y., J. D. Sherman, S. P. Lanning, N. K. Blake, J. M. Martin, and L. E. Talbert. 2012. Genetic analysis of long green leaf duration in spring wheat. Crop Sci. In Press. DOI:10.2135/cropsci2011.05.0269.
  • Noriel, A.J., X.-C. Sun, W. Bockus and G.-H. Bai. 2011. Resistance to tan spot and insensitivity to Ptr ToxA in wheat. Crop Sci. 51:1059-1067
  • Wang, H., K.P. Smith, E. Combs, T. Blake, R. Horsley, and G.J. Muehlbauer. 2011. Effect of population size and unbalanced data sets on QTL detection using genome-wide association mapping in barley breeding germplasm. Theor. Appl. Genet. DOI 10.1007/s00122-011-1691-8.
  • Lowe, I., D. L. Jankuloski, S. Chao, X. Chen, D. See and J. Dubcovsky. 2011. Mapping and validation of QTL which confer partial resistance to broadly virulent post-2000 North American races of stripe rust in hexaploid wheat. Theor Appl Genet. 123:143-157.
  • Prasad, P.V.V., S.R. Pisipati, I. Momcilovic, and Z. Ristic. 2011. Independent and combined effects of high temperature and drought stress during grain filling and plant yield and chloroplast EF-Tu expression in spring wheat. Journal of Agronomy and Crop Science 197: 430-441.
  • Pradhan G.P., P.V.V. Prasad, A.K. Fritz, M.B. Kirkham, and B.S. Gill. 2011. High temperature tolerance in Aegilops species and its potential transfer to wheat. Crop Science In press.
  • Hao, Y., Z.Chen, Y.Wang, D. Bland, J. Buck, G. Brown-Guedira and J. Johnson. 2011. Characterization of a novel major QTL for adult plant resistance to stripe rust in US soft red winter wheat. Theor. Appl. Genet. In press.
  • Iwata, H. and J.-L. Jannink, 2011. Accuracy of genomic selection in barley breeding programs: a simulation study based on the real SNP data. Crop Sci. 51:1915-1927.
  • Li. P., J. Chen, and Pute Wu. 2011. Evaluation of Grain Yield and Three Physiological Traits in 30 Spring Wheat Genotypes across Three Irrigation Regimes. Crop Sci. 52:1-12.
  • Pradhan G.P., P.V.V. Prasad, A.K. Fritz, M.B. Kirkham, and B.S. Gill. 2011. Response of Aegilops species to drought stress during reproductive stages of development. Functional Plant Biology. In press.
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