Source: UNIVERSITY OF CALIFORNIA, DAVIS submitted to
VALIDATION, CHARACTERIZATION AND DEPLOYMENT OF QTL FOR GRAIN YIELD COMPONENTS IN WHEAT
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
EXTENDED
Funding Source
Reporting Frequency
Annual
Accession No.
1011593
Grant No.
2017-67007-25939
Project No.
CA-D-PLS-2373-CG
Proposal No.
2016-06708
Multistate No.
(N/A)
Program Code
A1142
Project Start Date
Dec 15, 2016
Project End Date
Dec 14, 2019
Grant Year
2019
Project Director
Dubcovsky, J.
Recipient Organization
UNIVERSITY OF CALIFORNIA, DAVIS
410 MRAK HALL
DAVIS,CA 95616-8671
Performing Department
Plant Sciences
Non Technical Summary
More than 700 million tons of wheat are produced each year, providing more than one fifth of the calories and protein consumed by the human population. Current rates of improvement for wheat grain yield are not sufficient to feed a rapidly growing human population. Further increases in global wheat production will benefit from the identification and characterization of genes controlling wheat yield. The identification of these genes is a necessary first step to understand how these genes work, how they interact with each other and with the environment and how to combine them to accelerate the rates of wheat improvement for grain yield.In our previous Collaborative Agricultural Project (Triticeae CAP), we identified several wheat chromosome regions that have a positive effect on grain yield. However, the genes responsible for these beneficial effects remain unknown. The tools required for the identification and validation of these genes have been recently developed for wheat, including the first genome sequence and the development of sequenced mutant populations for gene validation. The application of these new tools to the well-characterized genetic populations developed in our previous project provides a unique opportunity to identify the genes controlling grain yield. Today, wheat is in a situation similar to that of rice after the release of its genome sequence in 2005, which resulted in an exponential increase in the number of identified genes in rice. In this project we propose to use these new tools to identify 15 genes controlling grain size, grain number, reproductive tiller number and overall grain yield. The chromosome regions controlling these traits have been identified in our previous grant. In this project, we will develop very large mapping populations segregating only for the chromosome region of interest and will use this genetic information to define precisely the candidate gene region. We will then use the recently released wheat genome sequence to identify all the genes present in the targeted region and to identify candidate genes. These candidate genes will be validated using available sequenced mutant populations and transgenic approaches including genome editing.These beneficial gene variants will be incorporated into elite breeding wheat lines to test their effect on grain yield in different environments. Lines differing only in the selected genes will be developed to test precisely the effect of the targeted genes. In addition, we will test the effect of different gene combinations on overall grain yield.A long-term constraint to future increases in wheat production in the USA is the limited number of trained plant breeders. In this project we will train the next generation of plant breeders, providing direct experience in field-based research, experimental design and bioinformatics tools. Our group has access to active breeding programs supported by the Universities, which will provide a perfect environment to train students in plant breeding. In addition, we will provide students online conferences and courses, face-to-face workshops, student seminars, and student discussion workshops. Each student will lead one gene identification and one gene deployment program. Students will see firsthand the challenges and rewards of transferring value from research to commercial varieties. Finally, the interaction with CIMMYT will provide students a global vision of plant breeding. The simultaneous training of a cohort of 15 PhD students will enhance the opportunities for collaboration and teach students the value of team work to solve complex problems. Results from this project will be disseminated in two ways. First, by releasing germplasm and varieties with alleles for increased yield. Growers will be able to see in their fields the benefits of this research. Isogenic lines carrying the selected alleles will be also showcased in field days and demonstration trials to show growers and industry concrete examples of the value generated by this research project. Results from comparative yield trials will be presented in local grower meetings, wheat commissions, and local agronomic journals to directly reach the growers. Second, results will be presented in publications in peer reviewed scientific journals and in national and international scientific conferences. Students will be encouraged to disseminate their work in posters, conferences and field day presentationsThe ultimate goal of this project is to accelerate the rate of wheat improvement for grain yield without jeopardizing its quality and nutritional value.
Animal Health Component
0%
Research Effort Categories
Basic
20%
Applied
80%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011549108050%
2011549108150%
Goals / Objectives
The overall goals for this project are the validation, characterization and deployment of QTL for grain yield components in wheat and the training of a new generation of plant breeders. The specific objectives of the project are to: 1) Characterize 15 QTL for grain yield and identify the underlying genes. 2) Validate the candidate genes using mutants and transgenic approaches.3) Deploy beneficial alleles in commercial varieties and advanced breeding lines. 4) Develop genomics tools to characterize the regulatory regions of the wheat genome. 5) Train a new cohort of 15 plant breeders, and make the training resources widely available.
Project Methods
Methods for Objective 1. To identify the genes underlying the yield QTL we will use a map-based cloning approach. First we will define well the phenotypes by reducing the genetic and environmental variability in segregating populations. To reduce the genetic variability among segregating lines we will use heterogeneous inbred families (HIFs). We will adjust the number of replications based on the observed variability between and within isogenic lines to maintain high statistical power. Lines with critical recombination events will be self-pollinated and homozygous recombinant and non-recombinant sister plants will be used to produce seeds for field experiments. We will use a two stage high-density mapping strategy. The flanking markers will be used to delimit the QTL region in the current assembly of the wheat genome and to identify candidate genes. We will use the exome and regulatory capture platforms to identify a large number of polymorphisms in the selected HIFs and deliver them to the respective PhD students. The list of candidate genes and putative causal mutations will be prioritized based on their significance in the AM panels, known function of the genes in other species and expression profiles. Methods for Objective 2. To prioritize candidate genes identified in the targeted regions for validation, we will integrate information from model species, wheat gene expression databases, and whole-genome imputation methods based on genotypic and phenotypic data generated in the TCAP project. We will also take advantage of other biparental populations and AM panels segregating for the same QTL. Natural variation among these lines will be used to identify historic recombination events to dissect the target regions. Candidate genes will be validated using mutants from our tetraploid and hexaploid sequenced TILLING populations, which include >10 million EMS mutations in gene regions. For validation purposes we will prioritize the tetraploid mutant population, because it is easier to combine mutations in two genomes than in three. Mutants will be backcrossed twice to the non-mutagenized Kronos to reduce mutation load. The hexaploid TILLING population will be used if appropriate mutations are not identified in tetraploid wheat. If mutations are not found or when closely linked paralogs need to be mutagenized, we will use CRISPR-Cas9 genome editing to generate knock-out mutants of the target genes. Methods for Objective 3. In collaboration with the local wheat breeder, each PhD student will select at least one QTL to deploy into his/her home breeding program. Using backcrossing or forward breeding strategies the selected allele will be introgressed into commercial varieties or advanced breeding lines. The student can select the QTL from his/her cloning project or from previously published studies. The PhD student can also select a mutant with known positive effects on wheat yield components. Alternatively, students can pursue the rapid pyramiding of multiple QTL for yield components using genomic selection approaches. The PhD students will work in close collaboration with the wheat breeders to select recurrent parents and strategies for forward breeding approaches. The students will collaborate with the regional genotyping labs in the development of high-throughput markers and in the screens of the large populations required to implement forward breeding marker assisted selection (MAS) strategies. PhD students will also collaborate with CIMMYT to test their isogenic lines in Obregon. Students working on winter wheat will transfer their QTL to one spring advanced line from CIMMYT-ESWYT panel through backcrossing. Methods for Objective 4. We will characterize sequence variation in the regulatory regions using a dedicated capture platform. We will also characterize chromatin structure in these regulatory regions using a nuclease sensitivity assay. These results will be integrated with RNA-Seq data and with candidate genes identified in this study to characterize gene regulatory networks controlling yield-related traits. To identify the regulatory regions, we will use the last version of the wheat genome annotation. We will target up to 1.5 kb of genomic regions upstream and 0.5 kb downstream from wheat gene models, introns not included in the previous exon capture and regions including miRNA precursors will be selected to design a 100 Mb Nimblegen SeqCap EZ capture assay (RegCap assay). Parental lines of the different HIF populations will be re-sequenced using the RegCap assay. A published bioinformatics pipeline will be applied for variant calling. Regulatory SNP variation will be made available through the T3 and Ensembl Plants databases. To delimit critical sequences within these wheat regulatory regions, we will develop and perform Micrococcal Nuclease (MNase) sensitivity assays. By mapping a wide range of fragment sizes, we will establish the genomic distributions of both nucleosomes and numerous non-histone proteins. MNase hyper-sensitive and hyper-resistant regions will be added to the annotation of the wheat genome and made available through the T3 and Ensembl Plants databases. To manage the large amount of genotypic and phenotypic information generated in this project, we will take advantage of "The Triticeae Toolbox" (T3) database. T3 will be improved to facilitate the identification and validation of candidate genes and to link current phenotypic, genotypic and genomics data. T3 will develop tools to take advantage of the extensive phenotypic and genotypic data sets generated in the previous TCAP project. T3 will provide tools to impute genotyping datasets up to full set of exome polymorphisms, to implement GWAS on each phenotyping trial and trait, and to perform meta-analyses to identify genomic regions enriched and depleted in QTL signal. This information will be linked to JBrowse tracks, one including the TILLING mutants and the other showing local recombination rates based on recombination events tallied in the wheat NAM populations. We will also link genes identified in the candidate gene region with new tools that discriminate expression among wheat homoeologs.Methods for Objective 5: This project will provide support and integrated training in these areas to 15 PhD students. PhD students will have a field-based component and will be trained in experimental design and bioinformatics through online conferences and courses, face-to-face workshops, student seminars, and student discussion workshops. Each student will lead a QTL dissection project, which will provide training in genetic studies, marker development and integration of genomic resources to gene identification and validation. Each student will also have a QTL deployment project to give them the opportunity to work in close collaboration with breeders and genotyping labs. Students will see firsthand the challenges and rewards of transferring value from research to commercial varieties. Finally, the interaction with CIMMYT will provide students a global vision of plant breeding. The simultaneous training of a cohort of 15 PhD students will enhance the opportunities for collaboration and teach students the value of team work to solve complex problems. As in the previous TCAP, graduate students not specifically funded by the project will also be invited to participate in the educational activities.

Progress 12/15/17 to 12/14/18

Outputs
Target Audience:The audiences targeted during the second year of the project include: 1) Wheat growers and wheat grower associations. WheatCAP breeding programs presented their results to state wheat commissions, grower associations and individual growers during field days and annual meetings. Wheat growers will be the primary beneficiaries of new varieties developed by the WheatCAP. 2) Wheat milling and baking industry.WheatCAP results were presented to the Wheat Quality Council and other Quality Collaborative Programs across the USA. Presentation were also made to individual milling and baking companies. 3) Wheat researchers working in basic and applied aspects of wheat. Results from the WheatCAP were presented to other researchers in 54 papers published in peer-reviewed journals and at national conferences including Plant and Animal Genome and ASA-CSSA meetings. 4) International wheat research community. WheatCAP researchers made presentations in different countries and published their results in internationally recognized scientific journals. WheatCAP participants sent improved wheat lines to the CIMMYT hub in Mexico. WheatCAP PD participated in the IWYP annual meeting in the UK. 5) Wheat breeders in the public and private sector. Varieties and germplasm generated by WheatCAP breeders have been made available to all members of the WheatCAP team and to public and private sector breeding programs that requested seeds for crossing. Markers for specific yield-enhancing genes are public information through T3. Kronos TILLING mutants for 110 lines were distributed to 15 laboratories in 2018. All mutations are accessible and searchable in a public database and the seeds of the mutant lines are distributed without IP limitations. The audiences targeted by the educational part of this project include: 1) Graduate and undergraduate students interested in plant breeding (including students outside the project). Education materials including videos of the presentations at the UCD Davis workshop on positional cloning and the KSU workshop on RNAseq have been updated in the Plant Breeding Training Network (PBTN) web site and are freely available to the public. 2) Educators interested in online tools for plant breeding and genetics. The results of surveys generated by WheatCAP and previous TCAP are available through the WheatCAP website. 3) Breeding companies interested in the training of their workforce. WheatCAP requested input from private breeding companies regarding the needs of new breeders, and those recommendations are being implementedin webinars and courses. 4) Wheat growers and grower organizations through field days and other venues conducted by participating breeders. In additional to the information regarding the new wheat varieties, we educate glowers, private breeders and seed handlers about the opportunities and limitation of new technologies. This information has facilitated a wide acceptance of new marker technologies. Changes/Problems:The subcontracts for the second year for the 19 institutions was completed on time and the funding was available to all collaborators in early 2018. The 2018 financial report covers expenses up to July 31, 2018 so there are still 4.5 months of spending this year. The current spending is at 37% of the budget but, in reality, it is closer to 50%. This distortion is due to the forward funding received in year two, which is being saved for the fifth year of the project as originally planned. There have been no changes in the budgets or original objectives. The budget of USDA-ARS Ithaca will continue to be transferred to Cornell University to provide T3 more flexibility and to simplify administration as approved last year for the complete duration of this grant. The only minor change in personnel was the retirement of Dr. Shiaoman Chao, who was in charge of the USDA-ARS small grains genotyping laboratory in Fargo, ND. Currently, Dr. Justin Faris is overseeing the laboratory. The scientist position was posted this past July and the interview and hiring process will be ongoing this fall to fill this position. What opportunities for training and professional development has the project provided?A central objective of the WheatCAP project is to train PhD students in molecular plant breeding. By leveraging funds from participating universities, the WheatCAP participants have exceeded the target of 15 students. The WheatCAP is currently training 18 PhD students and 4 MS students (45% female). Three additional students have graduated (1 MS and two PhD students that started their projects supported by TCAP completed them with WheatCAP support). Student education progress was monitored by an annual survey. The information generated by the surveys was used by the education team to adjust the project to the educational needs of the students. The annual survey results are posted online at the following link: https://www.triticeaecap.org/2018-graduate-student-survey/ In 2018, Wheat-CAP students participated in workshops that taught them the technical skills required for their positional cloning projects, and soft skills to help enhance their science communication abilities. The first workshop was hosted by WheatCAP director Jorge Dubcovsky at UC-Davis (January 8-12) and introduced the students to the overall strategy of positional cloning. The workshop hosted 27 participants from around the country. This workshop was essential to ensure that all the students have a clear understanding of the methods and complexities of the proposed projects. A second workshop was hosted at Cornell University (June 25-29) to teach the students how to communicate science to the public. This workshop was hosted by Sarah Evanega, director of Alliance for Science, in collaboration with the USDA IWYP funded Gene Editing research project. Seven Wheat-CAP students attended the workshop with several other students from different research projects, and they learned how to relate their research to the public through storytelling methods. A third workshop was hosted by WheatCAP co-Director Eduard Akhunov and Alina Akhunova at Kansas State University (July 9-13) on the use of RNA-Seq/Bioinformatics to identify candidate genes controlling the student's trait of interest. Twenty-two individuals participated in this workshop. Lectures from the two workshops were recorded and are posted on the PBTN https://passel.unl.edu/communities/pbtn and WheatCAP website and in T3. In addition to the workshops, the students participated in two online courses. The first one was held this summer (June - August) and was designed by Jean-Luc Jannink from Cornell University. The course trained the students on the use of T3 and GrainGenes databases for their research projects. This online course hosted eight online lectures and all lectures are posted on PBTN. Lastly, another online course was hosted this summer (June - August) by Loriana Sekarski (corporate soft skill consultant, Bonsai) to teach soft skills to the WheatCAP students. This course focused on having the students identify their strengths, teaching them how to leverage these strengths, develop their brand, and network efficiently. Educational activities also included the update of the infrastructure of the online PBTN education delivery platform. Leah Sandall upgraded the Plant and Soil Sciences eLibrary (PASSeL), which houses PBTN, to make both sites mobile-friendly.These revisions will result in PBTN being easily accessible by all web-browsing devices. The new target date for completion of the mobile-friendly upgrades is January 2019. Lastly, both Leah and DeAnna Crow, administrative assistant, have been conducting routine maintenance on PBTN, and have been formatting the recorded workshop and online lectures for posting on the website. How have the results been disseminated to communities of interest?Results generated by WheatCAP researchers have been disseminated in multiple ways. First, results have been published in 54 peer-reviewed publications in prestigious scientific journals. Results have been also presented at multiple scientific meetings including the ASA-CSSA meeting, the Plant and Animal Genome meeting. The WheatCAP results were presented in the IWYP 2018 conferences in the UK. The individual QTL cloning projects are described in the WheatCAP web site. These descriptions include the targeted trait, the chromosome region of the QTL and the flanking markers used to develop the high-density maps. https://www.triticeaecap.org/qtl-cloning-projects/. Marker assisted selection protocols are being delivered to the MASwheat web site (http://maswheat.ucdavis.edu/). New genomics resources generated by WheatCAP have been widely advertised through GrainGene's list server, conferences, and computer demos. Resources have been made widely available to the international wheat research community. Results have been communicated directly to growers attending field days hosted by the 15 breeding programs that participate in WheatCAP. Results have been also shared with state wheat commissions and other wheat grower associations. Results affecting quality have been presented in Wheat Quality Council and in quality collaborative program in different states. These meetings include breeders, handlers, millers and bakers. Educational tools have been distributed throughonline resources and courses are accessible through PBTN. What do you plan to do during the next reporting period to accomplish the goals? Education:In 2019, the Wheat-CAP students will host a Pioneer Symposia in San Diego, CA on January 11th, a day before the 2019 PAG conference begins. The topic of the Pioneer Symposia will be focused on how genomic technology is being used to increase yield. Jean-Luc Jannink is scheduled to host a workshop at Cornell University this upcoming summer that will be focused on database management, and he will introduce the students to new informatics tools being developed by the Genomic Open-source Breeding Informatics Initiative (GoBii) project. The soft skill training will continue in year three with Sarah Evanega leading another Science Communications workshop, and Loriana Sekarski continuing to lead the online soft skill course. T3:The T3 group will collaborate with that Edward Buckler lab and the Akhunov Lab in bringing the genome data storage and imputation method called PHG to wheat. Previously, the T3 team tested the 62 wheat-exome reference of Jordan et al. (2015) for imputation using Beagle4 (Browing & Browning, 2009). The collaboration with the Buckler lab will expand the reference set used for imputation and will facilitate the comparison of the two methods (Beagle4 and PHG). When new wheat lines are uploaded to T3 with genotype data of adequate density, they will be imputed. The imputed data will be available for download along with imputation statistics summarizing the reliability of imputed scores. Internally, the imputed scores will be used for GWAS analyses. GWAS analyses using imputed scores will take the reliability of those scores into account, as advocated by Guan and Stephens (2008). To date, all T3 functions (e.g., clustering by genotype, genomic prediction, haplotype tracking), have been run on original genotypes. Genotype imputation will be initially most important for T3 for the GWAS function, and that will be implemented first. Later, users will have options for downloading imputed genotypes and for applying other functions using genotypes on imputed rather than original genotypes. Thus, imputed genotypes will be stored in parallel tables to the original genotypes, but functions will query the relevant tables, as requested by users. The T3 team is developing a report to provide links from T3 to Knetminer / Wheat (http://knetminer.rothamsted.ac.uk/). The report will enable T3 users interested in a particular gene to explore knowledge on that gene culled from the literature and assembled into a network that helps identify if a the gene can be considered a likely candidate affecting a trait. In collaboration with the John Innes in the UK, WheatCAP is running analyses to design PCR primers for polymorphisms identified among Wheat CAP parents. Links to those primers will be made available through T3. When the Akhunov Lab releases new data from either exome or regulatory capture assays, T3 will make those available through T3. Likewise, T3 will incorporate data from MNase and ATAC-Seq into new JBrowse tracks, giving users prior information on which variants are likely to be exposed to DNA regulatory and transcription machinery. Genomics Resources: In the next year, the KSU group will continue its focus on re-sequencing the regulatory regions of a diverse set of wheat lines using the newly designed capture assay for wheat promoter regions. They will compare chromatin accessibility profiles obtained using ATAC-seq and MNase approaches. Chromatin accessibility profiles for developing spikes and embryos of hexaploid wheat and their relationship to gene expression will be obtained. The analyses of regulatory capture data generated for Wheat CAP parental lines and diversity panel will be completed and deposited into T3. The information about regulatory sequence variation will be integrated with gene expression, with a focus on candidate genes for the grain yield components targeted in this study. To connect the expression and diversity data, RNA-seq profiling of developing spike tissues will be implemented across several wheat accessions in collaboration with KSU IGF. The KSU group will collaborate with the T3 team on the analyses of genetic diversity, chromatin accessibility and gene expression data and in the development of bioinformatics tools to facilitate the access of this data to users. In collaboration with the genotyping laboratories, the KSU group will develop an updated rhAmpSeq assay. This assay will incorporate SNPs relevant for US breeding programs selected from the next-generation Practical Haplotype Graph (PHG) constructed using a representative sample of exome-captured data from 217 US wheat lines. Plans for the cloning projects: All cloning projects will continue to narrow down the candidate gene regions by screening larger populations to identify recombination events between the markers flanking the QTL. These recombinant lines will be evaluated in the field to determine the position of the QTL within the candidate interval. New markers will be developed in this candidate gene region using the exome capture data generated in year 1. The position of the QTL relative to the new recombination events identified in the candidate gene interval will be established in the third year. For the candidate genes already identified within the target intervals, the focus will shift to the validation of the candidate genes.Validation activities will include reduction of the candidate regions by additional recombinants, characterization of natural haplotype variation withinthe region, characterization of mutants in the sequenced TILLING populations, and complementation experiments using transgenics.To determine if a candidate gene is essential for the observed phenotypes, loss-of-function mutations in the A and B genome homoeologs of the candidate gene will be combined to generate complete loss-of-function mutants. If no loss-of-function mutations are identified, knock out mutations will be generated using CRISPR-Cas9. If feasible, CRIPR-Cas9 will be used to edit the same polymorphisms as the one observed in nature, to validate the causal polymorphisms. To determine if the candidate gene is sufficient to cause the observed phenotype, transformation will be used to demonstrate complementation. The mutant lines will be transformed with the functional allele of the candidate gene under its natural promoter.

Impacts
What was accomplished under these goals? Wheat-CAP overall productivity: During the second year of the WheatCAP, 47 peer-reviewed papers (plus 7 in press) were published acknowledging the USDA-NIFA support. WheatCAP breeders have directly benefited the wheat growers and the wheat industry by releasing 14 commercial wheat varieties, 8 improved germplasm, and 5 mapping populations. The complete lists of released varieties and publications are available at https://www.triticeaecap.org/publications-and-germplasm/ . The project completed the training of three graduate students and other 22 advanced in their classes and projects. T3 database: T3 added 24 phenotyping trials including experiments from TCAP, Winter Wheat Scab Nursery, and Mason-Dixon Yield Trials. The 2017_WheatCAP_UCD genotype trial was added, which includes exome capture of all parents in the Wheat CAP project. The T3 team developed a tool to select markers based on their polymorphism within subsets of lines. A report page was developed to show the Variant Effects Predictor values for the RefSeq_v1 assembly. The Variant Effect Predictor can be used to prioritize genomic variants in coding and non-coding regions. The report also includes links to the Sorting Tolerant from Intolerant (SIFT) score provided by Ensembl Plants. The T3 team added browse and search functions for genome annotations from RefSeq_v1, TGACv1, and the David Edwards lab Wheat Pangenome. The JBrowse database was updated for RefSeq_v1 and incorporated variety tracks. T3 developed a BLAST server linked to JBrowse showing Variant Effect Predictor values. A JBrowse track was added showing the local recombination rate. The T3 team added tutorials for Variant Effects, TASSEL, Flapjack, and R scripts. An interface from T3 to the graphical genotype viewer Flapjack was developed using Breeding API. Flapjack has functionality to analyze and provide decision support for marker assisted backcrossing, which should help WheatCAP students in incorporating their QTL into CIMMYT backgrounds. Genomics resources:Sequenced tilling populations: WheatCAP has provided access to the sequenced mutant populations of tetraploid and hexaploid wheat sequenced mutant populations. In the first 8 month of 2018, WheatCAP distributed 110 samples to 15 laboratories. Exome capture of parental lines of the WheatCAP mapping populations: WheatCAP re-sequence the coding sequences of 47 wheat lines used as the parents of the Wheat CAP mapping populations. On average, 57 million 150-bp paired-end reads were generated for each line and mapped to the latest version of the wheat genome reference (IWGSC, v. 1.1) providing 50x coverage of the targeted genomic regions. The variant calling used the GATK-based pipeline to discover 1,043,576 SNPs in the population. The data was deposited in Grain Genes and T3 databases. Developing the Practical Haplotype Graph (PHG) tool for wheat: The KSU lab and T3 developed a PHG for wheat. PHG is an effective SNP data storage and retrieval tool that requires a representative set of wheat lines that capture haplotypic diversity of wheat for predicting missing genotypes. The sequence data generated for 47 Wheat CAP lines was used to start building the first-generation haplotype graph of wheat. To increase the utility of PHG for US breeding programs, a panel 217 US wheat cultivars that represent genetic diversity of modern US breeding programs was assembled. The first 96 lines have been sequenced by exome capture. Low-cost genotyping assay based on rhAmpSeq (IDT): The KSU lab collaborated with E. Buckler's group to develop a low-cost genotyping assay for wheat based on rhAmpSeq technology developed by IDT. For this purpose, nearly 7 million SNPs obtained for 800 exome-captured accessions were used to select 2,999 genome-wide distributed common SNPs. The assay was supplemented with 120 functional markers associated with various agronomic traits identified by the Wheat CAP or wheat community. Exome capture genotype imputation resource: The first generation haplotype map of wheat was used to impute SNPs in the winter wheat association-mapping panel to demonstrate that increase in the SNP marker density substantially improves the precision of trait mapping and improves the accuracy of genomic prediction. Regulatory sequence capture: The design of the regulatory sequence capture targeting 250 Mb of unique genomic regions including predicted miRNA binding sites and 2 kb upstream of each gene model in the wheat genome was completed. The assay was tested on a set of 30 wheat lines from the US and UK (published in 2018). 12 Wheat CAP parental lines and 200 diverse wheat accessions. On average, 46.1 million reads were generated for each accession providing about 25x coverage of the wheat promoter regions. Chromatin accessibility: MNase and ATAC-seq chromatin accessibility assays were optimized for wheat. The MNase assay was used to identify functionally active regions of the wheat genome. For this purpose, the KSU group have prepared libraries from the MNase treated nuclei isolated from wheat leaves and roots to obtain 10x coverage of the wheat genome. The sequence reads were aligned to the reference genome and used to identify regions with open chromatin. Consistent with expectations, joint analyses of public RNA-seq data generated for cv. Chinese Spring and MNase sensitivity score showed strong correlation. Wheat NAM population: The spring wheat NAM population was developed, genotyped using 90K iSelect, and exome capture assays and used to characterize the distribution of 102,000 recombination breakpoints across the wheat genome. The NAM population was also used to identify QTL controlling the distribution of recombination along the chromosomes. Results were published in 2018. Genotyping Laboratories: The genotyping laboratories supported the WheatCAP activities by providing genotyping services to breeders and researchers who seek to improve the productivity and quality of wheat varieties. Since the WheatCAP project was initiated, the Fargo lab has provided services for processing Illumina 90k SNP arrays for 30 projects consisting of over 8,000 samples and generating 736 million data points for wheat. The labs at Manhattan and Raleigh have produced similar numbers of data points. The Pullman lab has developed primer pools for amplicon sequencing of hundreds of markers across the genome. Each of the regional labs is collaborating to expand exome capture data for elite US cultivars and to develop inexpensive haplotype-based approaches to genotyping. The genotyping labs also provided genotyping services using SSRs and KASP markers for marker-assisted selection of specific agronomically important traits to all breeding programs in their respective regions. CIMMYT HUB. Matthew Reynolds The CIMMYT hub started to test the lines generated by the WheatCAP. In 2018, they tested Kronos homozygous mutants with four different allelic combinations of Elf3 allele from T. monococcum for increased spikelet number and the gw-A2 mutant allele for increased grain size. The lines carrying the ELF3 allele from Triticum monococcum accession DV92 showed an 8.6% higher yield than the lines carrying the wild type allele. The lines carrying the Gw-A2 mutation showed a 7% increase in kernel size, which is consistent with previous results reported in CA and the UK. The line combining the ELF3 allele from DV92 and the Gw-A2 mutation showed the highest yield. QTL cloning projects:All QTL cloning project advanced their mapping projects by identifying recombination events within their candidate regions and evaluating these critical recombinant lines in greenhouse and field experiments. Using these data, most projects defined the QTL candidate regions more precisely within the reference wheat genome. Candidate genes have been identified for four QTL cloning projects and validation experiments of the candidate genes have been initiated using mutant lines.

Publications

  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Anderson, J.A., J.J. Wiersma, G.L. Linkert, S. Reynolds, J.A. Kolmer, Y. Jin, M. Rouse, R. Dill-Macky, G.A. Hareland, and J.-B. Ohm. 2018. Registration of 'Norden' hard red spring wheat. J. Plant Registrations. 12:9096.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Anderson, J.A., J.J. Wiersma, G.L. Linkert, S. Reynolds, J.A. Kolmer, Y. Jin, M. Rouse, R. Dill-Macky, G.A. Hareland, and J.-B. Ohm. 2018. Registration of 'Linkert' spring wheat with good straw strength and adult plant resistance to the Ug99 family of stem rust races. J. Plant Registrations 12:208214.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Anderson, J.A., J.J. Wiersma, G.L. Linkert, S. Reynolds, J.A. Kolmer, Y. Jin, M. Rouse, R. Dill-Macky, G.A. Hareland, and J.-B. Ohm. 2018. Registration of 'Bolles' hard red spring wheat with high grain protein concentration and superior baking quality. J. Plant Registrations 12:215-221.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Ando, K., S. Rynearson, K. T. Muleta, J. Gedamu, B, Girma, N. Bosque-P�rez, M. S. Chen, M. O. Pumphrey. 2018. Genome-Wide Associations for Multiple Pest Resistances in a Northwestern United States Elite Spring Wheat Panel. Plos One 13: e0191305.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Ayana GT, Ali S, Sidhu JS, Gonzalez Hernandez JL, Turnipseed B and Sehgal SK (2018) Genome-wide association study for spot blotch resistance in hard winter wheat. Front. Plant Sci. 9:926. doi:10.3389/fpls.2018.00926.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Bai, G., Z. Su, J. Cai. 2018. Wheat resistance to fusarium head blight. Can J. Plant Pathol. doi.org/10.1080/07060661.2018.1476411.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Belamkar, V, M.J. Guttieri, W. Hussain, D. Jarqu�n, I. El-basyoni, J. Poland, A. J. Lorenz, P.S. Baenziger. 2018. Genomic Selection in Preliminary Yield Trials in a Winter Wheat Breeding Program. G3: Genes, Genomes, Genetics. 8: 2735. doi:10.1534/g3.118.200415.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Blake, N. K., A. C. Varella, B. Bicego, J. M. Martin, J. P. Cook, H.-Y. Heo, R. Acharya, J. D. Sherman, D. Nash, L. E. Talbert. 2018. Maturity traits related to climate adaptation impact quality characteristics in hard red spring wheat. Crop Sci. 58:1954-1963.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Case, A.J., S. Bhavani, G. Macharia, Z. Pretorius, V. Coetzee, F. Kloppers, P. Tyagi, G. Brown-Guedira, B.J. Steffenson. 2018. Mapping adult plant stem rust resistance in barley accessions Hietpas 5 and GAW 79. Theor Appl Genet. doi.org/10.1007/s00122-018-3149-8
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Chen, S., Y. Guo, J. Briggs, F. Dubach, S. Chao, W. Zhang, M.N. Rouse, J. Dubcovsky. 2018. Mapping and characterization of wheat stem rust resistance genes SrTm5 and Sr60 from Triticum monococcum Theor. Appl. Genet. 131: 625-635.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Chen, S., W. Zhang, S. Bolus, M.N. Rouse, J. Dubcovsky. 2018. Identification and characterization of wheat stem rust resistance gene Sr21 effective against the Ug99 race group. PLOS Genetics. 14: e1007287.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Cook, J.; Heo, H.-Y. Varella, A., Lanning, S., Blake, N, Sherman, J. D, Martin, J., See, D. R, Chao, S., L. Talbert. 2018. Evaluation of a QTL mapping population comprised of hard red spring and winter wheat alleles using various marker platforms. Crop Sci. 58:701-712.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Dong H, R. Wang, Y. Yuan, J. Anderson, M. Pumphrey, Z. Zhang, J. Chen. 2018. Evaluation of the potential for genomic selection to improve spring wheat resistance to Fusarium head blight in the Pacific Northwest. Frontiers in Plant Science. 9: 911.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Edae, E. A., M.O. Pumphrey, and M.N. Rouse. 2018. A genome-wide association study of field and seedling response to individual stem rust pathogen races reveals combinations of race-specific genes in North American spring wheat. Frontiers in Plant Science 9:52.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Elbasyoni I.S., A.J. Lorenz, M. Guttieri, K. Frels, P.S. Baenziger, J. Poland, E. Akhunov. 2018. A comparison between genotyping-by-sequencing and array-based scoring of SNPs for genomic prediction accuracy in winter wheat. Plant Sci. 270:123-130.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: El-Feki, W.M., P.F. Byrne, S.D. Reid, and S.D. Haley. 2018. Mapping quantitative trait loci for agronomic traits in winter wheat under different soil moisture levels. Agronomy 8: 133.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Frels, K., M. Guttieri, B. Joyce, B. Leavitt, P.S. Baenziger. 2018. Evaluating canopy spectral reflectance indices to estimate nitrogen use traits in hard winter wheat. Field Crops Research 217:82. DOI : 10.1016/j.fcr.2017.12.004
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Gardiner, L.-J., T. Brabbs, A. Akhunova, K. Jordan, H. Budak, T. Richmond, S. Singh, L. Catchpole, E. Akhunov, A. Hall. 2018. Integrating genomic resources to present full gene and promoter capture probe sets for bread wheat. bioRxiv. 363663.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Gizaw, S.A., J.G.V. Godoy, K. Garland-Campbell, A.H. Carter. 2018. Using spectral reflectance as proxy phenotypes for genome-wide association studies of yield and yield stability in Pacific Northwest winter wheat. Crop Science 58:1232-1241.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Godoy, J., S. Rynearson, X. Chen, M. Pumphrey. 2018. Genome-wide association mapping of loci for resistance to stripe rust in North American elite spring wheat germplasm. Phytopathology. 108:234-24.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Godoy, J., S. Gizaw, S. Chao, N. Blake, A. Carter, R. Cuthbert, J. Dubcovsky, P. Hucl, K. Kephart, C. Pozniak, P.V. V. Prasad, M. Pumphrey, and L. Talbert. 2018. Genome-wide association study of agronomic traits in a spring-planted North American elite hard red spring wheat panel. Crop Science 58:1232-1241.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Haixiao, D., R. Wang, Y. Yuan, J. Anderson, M.O. Pumphrey, Z. Zhang, J. Chen. 2018. Evaluation of the potential for genomic selection to improve spring wheat resistance to fusarium head blight in the Pacific Northwest. Frontiers in Plant Science 9:911. doi:10.3389/fpls.2018.00911.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Haley, S.D., J.J. Johnson, F.B. Peairs, J.A. Stromberger, E.E. Hudson-Arns, S.A. Seifert, V.A. Anderson, J.B. Rudolph, G. Bai, X. Chen, R.L. Bowden, Y. Jin, J.A. Kolmer, M.-S. Chen, and B.W. Seabourn. 2018. Registration of Langin Hard Red Winter Wheat. J. Plant Reg. 12:232236.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Haley, S.D., J.J. Johnson, F.B. Peairs, J.A. Stromberger, E.E. Hudson-Arns, S.A. Seifert, V.A. Anderson, J.B. Rudolph, G. Bai, X. Chen, R.L. Bowden, Y. Jin, J.A. Kolmer, M.-S. Chen, and B.W. Seabourn. 2018. Registration of Avery wheat. J. Plant Reg. doi:10.3198/jpr2017.11.0080crc.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Hao, Q., W. Wang, X. Han, J. Wu, B. Lyu, F. Chen, A. Caplan, C. Li, J. Wu, W. Wang, Q. Xu, D. Fu. 2018. Isochorismate-based salicylic acid biosynthesis confers basal resistance to Fusarium graminearum in barley. Molecular Plant Pathology: 19: 19952010.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Hegarty, J.M., I.A. del Blanco, L. Gallagher, J. Dubcovsky. 2018. Registration of UC Tahoe, a California adapted two-rowed spring barley for craft-scale malting. Journal of Plant Registration 12:163167.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Heo, H.-Y., N. K. Blake, S. P. Lanning, P. F. Lamb, D. Nash, D. M. Wichman, K. D. Kephart, R. N. Stougaard, J. H. Miller, G. V. P. Reddy, J. L. Eckhoff, C. Chen, F. Menalled, E. Davis, and L. E. Talbert. 2018. Registration of NS Presser CLP wheat. J. Plant Reg12:70-73.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Jordan, K.J., S.Wang, F. He, S. Chao, Y. Lun, E. Paux, P. Sourdille, J. Sherman, A. Akhunova, N. K. Blake, M.O. Pumphrey, K. Glover, J. Dubcovsky, L. Talbert, E. Akhunov. 2018. The genetic architecture of genome-wide recombination rate variation in allopolyploid wheat revealed by nested association mapping Plant J. 95: 10391054.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Kippes, N., M. Guedira, L. Lin, G.L. Brown-Guedira and J. Dubcovsky. 2018. Single nucleotide polymorphisms in a regulatory site of VRN-A1 first intron are associated with differences in vernalization requirement in winter wheat. Molecular Genetics and Genomics. doi.org/10.1007/s0043.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Kidwell, K.K, J. S. Kuehner, G.B. Shelton, V.L. DeMacon, S. Rynearson, X.M. Chen, S. O. Guy, J.M. Marshall, D.A. Engle, C.F. Morris, and M.O. Pumphrey. 2018. Registration of 'Dayn" Hard White Spring Wheat. J. Plant Registrations 12:222-227.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Lei, L, G. Li, H. Zhang, C. Powers, T. Fang, Y. Chen, X. Zhu, B. Carver, L. Yan. 2018. Nitrogen use efficiency was regulated by interacting proteins relevant to development in wheat. Plant Biotechnol J. 16: 1214-1226.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Liu M, L. Lei, F. Miao, C. Powers, X. Zhang, J. Deng, M. Tadege, B.F. Carver, L. Yan. 2018. The STENOFOLIA gene from Medicago alters leaf width, flowering time and chlorophyll content in transgenic wheat. Plant Biotechnol J. 16:186-196.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Liu W., Y. Naruoka, K. Miller, K. Garland-Campbell, A.H. Carter. 2018. Characterizing and validating stripe rust resistance loci in US Pacific Northwest winter wheat accessions (Triticum aestivum L.) by genome-wide association and linkage mapping. The Plant Genome 11:170087.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Liu, Y., R. Wang, Y. Hu, and J. Chen. 2018. Genome-wide linkage mapping of quantitative trait loci for late-season physiological and agronomic traits in spring wheat under irrigated conditions. Agronomy 60: doi:10.3390/agronomy8050060.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Huang, M., N. Mheni, G. Brown-Guedira, A. McKendry, C. Griffey, D. Van Sanford, J. Costa, C Sneller. 2018. Genetic analysis of heading date in winter and spring wheat. Euphytica, 214: 128.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Lozada, D.N., Mason, R.E., Sukumaran, S., Dreisigacker, S. 2018 Validation of grain yield QTL from soft winter wheat using a CIMMYT spring wheat panel. Crop Science. doi:10.2135/cropsci2018.04.0232
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Mason, R.E., J.W. Johnson, M. Mergoum, R.G. Miller, D.E. Moon, J. Carlin, S.A. Harrison, M.A. Babar, P. Murphy, A.M.H. Ibrahim, R. Sutton, and A.R. Blount. 2018. AR11LE24 is a soft red winter wheat adapted to the mid-south region of the United States. Journal of Plant Registrations. doi: 10.3198/jpr2017.09.0060crc
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Mo, J., T. Howell, H. Vasquez-Gross, L.A. de Haro, J. Dubcovsky, S. Pearce. 2018. Mapping causal mutations by exome sequencing in a wheat TILLING population: a tall mutant case study. Mol. Genet. Genom. 293: 463-477.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Mo, Y., L.S. Vanzetti, I. Hale3, E.J. Spagnolo, F. Guidobaldi, J. Al-Oboudi, N. Odle, S. Pearce, M. Helguera, J. Dubcovsky. 2018. Identification and characterization of Rht25, a locus on chromosome arm 6AS affecting wheat plant height, heading time, and spike development. Theor Appl Genet doi: 10.1007/s00122-018-3130-6
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Qureshi, N., H. Bariana, P. Zhang, R. McIntosh, D. Wong, M. Shankar, M.J. Hayden, J. Dubcovsky, and U. Bansal. 2018. Genetic relationship of stripe rust resistance genes Yr34 and Yr48 in wheat and identification of linked KASP markers. Plant Disease.102: 413-420.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Shao M., G. Bai, T.W. Rife, J. Poland, M. Lin, S. Liu, H. Chen, T. Kumssa, A. Fritz, H. Trick, Y. Li, and G. Zhang. 2018. QTL mapping of pre?harvest sprouting resistance in a white wheat cultivar Danby. Theor. Appl. Genet. 131: 1683-1697.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Sherman, J. D., A. C. Varella, S. P. Lanning, J. M. Martin, H. Y. Heo, D. Nash, N. K. Blake, J. P. Cook, L. E. Talbert. 2018. Effect of a gene for high dough strength on whole wheat baking parameters of hard white spring wheat. Cereal Chem. 95:411-417.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Su, Z., S. Jin, D. Zhang, G. Bai. 2018. Development and validation of diagnostic markers Fhb1 region, a major QTL for Fusarium head blight resistance in wheat. Theor. Appl. Genet. doi.org/10.1007/s00122-018-3159-6.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Xue S., J. Kolmer, S. Wang, L. Yan. 2018. Mapping of leaf rust resistance genes and molecular characterization of the 2NS/2AS translocation in the wheat cultivar Jagger. G3 8: 2059-2065.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Yuan, C., J. Wu, B. Yan, Q. Hao, C. Zhang, B. Lyu, F. Ni, A. Caplan, J. Wu, D. Fu. 2018. Remapping of the stripe rust resistance gene Yr10 in common wheat. Theor. Appl. Genet. 131: 12531262.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Zhang G., Z. Hua. 2018. Genome comparison implies the role of Wsm2 in membrane trafficking and protein degradation. PeerJ. DOI 10.7717/peerj.4678.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Zhang, J., S.A. Gizaw, E. Bossolini, J. Hegarty, T. Howell, A.H. Carter, E. Akhunov, J. Dubcovsky. 2018. Identification and validation of QTL for grain yield and plant water status under contrasting water treatments in fall-sown spring wheats. Theor. Appl. Genet. 131: 17411759.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2018 Citation: Cobo, N., L. Pfl�ger, X. Chen, J. Dubcovsky. 2018. Mapping QTL for resistance to new virulent races of wheat stripe rust from two Argentinean wheat varieties. Crop Science. In press
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2018 Citation: Dhakal, S., C.-T. Tan, V. Anderson, H. Yu, M.P. Fuentealba, J.C. Rudd, S.D. Haley, Q. Xue, A.M.H. Ibrahim, L. Garza, R. Devkota, S.-Y. Liu. 2017. Mapping and KASP marker development for wheat curl mite resistance in TAM 112 wheat using linkage and association analysis. Molecular Breeding. In press.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2018 Citation: Gizaw SA, Godoy JG, Pumphrey MO, Carter AH. 2018. Use of spectral reflectance indices in indirection selection and genome wide association studies of drought resistance and yield potential in North American spring wheat (Triticum aestivum L.). Crop Sci. In press.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2018 Citation: Gizaw, S.A., J. Godoy, K. Garland-Campbell, A.H. Carter. 2018. Genome-wide association study of yield and component traits in Pacific Northwest winter wheat (Triticum aestivum L.). Crop Sci. In press.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2018 Citation: Huang M., B. Ward, C. Griffey, D. Van Sanford, A. McKendry, G. Brown-Guedira, P. Tyagi, C Sneller. 2018. The accuracy of genomic prediction between environments and populations for soft wheat traits. Crop Sci. In press.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2018 Citation: Jernigan K.L., J. Godoy, M. Huang, Y. Zhou, C.F. Morris, K. A. Garland-Campbell, Z. Zhang, A.H. Carter 2018. Association mapping for end-use quality in Pacific Northwest adapted soft white winter wheat. Frontiers in Plant Science. In press.
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2018 Citation: Su, Z., S. Jin, D. Zhang, G. Bai. 2018. Development and validation of diagnostic markers Fhb1 region, a major QTL for Fusarium head blight resistance in wheat. Theor. Appl. Genet. In press.


Progress 12/15/16 to 12/14/17

Outputs
Target Audience:The audiences targeted during the first year of the project include: 1) Wheat growers and wheat grower associations. WheatCAP breeding programs presented their results to state wheat commissions, grower associations and individual growers during field days and annual meetings. Wheat growers will be the primary beneficiaries of new varieties developed by the WheatCAP. 2) Wheat milling and baking industry.WheatCAP results were presented to the Wheat Quality Council and other Quality Collaborative Programs across the USA. Presentation were also made to individual milling and baking companies. 3) Wheat researchers working in basic and applied aspects of wheat. Results from the WheatCAP were presented to other researchers in 51 papers published in peer-reviewed journals and at national conferences including Plant and Animal Genome and ASA-CSSA meetings. 4) International wheat research community. WheatCAP researchers made presentations in different countries and published their results in internationally recognized scientific journals. 5) Wheat breeders in the public and private sector. Varieties and germplasm generated by WheatCAP breeders have been made available to all members of the WheatCAP team and to public and private sector breeding programs that requested seeds for crossing. Markers for specific yield-enhancing genes are public information through T3. The complete sequenced TILLING mutant population was distributed to Europe, Canada, China andMexico (CIMMYT). All mutations are accessible and searchable in a public database and the seeds of the mutant lines are distributed without IP limitations. More than 3000 mutant accessions have been already distributed to researchers from multiple countries. The audiences targeted by the educational part of this project include: 1) Graduate and undergraduate students interested in plant breeding (including students outside the project). Education materials have been updated in the Plant Breeding Training Network (PBTN) web site and are freely available to the public. 2) Educators interested in online tools for plant breeding and genetics. The results of surveys generated by WheatCAP and previous TCAP are available through the WheatCAP website. 3) Breeding companies interested in the training of their workforce. WheatCAP requested input from private breeding companies regarding the needs of new breeders, and those recommendations are being implementedin webinars and courses. 4) Wheat growers and grower organizations through field days and other venues conducted by participating breeders. In additional to the information regarding the new wheat varieties, we educate glowers, private breeders and seed handlers about the opportunities and limitation of new technologies. This information has facilitated a wide acceptance of new marker technologies. Changes/Problems:The subcontracts to the 19 institutions have been completed and the funding was available to all collaborators by March 2017. There has been very limited time to start invoicing the project so the financial report (up to July 31, 2017) show a slower than expected spending during the first six months of the project. Approximately 18% of the budget has been spent and an additional 10% is pending processing of invoices. This has not caused any delays in the scientific objectives. All participants were able to initiate the crosses and research activities before they received the initial funding by taking advantage of their stable personnel and financial resources from the previous T-CAP. Two programs (NC and WA) have suffered delays in recruiting their PhD students, who will start in early 2018. Meanwhile, research activities in these two programs are being performed by other students currently working in these programs. From the second year, the budget of USDA-ARS Ithaca will be transferred to Cornell University to provide T3 more flexibility in the hiring. None of the original objectives or responsibilities are modified. What opportunities for training and professional development has the project provided?We have leveraged the WheatCAP funding to hire 15 PhD students and 5 MS students (45% female) with two additional PhD hires pending at Washington State University and North Carolina State University. This number exceeds the 15 students proposed in the initial project. All incoming WheatCAP students are being self-evaluated with an anonymous survey to assess their education level. An interactive online discussion forum has been created for WheatCAP participants to post questions and answers that are important to the success of the WheatCAP student projects. Once students start the fall 2017 semester at their respective institution, video conferencing using the Zoom webinar software will be commenced to provide a live forum where WheatCAP students can discuss their projects. Education activities has also included updating our online education delivery platform infrastructure.The active wheat breeding programs are providing the students a hands-on experience of the field and lab skills required to run a breeding program, whereas the positional cloning projects provide a rigorous training in genetics and genomics. The first workshop for graduate students has been scheduled for January 2018. This workshopwill be focused on positional cloning workshop at UC Davis. The workshop will be held in conjunction with the USDA-funded Wheat CRISPR project led by Dr. E. Akhunov. The workshop will be taught by Dr. J. Dubcovsky (PD), Dr. E. Akhunov (Co-director), Dr. Jean-Luc Jannink (T3), Dr. Junli Zhang (project coordinator), PhD student Hans Vasquez-Gross (Tilling), Dr. Sen Tanner (GrainGenes) and Dr. Sarah Davidson (scientific communication). Because many of the student's first semester will be fall 2017, we delayed the first WheatCAP online course to provide the students an opportunity to acclimate to their home institution course work. Our first online course will start January 2018 and will teach students the basics of using tools available in the T3 and GrainGenes databases.The eXtension website will provide courses with an established delivery infrastructure and user technical support.All current and future online courses on the Plant Breeding Training Network (PBTN) will be housed in eXtension and will be are freely available to the public. How have the results been disseminated to communities of interest?Results generated by WheatCAP researchers have been disseminated in multiple ways. First, results have been published in 51 peer-reviewed publications in prestigious scientific journals. Results have been also presented at multiple scientific meetings including the ASA-CSSA meeting, the Plant and Animal Genome meeting. WheatCAP researchers provided the two first keynote lectures at the 2017 annual meeting of the National Association of Plant Breeders, hosted by UC Davis. The individual QTL cloning projects are described in the WheatCAP web site. These descriptions include the targeted trait. The chromosome region of the QTL and the flanking markers used to develop the high-density maps. Marker assisted selection protocols are being delivered to the MASwheat web site (http://maswheat.ucdavis.edu/). New genomics resources generated by WheatCAP have been widely advertised through GrainGene's list server, conferences, and computer demos. Resources have been made widely available to the international wheat research community. Results have been communicated directly to growers attending field days hosted by the 15 breeding programs that participate in WheatCAP. Results have been also shared with state wheat commissions and other wheat grower associations. Results affecting quality have been presented in Wheat Quality Council and in quality collaborative program in different states. These meetings include breeders, handlers, millers and bakers. Educational tools have been distributed throughonline resources and courses are accessible through PBTN. What do you plan to do during the next reporting period to accomplish the goals? Plans for the second year of the project Education: The first educational activity of 2018 will be the positional cloning workshop at UC Davis. An online course is also planned for the first quarter of 2018 that will teach students to use the tools available in T3 and GrainGenes databases. All current and future online courses on the PBTN will be housed in eXtension and are freely available to the public. T3: Filters for the exome capture data by genomic region and by gene annotation will be finalized in the next month. Annotations will come from the TGACv1 reference because the annotations from IWGSC RefSeq1 are not yet published. The annotations will be updated once IWGSC RefSeq1 is released. The Akhunov Lab is processing polymorphisms through "Variant Effect Predictor" and SIFT pipelines. When these analyses are done, we will make results available to WheatCAP members for visualization and as filtering criteria. This sequence resource will be BLAST searchable leading to reports and JBrowse visualizations of all polymorphisms detected within a segment surrounding BLAST hits. This will facilitate the identification of natural loss-of-function variants among our accessions. Whole genome and whole exome capture data are becoming common even in wheat. The original database structure for genotype data in T3 was designed for Illumina Golden Gate assay. To better handle massive genomic data, we will transition T3 genotype storage to the Genomic and Open-source Breeding Informatics Initiative (GOBII, gobiiproject.org) platform. This will enable us to integrate legacy and ongoing sequence data into a unified framework Genomics Resources: The next year we will re-sequence the regulatory regions of a diverse set of wheat lines using the newly designed capture assay for wheat promoter regions. Two hundred lines that have been previously evaluated for gene expression will be used for exon capture. The MNAse and ATAC-seq approaches will be used to characterize the chromatin accessibility in nuclei of different wheat tissues. We will develop a catalog of functionally active regions of the wheat genome. Cloning projects: All positional cloning projects will develop large populations from the HIFs identified in year one. These populations will be screened with QTL flanking marker to identify lines carrying recombination events in the critical QTL region. Progeny tests will be performed for these recombinant lines, and homozygous recombinant and non-recombinant sister lines will be identified for each recombination event. Seeds will be increased and evaluated in highly replicated field experiments. This information will be used to complete the first step of the high density mapping projects. Haplotype analysis will be performed in the delimited region and association studies will be performed to validate the mapping results. Once the QTL is delimited to a reasonable size, the recently released IWGSC RefSeq v1.0 will be used to select potential candidate genes. The exome capture data will be used to identify genes that have loss-of-function mutations within the candidate region. All positional cloning projects will advance the backcrossing of their target QTL to the selected CIMMYT lines and to their own high-yielding adapted lines. Programs that identify candidate genes, will select truncation or loss-of-function mutations in the A and B genome homoeologs of the candidate gene in the tetraploid TILLING database. Mutants will be backcrossed to Kronos to reduce background mutations, and homoeologs will be intercrossed to generate null-mutants. The phenotypic effects of the single and double mutants will be evaluated. A web forum will be developed for students on the project to discuss their cloning projects and strategies to get a better resolution of their phenotypes. This will be especially helpful in that some programs are more advanced and students may be able to provide helpful advice to their colleagues.

Impacts
What was accomplished under these goals? The WheatCAP project has directly benefited the wheat growers and wheat industry by releasing 19 new commercial wheat varieties with improved yield, quality and disease resistance. The project has also released mapping and mutant populations that accelerate the identification of valuable agronomic genes and their characterization. The WheatCAP project has developed multiple genomic resources that have accelerated the pace of discovery of valuable traits and linked markers. The wheat breeding programs have used these new resources to accelerate the mapping of genes affecting grain yield components and to accelerate their deployment. These results have been reported in 51 peer-reviewed publications. All the information from the project has been organized in the public database T3. The WheatCAP has been essential to coordinate the activities of the major wheat breeding and research programs across the USA avoiding unproductive duplications. Finally, the WheatCAP has initiated the training of a new cohort of 20 graduate students in wheat breeding and molecular genetics. 1) Major activities completed / experiments conducted We completed the development of several genomic resources. The exome capture assay targeting 162 Mb of the wheat genome was used to re-sequence the coding sequences of 1535 tetraploid and 1200 hexaploid mutants. The 10,000,000 mutations identified are being used by IWYP participants to identify mutations affecting different grain yield components. The design for the regulatory sequence capture assay targeting 250 Mb of unique genomic regions was completed and submitted to Nimblegen Inc. for synthesis. This assay includes 2 kb upstream of each gene model in the wheat genome and predicted miRNA binding sites. The exome capture was also used to re-sequence the gene coding regions of 36 wheat lines used as the parents of the Wheat CAP mapping populations. This has generated roughly one million SNPs that are being used by project participants for high-density mapping and cloning of grain yield components. Markers developed through this project will be of use to wheat breeders throughout the world. The spring wheat NAM populations were genotyped using 90K iSelect, GBS and exome capture assays and used to characterize the distribution of 102,000 recombination breakpoints across the wheat genome. The data was used to identify genes controlling recombination rate variation across the wheat genome and to map the crossover frequency distribution across the wheat genome. This last information is very useful for the positional cloning projects. The genotyping labs have been working on development of amplicon sequencing approaches for genotyping. A protocol for next generation sequencing trait-linked markers published by researchers at the genotyping lab at Manhattan, KS was modified for use with genome-wide markers. The group at Pullman, WA selected 768 markers from the iSelect arrays. A high degree of success was observed for primer pools using targeted amplicon sequencing. The 15 breeding programs have selected their targeted chromosome regions affecting grain yield and have identified advanced generation lines heterozygous for those QTL regions. These heterozygous lines have been used to develop heterogeneous inbred families (HIF) and to initiate the high-density mapping of the targeted QTL. The breeding programs have initiated the introgression of yield QTL into 5 lines selected by CIMMYT for high biomass and 15 lines selected for broad adaptability and high yield potential. The rationale for this selection was the dependence of yield gains on simultaneous increases in "source" and "sink". Since many of the selected QTL affect the sink side of the equation (more and larger grains), we selected high biomass lines to maximize our chances of an adequate carbon and nutrient supply from the "source". The targeted QTLs are also being introgressed in the local breeding programs. Several yield component traits are being combined to study their epistatic interactions. 2) Data collected We have expanded the number of phenotyping trials accessible through T3 by adding data from US Cooperative Uniform Nurseries.The number of phenotypic data points in T3 increased by 44%. T3 also developed a whole database GWAS analysis pipeline. Genes are sorted by cumulative evidence of association and automated links are made to four external databases. We have added a JBrowse track to the recently published wheat pan-genome and compared all DNA variants stored in T3 against this resource. Sequencing data from exome captures was collected from the 36 parental lines used in the project. On average, 57 million 150-bp paired-end reads were generated for each line and mapped to the latest version of the wheat genome reference. The variant calling using the GATK-based pipeline identified 976,558 SNPs and small indels. The exome capture has been also used to re-sequence most of the genes from a collection of 1,535 tetraploid mutants and 1200 hexaploid mutants, generating a database of more than 10,000,000 sequenced mutations. The first sequencing studies of the regulatory regions in the wheat genome have been completed using MNase and ATACseq strategies. 3) Summary statistics and discussion of results Members of the WheatCAP team have published 51 peer-reviewed publications acknowledging the support from the WheatCAP or the previous T-CAP. None of these publications has been included in any previous T-CAP report. Breeders from WheatCAP have released 19 commercial varieties (10 with PVP and 9 pending or public releases), 3 germplasm and 5 mapping or TILLING populations. A complete list of these publications and released varieties is available on the WheatCAP web site (http://www.triticeaecap.org/ ). The same web site includes links to each of the 15 positional cloning projects (http://www.triticeaecap.org/qtl-cloning-projects/). More than 10,000,000 induced mutations and 1,000,000 natural mutation have been sequenced and incorporated into public databases. 4) Key outcomes or other accomplishments realized. Accomplishments realized through the WheatCAP project include changes in knowledge, as breeders understand the fundamental genetics of their primary selection target of grain yield. Changes in action has occurred by the incorporation of molecular-based approaches into variety development programs. Change in condition can be seen by the training of 20 new professional plant breeders through the WheatCAP collaborative Ph.D. training program. The new genomic resources have changed the way wheat-breeding programs conduct genetic research in wheat. Most of the genetic and phenotypic data is now located in a single site (T3) with adequate tools to analyze this data. Thus, many experiments can be performed first in silico, and then tested in the lab or the field, increasing the speed and efficiency to generate hypothesis and design experiments. The availability of the induced mutant database has changed the way researchers conduct functional genetic analysis and validate candidate genes in wheat. Non-functional copies of all three homoeologs can be rapidly identified by an online search tool and seeds can be obtained by a simple email to the seed distribution laboratories. Therefore, variation previously hidden by redundancy of the wheat genome can now be released by combining loss-of-function mutations in all three homoeologs. This has accelerated the translation of discoveries made in the diploid grasses into polyploid wheat. The existence of a coordinated project has changed the way programs interact with each other. The WheatCAP project has allowed sharing of data and expertise leading to enhanced collaboration, which is evident in the multi-program authorship in most of the project publications. This has also accelerated the speed of discovery as evidenced by the large number of publication and germplasm releases in the first year of this project.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Addison, C.K., R.E. Mason, G. Brown-Guedira, M. Guedira, Y. Hao, D.L Lozada, A.M. Acuna, N.A. Arguello, N. Subramanian, J. Johnson, A.M.H. Ibrahim, R. Sutton, S.A. Harrison. 2016. QTL and major genes associated with grain yield in soft red winter wheat adapted to the southern United States. Euphytica. 209: 665-677
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Arruda, M.P., P. Brown, G. Brown-Guedira, A.M. Krill, C. Thurber, K.R. Merrill, B.J. Foresman, F.L. Kolb. 2016. Genome-wide association mapping of Fusarium head blight resistance in wheat using genotyping-by-sequencing. Plant Genome 9(1) doi: 10.3835/plantgenome2015.04.0028
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Assanga, S.O., G. Zhang, C.-T. Tan, , J.C. Rudd, A. Ibrahim, Q. Xue, S. Chao, M.P. Fuentealba, S.Y. Liu. 2016. Saturated genetic map of wheat streak mosaic virus resistance gene wsm2 in wheat. Crop Sci. 57:332-339.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Babiker, E.M., T.C. Gordon, S. Chao, M.N. Rouse, R. Wanyera, M. Newcomb, G. Brown-Guedira, Z.A. Pretorius, J.M. Bonman. 2016. Genetic mapping of resistance to the Ug99 race group of Puccinia graminis f. sp. tritici in a spring wheat landrace CItr 4311. Theor Appl Genet 2016:1-10.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Babiker, E.M., T.C. Gordon, S. Chao, M.N. Rouse, R. Wanyera, M. Acevedo, G. Brown-Guedira, M. Bonman. 2016. Molecular mapping of stem rust resistance loci effective against the Ug99 race group of the stem rust pathogen and validation of a single nucleotide polymorphism marker linked to stem rust resistance gene Sr28. Phytopathology 107:208-215
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Babiker, E.M., T.C. Gordon, J.M. Bonman, S. Chao, M.N. Rouse, G. Brown-Guedira, S. Williamson, Z.A. Pretorius. 2016. Rapid identification of resistance loci effective against Puccinia graminis f. sp. tritici race TTKSK in 33 spring wheat landraces. Plant Dis. 1002: 331-336.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Carter A.H., S.S. Jones, K.A. Balow, G.B. Shelton, A. Burke, S.R. Lyon, R.W. Higginbotham, X.M. Chen, D.A. Engle, T.D. Murray, C.F. Morris. 2017. Registration of Jasper soft white winter wheat. J. Plant Reg. 10.3198/jpr2016.09.0051crc.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Carter A.H., S.S. Jones, S.R. Lyon, K.A. Balow, G.B. Shelton, A. Burke, R.W. Higginbotham, X.M. Chen, D.A. Engle, C.F. Morris. 2017. Registration of Sequoia hard red winter wheat. Journal of Plant Registrations 10.3198/jpr2016.09.0052crc.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Carter A.H., K.K. Kidwell, A. Burke, G.B. Shelton, R.W. Higginbotham, V. DeMacon, M.J. Lewien, X.M. Chen, D.A. Engle, C.F. Morris. 2017. Registration of Earl hard white winter wheat. Journal of Plant Registrations 11:275-280
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Cai J., S. Wang, T Li, G. Bai. 2016. Multiple minor QTLs are responsible for Fusarium head blight resistance in Chinese wheat landrace Haiyanzhong. PloS ONE 11:e0163292
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Chao, S., M.N. Rouse, M. Acevedo, A. Szabo-Hever, H. Bockelman, J.M. Bonman, E. Elias, D. Klindworth, and S. Xu. 2017. Evaluation of genetic diversity and host resistance to stem rust in USDA NSGC durum wheat accessions. Plant Genome 10. doi: 10.3835/plantgenome2016.07.0071
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Chen, J., M. J. Guttieri, J. Zhang, D. Hole, E. Souza, B. Goates. 2016. 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: 2017 Citation: Chen, J., J. Wheeler, N. Klassen, W. Zhao, K. OBrien, C. Jackson, J. M. Marshall, X.M. Chen. 2017. Release of UI Sparrow soft white winter wheat. Journal of Plant Registration, In Press.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Cook, J. P., N. K. Blake, H. Y. Heo, J. M. Martin, D. K. Weaver, and L. E. Talbert. 2017. Phenotypic and haplotype diversity among tetraploid and hexaploid wheat accessions with potentially novel insect resistance genes for wheat stem sawfly. Plant Genome 10. doi:10.3835/plantgenome2016.03.0026.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Dong, Z, J. Zhang, J. M. Hegarty, W. Zhang, S. Chao, X. Chen, Y. Zhou, and J. Dubcovsky. 2017. Validation and characterization of a QTL for adult plant resistance to stripe rust on wheat chromosome arm 6BS (Yr78). Theor. Appl. Genet. DOI 10.1007/s00122-017-2946-9.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Fang, T., B.F. Carver, R.M. Hunger, L. Yan. 2017. Mis-spliced Lr34 transcript events in winter wheat. PLoS ONE 12:e0171149.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Gao, L., M.N. Rouse, P. Mihalyov, P. Bulli, M. Pumphrey, J.A. Anderson. 2017. Genetic characterization of stem rust resistance in a global spring wheat germplasm collection. Crop Science. 57:1-15.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Guedira, M., M. Xiong, Y.F. Hao, J. Johnson, S. Harrison, D. Marshall, G. Brown-Guedira. 2016. Heading date QTL in winter wheat (Triticum aestivum L.) coincide with major developmental genes VERNALIZATION1 and PHOTOPERIOD1. PLoS ONE, 11: e0154242
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Guttieri, M.J., K. Frels, T. Regassa, B.M. Waters, P.S. Baenziger. 2017. Variation for nitrogen use efficiency traits in current and historical Great Plains hard winter wheat. Euphytica 213:87. DOI :10.1007/s10681-017-1869-5.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Haley S.D., J.J. Johnson, F.B. Peairs, J.A. Stromberger, E.E. Hudson-Arns, S.A. Seifert, V.A. Anderson, G. Bai, X. Chen, R.L. Bowden, Y. Jin, J.A. Kolmer, M. Chen, and B.W. Seabourn. 2017. Registration of Sunshine Hard White Winter Wheat. J. Plant Reg. doi:10.3198/jpr2016.12.0075crc
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Jernigan, K.L., C. F. Morris, R. Zemetra, J. Chen, K. Garland-Campbell, A.H. Carter. 2017. Genetic mapping of quantitative trait loci for end-use quality traits in a soft wheat RIL population. Journal of Cereal Science. 76:148-156
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Kidwell, K.K, M. O. Pumphrey, J. S. Kuehner, G. B. Shelton, V. L. DeMacon, S. Rynearson, X. M. Chen, S. O. Guy, D. A. Engle, B.-K. Baik, C. F. Morris, and N. A. Bosque-P�rez. 2017. Registration of 'Glee" Hard Red Spring Wheat. Journal of Plant Registrations. In press
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Kissing Kucek, L., E. Dyck, J. Russell, E. Clark, J. Hamelman, S. Burns-Leader, S. Senders, J. Jones, D. Benscher, M. Davis, G. Roth, S. Zwinger, M.E. Sorrells, J.C. Dawson. 2017. Evaluation of wheat and emmer varieties for artisanal baking, pasta making, and sensory quality, J. Cereal Science, 74:19-27.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Krasileva, K.V., H. Vasquez-Gross, T. Howell1, P. Bailey, F. Paraiso, L. Clissold, J. Simmonds, R. H. Ramirez-Gonzalez, X. Wang, P. Borrill, C. Fosker, S. Ayling, A. Phillips, C. Uauy, J. Dubcovsky. 2017. Uncovering hidden variation in polyploid wheat. Proc. Natl. Acad. Sci. U.S.A. 114: E913E921.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Liu, Y., J.Zhang, Y. Hu, and J. Chen. 2017. Dwarfing genes Rht4 and Rht-B1b affect plant height, agronomic traits, and kernel quality traits in common wheat under two water regimes. Field Crops Research 204: 242-248.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Liu, Y., B.C. Bowman, Y. Hu, X. Liang, W. Zhao, J. Wheeler, N. Klassen, H. Bockelman, J. M. Bonman, J. Chen. 2017. Evaluation of agronomic traits and drought tolerance of winter wheat accessions from the National Small Grain Collection. Agronomy. 7(51) doi:10.3390/agronomy7030051
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Liu, M., L. Lei, C. Powers, Z. Liu, K.G. Campbell, X. Chen, R.L. Bowden, B.F Carver, L. Yan. 2016. TaXA21-A1 on chromosome 5AL is associated with resistance to multiple pests in wheat. Theoretical and Applied Genetics. 129:345-355.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Kruse, E.B., S.W. Carle, N. Wen, D.Z. Skinner, T.D. Murray, K.A. Garland-Campbell, A.H. Carter. 2017. Genomic regions associated with tolerance to freezing stress and snow mold in winter wheat. G3 7: 775-780 Early Online Published January 30, 2017
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Lan, C., I. Lowe Hale, S.A. Herrera-Foessel, B.R. Basnet, M.S. Randhawa, J. Huerta-Espino, J. Dubcovsky and R.P. Singh. 2017. Characterization and mapping of leaf rust and stripe rust resistance loci in hexaploid wheat lines UC1110 and PI610750 under Mexican environments. Frontiers in Plant Science doi: 10.3389/fpls.2017.01450
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Li C-L., G. Bai, B. F. Carver, S. Chao and Z. Wang. 2016. Single nucleotide polymorphisms linked to quantitative trait loci for grain quality traits in wheat. The Crop J. 4:111.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Lin M., D. Zhang, S. Liu, G. Zhang, J. Yu, A. K. F. and G. Bai. 2016. Genome-wide association analysis on pre-harvest sprouting resistance and grain color in U.S. winter wheat. BMC Genomics 17:794
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Lozada, D.N., R.E. Mason, M.D.A. Babar, B.F. Carver, G. Brown-Guedira, K. Merrill, M.N. Arguello, A. Acuna, L. Vieira, A. Holder, C.K. Addison, D.E. Moon, R.G. Miller, and S. Dreisigacker. 2017. Association mapping reveals loci associated with multiple traits that affect grain yield and adaptation in soft winter wheat. Euphytica. In press.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Mihalyov, P.D., V.A. Nichols, P. Bulli, M.N. Rouse, M.O. Pumphrey. 2017. Multi-locus mixed model analysis of stem rust resistance in winter wheat. The Plant Genome. 10(2). doi: 10.3835/plantgenome2017.01.0001.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Muleta, K.T., M.N. Rouse, S. Rynearson, X. Chen, B. G. Buta, and M.O. Pumphrey. 2017. Characterization of molecular diversity and genome-wide mapping of loci associated with resistance to stripe rust and stem rust in Ethiopian bread wheat accessions. BMC Plant Biology. 17, 13
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Muleta, K.T., P. Bulli, S. Rynearson, X. Chen, and M. Pumphrey. 2017. Loci Associated with Resistance to Stripe Rust (Puccinia striiformis f. sp. tritici) in a Core Collection of Spring Wheat (Triticum aestivum). Plos One. doi: 10.1371/journal.pone.017908
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Muleta, K.T., P. Bulli, Z. Zhang, X. Chen, and M. Pumphrey. 2017. Unlocking diversity in germplasm collections by genomic selection: a case study based on quantitative adult plant resistance to stripe rust in spring wheat. The Plant Genome. 10(3) doi: 10.3835/plantgenome2016.12.0124
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Nirmala, J., J. Saini, M. Newcomb, P. Olivera, S. Gale, D. Klindworth, E. Elias, L. Talbert, S. Chao, J. Faris, S. Xu, Y. Jin, and M.N. Rouse. 2017. Identification and mapping of a unique stem rust resistance allele present in durum wheat that differentiates isolates in the Ug99 race group. G3: Genes, Genomes, Genetics, In press.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Pour, H.A., M.R. Bihamta, V. Mohammadi, S.A. Peyghambari, G.H. Bai and G.R. Zhang. 2017. Genotyping-by-sequencing (GBS) revealed molecular genetic diversity of Iranian wheat landraces and cultivars. Front. Plant Sci. On line first doi: 10.3389/fpls.2017.01293
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Sch�nhofen, A., X. Zhang, and J. Dubcovsky. 2017. Combined mutations in five wheat Starch Branching Enzyme II genes increase resistant starch but affect grain yield and bread-making quality. Journal of Cereal Science 75: 165-174.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Shi F., J. Tibbits, R.K. Pasam, P. Kay, D. Wong, J. Petkowski, K.L. Forrest, B.J. Hayes, A. Akhunova, J. Davies, S. Webb, G.C. Spangenberg, E. Akhunov, M.J. Hayden, H.D. Daetwyler. 2017. Exome sequence genotype imputation in globally diverse hexaploid wheat accessions. Theor Appl Genet. 130:1393-1404
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Su Z., S. Jin, Y. Lu, G. Zhang, S. Chao, G. Bai. 2016. Single nucleotide polymorphism tightly linked to a major QTL on chromosome 7A for both kernel length and kernel weight in wheat. Mol Breed. 36:15
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Subramanian, N., R.E. Mason, E.A. Milus, D.E. Moon, G. Brown-Guedira. 2016 Characterization of two adult-plant stripe rust resistance genes on chromosomes 3BS and 4BL in soft red winter wheat. Crop Science doi: 10.2135/cropsci2015.01.0043
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Tan, C.-T, S.O. Assanga, G. Zhang, J.C. Rudd, S. Haley, Q. Xue, A. Ibrahim, G. Bai, X. Zhang, P. Byrne, M.P. Fuentealba, S.Y. Liu. 2017. Development and validation of KASP SNP markers for wheat streak mosaic virus resistance gene Wsm2. Crop Sci. 57:340-349.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Tan, C.-T., H. Yu, Y. Yang, X. Xu, M. Chen, J.C. Rudd, Q. Xue, A. Ibrahim, L. Garza, S. Wang, M.E. Sorrells, S.Y. Liu. 2017. Development and validation of KASP markers for the greenbug resistance gene Gb7 and the Hessian fly resistance gene H32 in wheat. Theor Appl Genet: 1-18.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Turner, M.K., J.A. Kolmer, M.O. Pumphrey, P. Bulli, S. Chao, and J.A. Anderson. 2016. Association mapping of leaf rust resistance loci in a spring wheat core collection. Theor. Appl. Genet. 130:345361.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Varella, A. C., D. K. Weaver, J. P. Cook, N. K. Blake, M. L. Hofland, P. F. Lamb, L. E. Talbert. 2017. Characterization of resistance to the wheat stem sawfly in spring wheat landrace accessions from targeted geographic regions of the world. Euphytica 213:153.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Varella, A.; D. Weaver, R. Peterson, J. Sherman, M. Hofland, N. Blake, J. Martin, L. Talbert. 2017. Host plant quantitative trait loci affect specific sequences in oviposition by a stem-mining insect. Theor. Appl. Genet. 130:187-197.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Veenstra, L.D., J-L. Jannink, M.E. Sorrells. 2017. Wheat fructans: a potential breeding target for nutritionally improved, climate resilient varieties. Crop Science 57:16241640
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Wang, R., J. Chen, J. Zhang, W. Zhao, J. Wheeler, N. Klassen, J.A. Anderson, D.R. See and Y. Dong. 2017. Genome-wide association mapping of resistance QTL to fusarium head blight in spring wheat lines grown in Pacific Northwest and CIMMYT. Phytopathology. DOI: 10.1094/PHYTO-02-17-0073-R.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Zhou, Y., B. Conway, D. Miller, D. Marshall, A. Cooper, P. Murphy, S. Chao, G. Brown-Guedira and J. Costa. 2017. Quantitative trait loci mapping for spike characteristics in hexaploid wheat. Plant Genome. 10. doi:10.3835/plantgenome2016.10.0101