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, 2021
Grant Year
2020
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 12/15/19 to 12/14/20

Outputs
Target Audience:The audiences targeted during the fourth 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 are the primary beneficiaries of the new varieties developed by the WheatCAP researchers. 2) Wheat milling and baking industry.WheatCAP results were presented to the Wheat Quality Council and other Quality Collaborative Programs across the USA. Presentations were also made to individual milling and baking companies. 3) Scientist working in basic and applied aspects of wheat research. Results from the WheatCAP were presented to other researchers in 35 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, coPDs and students made Zoom presentations at National and International meetings. 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 publicly accessible through the T3 database. Kronos TILLING mutants were distributed to wheat breeders and researchers in the US and abroad. All mutations are accessible and searchable in a public database and the seeds of the mutant lines are distributed without IP limitations. A new database of 4.3 million mutations in the promoters of all the wheat genes has been made available through GrainGenes and T3. The audiences targeted by the educational activities of the WheatCAP include: 1) Graduate and undergraduate students interested in plant breeding (including students outside the project). Education materials from the WheatCAP workshops have been uploaded into the WheatCAP website. 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. 4) Wheat growers and grower organizations through field days and other venues conducted by participating breeders. In addition to the information regarding the new wheat varieties, we educate growers, private breeders and seed industry about the opportunities and limitations of new technologies. This information has facilitated wide acceptance of new marker technologies. Changes/Problems:The subcontracts for the fourth year for the 19 institutions was completed on time and the funding was available to all collaborators in early 2020. We have already completed the the subcontracts for year 5 and they will be available to collaborators before the end of 2020. 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. Dr. Luther Talbert, the wheat breeder for Montana retired and Jason Cook, the WheatCAP education coordinator was selected as a new breeder for MT, which will provide continuity to the WheatCAP project in Montana. Jason will supervise the MT PhD students. Dr. Scott Haley, the wheat breeder for Colorado retired and Esten Mason, the WheatCAP breeder for Arkansas got the position. The PI at Colorado State University is Stephen Pearce, so the retirement of Dr. S. Haley hadno impact in the direction of the WheatCAP project or the students at CSU. Arrangements have been made for the students from University of Arkansas to complete their degrees in one or the other University. The budget for year 5 for the University of Arkansas was transferred to Colorado State University where it will be merged with the WheatCAP budget from Stephen Pearce to avoid additional overhead. Esten Mason and Stephen Pearce will collaborate in the WheatCAP project at Colorado State University. What opportunities for training and professional development has the project provided?One of the main objectives of the WheatCAP project is to educate 15 PhD students in molecular plant breeding. By leveraging funds from participating universities, 26 PhD students and 9 MS students have been supported by the WheatCAP project (40% female). Seven PhD students and five MS students have graduated. Additionally, four new international graduate students are waiting for approval to enter the United States to join their respective WheatCAP research groups. As more students approach the completion of their graduate degree, a number of students have been recognized for their leadership, hard work and dedication towards the field of plant breeding and genetics. In 2020, WheatCAP graduate students Saarah Kuzay (UC Davis), Brittney Brewer-Jones (Montana State University) and Ella Taagen (Cornell University), received three out of 16 "NAPB 2020 Borlaug Graduate Scholars" awards. The Borlaug Graduate Scholars program was established by the National Association of Plant Breeders (NAPB) and funded through the Agronomic Science Foundation (ASF) to develop the plant breeding science profession by strengthening the next generation of leaders. Lastly, to date, student research progress has culminated in eight first author peer-reviewed manuscripts. Every year the education team assesses student progress using an annual survey to monitor student progress in learning concepts that are essential for completing their WheatCAP research project and preparing for future employment. The survey also serves as a guide to help plan future education activities. This year's survey included a question about how the Covid-19 pandemic has impacted student education and research progress, and asked how the WheatCAP project could help the students cope with the negative impacts of Covid-19. Overall, most of the students indicated the pandemic has caused delays in their research progress, and a few of the students said they had to drop projects. Additionally, students indicated they are suffering from isolation, because they are not able to interact with their peers on a regular basis. Based on the survey results, the education team will adjust the education activities to help the students' better cope with the Covid-19 pandemic. A summary of the survey results are presented in Appendix 5. Education activities in 2020, started off by hosting an in person soft skill workshop in San Diego, CA (January 10) in conjunction with the WheatCAP annual meeting and the PAG conference. The soft skill workshop was hosted by Bonsai, and focused on developing the students' leadership skills by identifying and leveraging their strengths, how to manage a team, and develop interpersonal communication skills. The T3 group co-hosted a PAG workshop: "Connecting Crop Phenotype and Genotype Data" in January 11 2020. For the week of March 15-21, the education team had planned to send the students to CIMMYT research sites located in Obregon and El Batan, Mexico where the students would have had an opportunity to attend a CIMMYT field day, tour research facilities and interact with international research scientist. Unfortunately, the CIMMYT workshop was canceled due to the Covid-19 pandemic to protect the safety of the students. It is uncertain if the CIMMYT trip can be rescheduled before the end of the WheatCAP grant. A second workshop was planned for the week of July 5-11 at the University of Minnesota and North Dakota State University where the students were going to visit public and private breeding programs, meet with growers, and end-use stake holders. The workshop was cancelled due to Covid-19. In lieu of our in person workshops, the students have been participating in online education activities. These activities include starting two writing groups where the students meet each week to discuss writing their manuscripts, provide edits and help each other overcome writers block. Students have also been acquiring video and photos from their summer field season for doing virtual field tours this fall. Other students are planning to augment the virtual field tours with webinars focused on topics of interest that include genomic selection and end-use quality. 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 35 peer-reviewed publications in prestigious scientific journals. The WheatCAP publications have been cross-referenced 2,153 times in Google Scholar (9/10/2020) in spite of the short term since their publication. A similar analysis of the publications generated by the previous T-CAP project (2011-2016) indicates 17,146 cross-references in Google scholar until 2020, documenting the high-impact of the publications generated by this group. https://www.triticeaecap.org/publications-and-germplasm/ Results have also been presented at multiple scientific meetings in the US including the ASA-CSSA meeting and the Plant and Animal Genome Conference. The WheatCAP PDs and students presented multiple Zoom conferences remotely due to the pandemic. The individual QTL cloning projects are described on 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 website (http://maswheat.ucdavis.edu/). Mutations in all wheat genes and forms to request seeds of the mutant lines are available at https://dubcovskylab.ucdavis.edu/wheat_blast. Expression datasets are accessible through https://wheat.pw.usda.gov/WheatExp/. New genomic resources generated by WheatCAP have been widely advertised through the GrainGenes 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 the 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 plans for 5th year: For the 2020-2021 year, the education group will be adaptive to the evolving situation caused by Covid-19. The first educational activity will occur on Sept. 8-9 where students will participate in an online workshop to learn how to you use 'Breedbase', a data management tool that will be the bases of the T3 database. Members of Jean-Luc Jannink's team will be leading the workshop, and the workshop will include participants from the US Wheat and Barley Scab Initiative. Another education activity, led by Priscilla Glenn (UC-Davis), is a 9-week webinar series slated to start on Oct. 5th. The series will include topics on wheat breeding, pathology, end-use quality, genomic selection and virtual field tours. Additionally, the education team is exploring the possibility of having webinars with company representatives to give the students an opportunity to learn more about what it is like to work in industry, and to help build networks for career advancement. Lastly, a soft skill training workshop is planned, which will include coaching on how to better cope with the impacts of the Covid-19 pandemic on student education and career advancement. T3 plans for 5th year: Some of the tools listed below are on T3 Classic and need to be ported to T3 Breedbase. Planned activities include Incorporate as many wheat datasets as possible, particularly from cooperative nurseries. In the coming year T3 will be focusing on fusarium head blight nurseries as T3 has some supplemental funding from the scab initiative. GWAS Results. T3 still run automated GWAS on all phenotyping trials in the background. As of yet, T3 has not identified the best interface to present these results through T3 Breedbase. Tutorials. There are quite a number of new functions through T3 Breedbase that need to be documented in a more user-friendly way, specified to the T3/Wheat instance. Adding links from accessions to GrainGenes and GRIN Global. The value of having this data in the cloud is that connections can be made from user data to web resources. Subset markers by Polymorphism. Given a selected set of wheat lines, identify those markers that are polymorphic in the set and select them. Optimize genomic prediction training set. This is needed if the user wants to phenotype a subset of lines such that prediction accuracy for a separate population of lines will be maximized. Variant Effects for specific genotype data sets. Use of algorithms from the literature for VEP and SIFT. Storage of metabolomic and transcriptomic data. These data are challenging because they are very high dimensional and do not have simple ontologies as do typical agronomic traits. Filter Outliers. Curation of phenotypic datasets Canopy Spectral Reflectance. Data from the TriticeaeCAP on CSR is still housed in T3 Classic. Predict cross variance. This can be used as a decision support tool for breeders designing crossing nurseries. During the 2020-2021 grant year T3 will get a functioning automated imputation engine up and running on T3 using the Practical Haplotype Graph. Genomics Resources plan for 5th year: The low-cost medium throughput genotyping assay for mapping and genomic selection applications will be developed and tested in collaboration with genotyping labs. The PHG will be build based on exome capture data generated for US wheat cultivars, and the accuracy of genotype imputation using low-coverage Skim-seq approach will be tested. The PHG resource along with low-cost medium throughput genotyping assay will be deployed in genotyping labs to accelerate genetic analysis of material from breeding programs. The KSU group will finalize development of the eQTL map of the wheat genome and deposit it to the T3 database. They will collaborate with a T3 development team on setting tools for filtering SNPs in T3 database using functional information from the eQTL and chromatin accessibility maps. They will create tissue-specific gene expression atlases using low-cost 3'-end RNA-seq profiling for parents of Wheat CAP mapping populations. The KSU team lead by E. Akhunov will establish the NIFA IWYP Winter Wheat Breeding Innovation (WWBI) Hub. In coordination with the consortium of public and private wheat breeders, and geneticists the WWBI Hub will identify and introduce beneficial traits affecting grain yield into elite germplasm. This Hub aims to accelerate delivery of key yield traits to U.S. growers to reverse the declining trend of U.S. winter wheat acreage and add significant value to the U.S. wheat industries. The WWBI Hub leadership will collaborate with Wheat CAP on selecting promising donor germplasm for introgression into winter wheat germplasm and evaluating effects of introgression on yield potential. In 2021, the UCD lab will complete the publication of the database for sequenced mutations in the promoters of all wheat genes. The UCD lab will also continue distributing the seeds from the EMS sequenced populations and will disseminate the new GRF4-GIF1 transformation technology and distribute the necessary vectors to accelerate the incorporation of genome editing technologies in wheat. These resources will contribute to the engineering of the wheat plant by combining beneficial alleles of genes that regulate different agronomic traits. ?Plans for CIMMYT for the 5th year: In 2021 the CIMMYT hub will repeat the Elf-Am3 x gw-A2 filed trials to generate a second year of data. This experiment will be performed as a RCBD with ten blocks using the seed generated in 2019. In addition the CIMMYT hub will initiate preliminary experiments to test and increase the isogenic lines for the: WAPO-A1 QTL high number of spikelets per spike introgressed into CIMMYT high-biomass lines GID3855011, 4314513, 4577963 Isogenic lines of QTn.mst-6B for number of reproductive tillers (MT) introgressed from McNeal into CIMMYT high-yielding lines Kingbird and BAJ#1 Isogenic lines of a QTL for spikelet number per spike on chromosome 5A and a QTL for productive tiller number on chromosome 6A from SYC Capstone introgressed into CIMMYT high-biomass line. GID3613474 Plans for the cloning projects for the 5th year: All cloning projects will continue to narrow down their 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 the narrowed candidate gene region using the exome capture data. Projects that have identified good candidate genes will shift their focus 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.Loss-of-function mutations in the A and B genome homeologs 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. For the two projects that have already validated their candidate genes the focus will be on the molecular mechanisms and in the identification of interacting genes.

Impacts
What was accomplished under these goals? WheatCAP overall productivity: During the fourth year, the WheatCAP project published 35 peer-reviewed papers acknowledging the USDA-NIFA support and identified 9 candidate genes for grain yield components. WheatCAP breeders released 22 new improved commercial varieties in all wheat market classes, 4 improved germplasm, and 5 mapping populations. Seventeen additional varieties reported in 2019 received PVP in 2020 (see https://www.triticeaecap.org/cumulative-list-of-varieties-and-germplasm-2017-2020/ ). Education: By leveraging funds from participating universities, 26 PhD students and 9 MS students have been supported by the WheatCAP project (40% female). Seven PhD students and five MS students have graduated. As more students approach the completion of their graduate degree, a number of students have been recognized for their leadership, hard work and dedication towards the field of plant breeding and genetics T3 database: The T3 team completed loading all data from T3 into the Breedbase platform developed by the Mueller lab. As of January 2020, datasets are no longer uploaded to "T3/Wheat Classic" but only to "T3/Wheat Breedbase". T3 Classic is still being maintained and is accessible at: https://triticeaetoolbox.org/wheat/. T3 Breedbase is accessibleat: https://wheat.triticeaetoolbox.org/ To date, T3/Wheat Breedbase contains 20,639 accessions with phenotype data and 11,473 with genotype data. A total of 2,618 phenotype trials (containing 818,155 observations) and 38 genotype trials have been uploaded to T3/BreedBase. SNP Primer Design pages have been ported to T3 Breedbase. A Galaxy project pipeline using PolyMarker developed by Junli Zhang from the UC Davis WheatCAP group is accessible at https://galaxy.triticeaetoolbox.org/. T3 Breedbase also hosts a KASP marker design program, which is a R Shiny program developed by Noah DeWitt from the NC WheatCAP group. Four large genotype datasets contributed by the Akhunov Lab (2017_WheatCAP, 2019_DiversityGBS, 2019_Diversity GBS Filtered, and 2019_HapMap) are on Breedbase. The T3 Breedbase platform has incorporated a Genomic Selection tool and a new germplasm search tool has been created that allows users to bulk search T3 Breedbase for existing germplasm records by name. Genomics resources: The UCD group completed the remapping of the Kronos exome capture to the Chinese Spring RefSeq v1.0 and called 4,774,529 sequenced mutations with an estimated error rate of 0.33% and a mutation density of 40 mutations per Kb. In addition they completed the sequencing of the promoter regions (2 kb) of all annotated high-confidence genes in 1,513 lines of the EMS mutagenized Kronos population and annotated 4,287,361 sequenced mutations with an estimated error rate of 0.21% (99.79% accuracy). The KSU group showed that chromatin accessibility is a strong predictor of the effect of SNP variation on phenotype.The chromatin accessibility map of the wheat genome was constructed and results are published (Jordan et al., 2020) and publicly accessible through T3. The KSU group used the same regulatory capture assay used in the Kronos EMS population to re-sequence 203 wheat accessions. A total of 9,418,016,463 paired-end 2x150 bp reads were generated for 203 accessions, with the mean of 46,394,170 reads per accession. On average, 87% of all reads were mapped to the genome uniquely with an average of 8% reads failed to map. After SNP filtering, they obtained 3,320,006 SNPs segregating in the regulatory and coding regions of genome. The KSU group used a panel 198 diverse spring wheat cultivars and landraces to map SNPs associated with variation in gene expression in seedlings and developing spikes. They identified 36,898 and 65,117 eQTL in the RNA-seq datasets from wheat seedlings and spikes, respectively. The Akhunov lab collaborates with T3 team and genotyping labs developed a Practical Haplotype Graph (PHG) tool for wheat. The 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 Dubcovsky lab in collaboration with the transformation facility at UCD developed a new transformation technology using a chimeric protein including the wheat GROWTH-REGULATING FACTOR 4 (GRF4) and its cofactor GRF-INTERACTING FACTOR 1 (GIF1). The results were published in Nature Biotechnology. The Akhunov lab tested successfully molecular inversion probe (MIP) assay for low-cost genotyping in wheat. Genotyping Laboratories:. USDA-ARS researchers in collaboration with the Akhunov lab have compiled exome capture sequencing data on a collection of 419 lines relevant to contemporary U.S. wheat breeding efforts. Lines were identified and sequenced by regional small grains genotyping labs in the Pacific Northwest region (Pullman, WA), the Central Plains hard red winter wheat growing region (Manhattan, KS), the Northern Plains hard red spring wheat growing region (Fargo, ND), and the Southeastern soft red winter wheat growing region (Raleigh, NC). Variant calling has identified 1.28 million SNPs and 73,000 indels in this set of lines. The NC lab worked with the program at Cornell to develop 28 KASP assays with improved genome specificity that were evaluated on 1,920 lines for a total of 53,760 data points. . In support of the graduate student project at NCSU, forty new genome-specific KASP assays were developed and evaluated on 768 plants for fine-mapping QTL on chromosome 3A, 5A and 3D in the LA95135 x SS-MPV57 population. The Manhattan lab optimized a new next-generation-sequencing based medium- to high-throughput genotyping system called multiplex restriction amplicon sequencing (MRASeq) for Illumina platform. The Manhattan lab also developed three near diagnostic KASP markers for the 1R translocation. In addition, the lab developed two diagnostic markers for leaf rust resistance gene Lr42 using RNA-seq, the new markers have been validated in more than 1000 germplasm lines and are highly diagnostic for Lr42 in different genetic backgrounds. Finally, the Manhattan lab analyzed >8,000 wheat samples from 15 genetics and breeding programs in 2020. The Fargo genotyping laboratory primarily runs Illumina Infinium Assays for genome-wide SNPs and KASP/SSR markers for specific targets. In 2019-2020, they processed 20,000 individual samples and delivered 600M data points to customers. Among the WheatCAP-related projects supported by the Western Regional Small Grains Genotyping Laboratory is the development and sequencing of exome capture libraries for lines contributed by the breeding programs, including 127 lines sequenced to an average depth of 42 million reads per sample. They developed a new genotyping technology based on two-step PCR approach that allows for multiplexing thousands of SNP markers for high-throughput genotyping. CIMMYT HUB: In the 2019-2020 growing season two experiments were performed in the CIMMYT HUB at Obregon to test the effect of the combined Elf-Am3 (T. monococcum) allele for increased grain number with the gw-A2 mutant allele for increased grain size. QTL cloning projects:During the fourth year of the project, candidate genes were identified, validated and/or published for nine QTLs: QTL for number of spikelets per spike on 7AL (WAPO-A1, UCD-KSU). Grain size QTL TaGW7 encoding a TONNEAU1-recruiting motif (TRM) protein (KSU). Grain weight QTL TaGS3 encoding G-protein subunit (KSU). Awn suppressor B1 (NCSU). 1RS/1BS QTL for yield under water stress (UCD). 7BL QTL for number of spikelets per spike (Oklahoma State University). 2BL QTL for spikelets per spike (UCD). 3AS QTL for spikelets per spike (FT-A2, UCD) Mutations ful-A2 and ful-B2 that increase SNS on the long arm of chromosomes of homeologous group 2 (UCD).

Publications

  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Bajgain P., Y. Jin, T.J. Tsilo, G.K. Macharia, S.E. Reynolds, R. Wanyera, and J.A. Anderson. 2020. Registration of KUWNSr, a wheat stem rust nested association mapping population. J Plant Regist. https://doi.org/10.1002/plr2.20043.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Bernardo, A., P.St. Amand, H.Q. Le, Z. Su, and G. Bai. 2020. Multiplex restriction amplicon sequencing: a novel next-generation sequencing-based marker platform for high-throughput genotyping. Plant Biotechnol. J., 18:254-265.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Bolus, S., E. Akhunov, G. Coaker and J. Dubcovsky. 2019. Dissection of cell death induction by wheat stem rust resistance protein Sr35 and its matching effector AvrSr35. Mol. Plant Microbe Int. 33: 308319
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Chen, J., J. Wheeler, N. Klassen, W. Zhao, K. OBrien, C. Jackson, J.M. Marshall, K. Schroeder, and X.M. Chen. 2020. Registration of UI Bronze Jade hard white winter wheat. Journal of Plant Registration, 1 8. https://doi.org/10.1002/plr2.20029.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Chen, S., M. N. Rouse, W. Zhang, X. Zhang, Y. Guo, J. Briggs, J. Dubcovsky. 2020. Wheat gene Sr60 encodes a protein with two putative kinase domains that confers resistance to stem rust. New Phytologists. 225:948-959.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: DeWitt, N., M. Guedira, E. Lauer, M. Sarinelli, P. Tyagi, D. Fu, Q. Hao, J.P. Murphy, D. Marshall, A. Akhunova, K. Jordan, E. Akhunov, and G. Brown-Guedira. 2020. Sequence based mapping identifies AWNS1, a candidate transcription repressor underlying awn suppression at the B1 locus in wheat. New Phytologist, 225:326-339.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Fang, T., L. Lei, G. Li, C. Powers, P.M. Hunger, B.F. Carver, and L. Yan. 2020. Development and deployment of KASP markers for multiple alleles of Lr34 in wheat Theor. Appl. Genet. 133:2183-2195.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Guttieri, M.J., R.L. Bowden, K. Reinhart, D. Marshall, Y. Jin, B. Seabourn. 2020. Registration of hard white winter wheat germplasms with adult plant resistance to stem rust, KS14U6380R5, KS16U6380R10, and KS16U6380R11. J. Plant Registrations. 14:210-217
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Cook, J.P., R. K. Acharya, J. M. Martin, N. K. Blake, I. J. Khan, H.-Y. Heo, K. D. Kephart, J. Eckhoff, L.E. Talbert, and J. D. Sherman. 2020. Genetic analysis of stay-green, yield and agronomic traits in spring wheat (Triticum aestivum L.). Crop Science. https://doi.org/10.1002/csc2.20302
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Debernardi, J.M., J.R. Greenwood, E.J. Finnegan, J. Jernstedt, J. Dubcovsky. 2020. Wheat APETALA2-like genes AP2L2 and AP2L5 control the initiation of axillary floral meristems and specify glume-lemma identity. The Plant Journal. 101:171-187
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Debernardi JM, Tricoli DM, Ercoli MF, Hayta S, Ronald P, Palatnik JF, Dubcovsky J (2020) A chimera including a GROWTH-REGULATING FACTOR (GRF) and its cofactor GRF-INTERACTING FACTOR (GIF) increases transgenic plant regeneration efficiency. Nature Biotechnology https://doi.org/10.1038/s41587-020-0703-0
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Halder J., J. Zhang, S. Ali, H.S. Gill, J.S. Sidhu, S. Talukdar, J. Kleinjan, B. Turnipseed, S.K. Sehgal. 2019. Mining and genomic characterization of resistance against to Tan spot, Stagonospora nodorum blotch (SNB), and Fusarium head blight in Watkins core collection of wheat. BMC Plant Biology. 19:480
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Jones, B.H., N.K. Blake, H.-Y. Heo, J.R. Kalous, J.M. Martin, J.A. Torrion and L.E. Talbert. 2020. Improving hexaploid spring wheat by introgression of alleles for yield component traits from durum wheat. Crop Science 60: 759-771. doi:10.1002/csc2.20011.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Jordan KW, He F, DeSoto MF, Akhunova A, Akhunov E. 2020. Differential chromatin accessibility landscape reveals structural and functional features of the allopolyploid wheat chromosomes. Genome Biol. 21:176.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Kan, C-C, H., Jia, C, Powers, B.F. Carver, and L. Yan. 2020. Genetic characterization and deployment of a major gene for grain yield on chromosome arm 1BS in winter wheat. Mol. Breed. 40:26.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Kippes, N., C. van Gessel, J. Hamilton, A. Akpinar, H. Budak, J. Dubcovsky and S. Pearce. 2020. Effect of phyB and phyC loss-of-function mutations on wheat transcriptome under short and long day photoperiods. BMC Plant Biology. 20: 297.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Klymiuk, V., A. Fatiukha, D. Raats, V. Bocharova, L. Huang, L. Feng, S. Jaiwar, C. Pozniak, G. Coaker, J. Dubcovsky, T. Fahima. 2020. Three previously characterized resistances to yellow rust are encoded by a single locus Wtk1. Journal of Experimental Botany. 71: 2561-2572.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Larkin, D. L., A.L. Holder, R.E. Mason, D.A. Moon, G. Brown-Guedira, P.P. Price, S.A. Harrison, and Y. Dong. (2020). Genome-wide analysis and prediction of fusarium head blight resistance in soft red winter wheat. Crop Science. doi:10.1002/csc2.20273
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Liu, G., X. Liu, Y. Xu, A. Bernardo, M. Chen, Y. Li, F. Niu, L. Zhao and G. Bai. 2020. Reassigning Hessian fly resistance genes H7 and H8 to chromosomes 6A and 2B of the wheat cultivar Seneca using genotyping?by?sequencing. Crop Sci. 60:14881498
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Liu S., G. Bai, M. Lin, M. Luo, D. Zhang, F. Jin, B. Tian, H.N. Trick, L. Yan. 2020. Identification of candidate chromosome region of Sbwm1 for Soil-borne wheat mosaic virus resistance in wheat. Sci Rep-UK 10:8119
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Niu, F., Y. Xu, X. Liu, L. Zhao, A. Bernardo, Y. Li, G. Liu, M. Chen, L. Cao, Z. Hu, X. Xu, and G. Bai. 2020. The Hessian fly recessive resistance gene h4 mapped to chromosome 1A of the wheat cultivar Java using genotyping-by-sequencing. Theor. Appl. Genet. https://doi.org/10.1007/s00122-020-03642-9.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Nyine M., E, Adhikari, M. Clinesmith, K. W. Jordan, A.K. Fritz, E. Akhunov. 2020. Genomic Patterns of introgression in interspecific populations created by crossing wheat with its wild relative. G3 (Bethesda) 10:3651-3661. doi: 10.1534/g3.120.401479
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Shaw, L. M., C. Li, D. P. Woods1, M. A. Alvarez, H. Lin, M. Y. Lau, A. Chen, and J. Dubcovsky. 2020. Epistatic interactions between PHOTOPERIOD1, CONSTANS1 and CONSTANS2 modulate the photoperiodic response in wheat. PLoS Genetics. 16: e1008812
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Sidhu J.S., D. Singh, H.S. Gill, N.K. Brar, Y. Qiu, J. Halder, R. Al Tameemi, B. Turnipseed and S.K. Sehgal. 2020. Genome-wide association study uncovers novel genomic regions associated with coleoptile length in hard winter wheat. Frontiers in Genetics. 10:1345.
  • Type: Journal Articles Status: Accepted Year Published: 2020 Citation: Strauss, N. M., A. Wiersma, P. DeMacon, E. Klarquist, A. Carter, K.A. Garland Campbell, E. Olson. 2020. Registration of the wheat D-Genome nested association mapping population. Journal of Plant Registrations. Accepted
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Maulana F., K-S. Kim, J.D. Anderson, M.E. Sorrells, T. J. Butler, S.-Y. Liu, P. S. Baenziger, P.F. Byrne, and X-F. Ma. 2020. Genomic selection of forage agronomic traits in winter wheat. Crop Sci. https://doi.org/10.1002/csc2.20304.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Muleta, K.T., X. Chen and M. Pumphrey. 2020. Genome-wide mapping of resistance to stripe rust caused by Puccinia striiformis f. sp. tritici in hexaploid winter wheat. Crop Science. DOI:10.1002/csc2.20058.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Taagen E., A.J. Bogdanove, and M.E. Sorrells. 2020. Counting on crossovers: Controlled recombination for plant breeding. Trends in Plant Science. 25:455-465.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Taagen, E., A.J. Bogdanove, M.E. Sorrells. 2020. Achieving controlled recombination with targeted cleavage and epigenetic modifiers. Trends in Plant Science. 25:513-514. https://doi.org/10.1016/j.tplants.2019.12.018
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Veenstra, L.D., J. Poland, Jannink, and M.E. Sorrells. 2020. Recurrent genomic selection for wheat grain fructans. Crop Science 60:1499-1512. DOI: 10.1002/csc2.20130.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Veenstra, L.D., N. Santantonio, J.L. Jannink, and M.E. Sorrells. 2019. Influence of genotype and environment on wheat grain fructan content. Crop Sciences. 59:190-198. DOI: 10.2135/cropsci2018.06.0363
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Wang, S., Q. Li, J. Wang, Y. Yan, G. Zhang, Y. Yan, H. Zhang, J. Wu, F. Chen, X. Wang, Z. Kang, J. Dubcovsky, and J.-Y. Gou. 2019. YR36/WKS1-mediated phosphorylation of PsbO, an extrinsic member of Photosystem II, inhibits photosynthesis and confers stripe rust resistance in wheat. Molecular Plant 12:1639-1650
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Zhao, L., N.R. Abdelsalam, Y. Xu, M.S. Chen, Y. Feng, L. Kong, and G. Bai, G. 2020. Identification of two novel Hessian fly resistance genes H35 and H36 in a hard winter wheat line SD06165. Theor. Appl. Genet. 133:2343-2353.
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Zhang, P., C. Guo, Z. Liu, A. Bernardo, H. Ma, P. Jiang, G. Song and G. Bai. 2020. Quantitative trait loci for Fusarium head blight resistance in wheat cultivars Yangmai 158 and Zhengmai 9023, Crop J. https://doi.org/10.1016/j.cj.2020.05.007
  • Type: Journal Articles Status: Published Year Published: 2020 Citation: Zhang, Y., A. Schonhofen, W. Zhang, J. Hegarty, C. Carter, T. Vang , D. Laudencia-Chingcuanco and J. Dubcovsky. 2020. Contributions of individual and combined Glu-B1x and Glu-B1y high-molecular-weight glutenin subunits to semolina functionality and pasta quality. Journal of Cereal Science 93: 102943.


Progress 12/15/18 to 12/14/19

Outputs
Target Audience:The audiences targeted during the third 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. Presentations were also made to individual milling and baking companies. 3) Scientist working in basic and applied aspects of wheat research. 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, coPDs and students made oral and poster presentations at the International Wheat Congress in Canada. 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 publicly accessible through the T3 database. Kronos TILLING mutants were distributed to wheat breeders and researchers in the US and abroad. 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 activities of the WheatCAP include: 1) Graduate and undergraduate students interested in plant breeding (including students outside the project). Education materials from the WheatCAP workshops have been uploaded into the Plant Breeding Training Network (PBTN) and the WheatCAP website. Links to the 2019 WheatCAP Plant Science Symposium organized by the WheatCAP students are available at https://www.triticeaecap.org/whpss/. 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 addition to the information regarding the new wheat varieties, we educate growers, private breeders and seed industry about the opportunities and limitations of new technologies. This information has facilitated 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 2019. The 2019 financial report covers expenses up to July 31, 2019 so there are still 4.5 months of spending this year. The funding for the fifth year has been retained by UCD and is available to be used as intended. 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 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 and her replacement by Jason Fiedler, who is already running the ND genotyping laboratory successfully. What opportunities for training and professional development has the project provided?One of the main objectives of the WheatCAP was to educate 15 PhD students in molecular plant breeding. By leveraging funds from participating universities, we have supported 29 graduate students (19 current PhD students, four current MS students and six graduated students). The efficiency of the WheatCAP education program was assessed by conducting an annual survey that evaluated students' progress in learning the concepts essential for completing their WheatCAP research projects and their future employment. The survey also served as a guide to help planning future education activities. Survey results are posted online at the following link: https://www.triticeaecap.org/2019-graduate-student-survey/. The first participatory education activity supported by WheatCAP in 2019 was the Plant Sciences Symposia sponsored by Corteva Agriscience that was held in San Diego, CA (January 11), and was hosted and organized by the WheatCAP students. The Plant Sciences Symposia series is a global network of student-organized and student-driven conferences designed to provide students an opportunity to harness their leadership and soft skills. Leading scientists and graduate students, most of whom were not associated with the WheatCAP project, were invited to speak on the conference topic: "Bridging the Gap: Using Functional Genomics to Unlock Yield Potential." Additionally, there was a discussion panel comprised of individuals who work in academia and industry that answered questions from the audience regarding their career and work experiences. The symposia provided an opportunity for WheatCAP students to develop their leadership skills, work together as a team, network with leading scientists and learn about the latest research focused on improving yield. The second participatory education activity organized by WheatCAP was a workshop hosted at Cornell University (July 8-12) designed to teach the students how to use bioinformatic and database tools to develop a practical haplotype graph (PHG). PHG is a new way to compile genomic data to infer high-density genotypes directly from low-coverage sequence data for use in genome wide association studies (GWAS) and genomic selection (GS). Dr. Jean-Luc Jannink, Dr. Edward Buckler and their research teams, hosted the workshop. The workshop also offered opportunities for the students to discuss their projects and make plans for future education opportunities. On September 4, 2019 most of the students involved in positional cloning projects participated in a Zoom meeting led by J. Dubcovsky to discuss strategies for validation of the candidate genes. The meeting and questions extended for one and a half hour and was recorded at https://vimeo.com/tcapfilms/review/357884325/02bbd0a8d1 Lastly, the Plant Breeding Training Network (PBTN) was successfully transferred to the new Plant and Soil Sciences eLibrary (PASSeL) website platform. Leah Sandall led this effort with assistance from DeAnna Crow. The transfer has made PBTN easily accessible on mobile devices as well as tablets and computers. Information and content on PBTN was updated and visitors have access to archived webinars, online learning opportunities and many other resources to support plant-breeding education. The new PBTN interface can be accessed directly: https://passel2.unl.edu/view/community/b6721f4789d7/1 or by visiting PASSeL: https://passel2.unl.edu and clicking on Communities. 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. The WheatCAP papers (01/2017-09/2019) have been cross-referenced in Google Scholar 924 times, documenting impact. Results have also been presented at multiple scientific meetings in the US including the ASA-CSSA meeting and the Plant and Animal Genome Conference. The WheatCAP PDs and students presented five of the selected oral presentations at the 1st International Wheat Congress, documenting the International recognition of the WheatCAP group. The individual QTL cloning projects are described on 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 website (http://maswheat.ucdavis.edu/). Mutations in all wheat genes and forms to request seeds of the mutant lines are available at https://dubcovskylab.ucdavis.edu/wheat_blast. Expression datasets are accessible through https://wheat.pw.usda.gov/WheatExp/. New genomic resources generated by WheatCAP have been widely advertised through the GrainGenes 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 the 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 plans for 4th year: In 2020, the WheatCAP students will participate in a Soft Skills workshop on January 10, in San Diego, CA, a day before the 2019 PAG conference begins. Topics for this workshop include developing skills for obtaining a job, preparation for a smoother transition from being a student to being a professional, and how to effectively work in teams and lead others. Additionally, we are planning a trip to CIMMYT located in Obregon, Mexico (March 16-20) to give the WheatCAP students an opportunity to learn about CIMMYT's international mission to solve global food shortages, tour their breeding programs and network with leading scientists who are working on international projects to end hunger. Lastly, the University of Minnesota will host a breeding workshop on July 6-10th that will include an overview of the UMN hard red spring wheat breeding program, discussion on genomic selection, an interactive milling and baking workshop with local businesses, possible tours of bakeries and mills in the Twin City area and interaction with Minnesota wheat stakeholders. T3 plans for 4th year: In an effort to make T3 more useful to breeders, we are transitioning the database to a new code base called Breedbase. Breedbase was originally developed out of the Boyce Thompson Institute at Cornell. It has been supported by the Bill and Melinda Gates Foundation. It is also being adopted by a USDA initiative called Breeding Insight which aims to bring improved breeding IT to the specialty crops and livestock breeding efforts funded by USDA-ARS. Thus, Breedbase has a lot of support that we think we can synergistically bring to WheatCAP. We intend to complete the transition by early 2020, while ensuring minimal disruption to normal use of T3. Part of the transition will also bring a new genotype storage solution to T3 that will be robust to increasing density of genotypic variants used in wheat breeding and research. Specifically, we will be using the GOBii platform. We have the wheat exome data currently stored on this platform as its first test. Users of T3 will not be aware of the platform switch other than through improved performance. By the end of next year, we plan to have an imputation platform in place that will allow wheat lines to be imputed from GBS, 90K or exome capture to whole-exome level variants. Imputation will be based on a PHG. We continue to incorporate as many wheat datasets as possible, particularly from cooperative nurseries. In the coming year we will be focusing on fusarium head blight nurseries as we have some supplemental funding from the scab initiative. We plan to incorporate two tools that may / may not conflict with the transition to BreedBase (which is the top priority). Success will depend on sufficient time to develop these features in the BreedBase context. A tool to predict the variance among progeny of a cross as a decision support for breeders designing crossing nurseries. Features to upload and interact with metabolomics and transcriptomics data. Genomics Resources plan for 4th year: The WheatCAP genomics group will collaborate in the development of the practical haplotype graph (PHG) by using SNP data generated using exome capture for more than 200 US wheat breeding lines and cultivars. This will make PHG highly relevant for genotype imputation in the US wheat breeding programs. These efforts will be combined with the development of a low cost SNP genotyping assay containing 2000-3000 SNPs, which will be used for fast, low-cost genotyping of breeding material for genomic selection. The SNPs used for this assay design were selected among variable sites with high MAF in the US wheat cultivars and breeding lines. This resource will allow for effective SNP imputation from the PHG and accurate prediction of traits for genomic selection in individual breeding programs. Using promoter capture data obtained from WheatCAP parental lines and 200 diverse wheat accessions, we will characterize the contribution of genetic variation in the regulatory regions to controlling gene expression. For this purpose, we will collect gene expression data from multiple tissues of WheatCAP parental lines and diversity panel, and correlate changes in gene expression levels with variation in the promoter regions. This data will be integrated with QTL mapping/gene cloning results of the WheatCAP to connect gene expression and promoter sequence variation with variation in yield component traits. We will expand the chromatin accessibility datasets from multiple wheat tissues using ATAC-seq strategy. The data will be combined with already generated MNase chromatin accessibility data, gene expression and promoter sequence variation to develop genomic resources for effective identification of causal variation controlling complex traits in wheat. These resources will lay a foundation for re-designing the wheat plant by combining multiple beneficial alleles of genes in the pathways that regulate major agronomic traits. Plans for CIMMYT for the 4th year: In August 2019, UCD sent a new set of Gw2 x Elf3 combinations in two different tetraploid genetic backgrounds selected by CIMMYT: CIRNO and GID 6420253. Seeds are being increased to perform a large experiment including these two genotypes and Kronos and the four lines per genotype in 2019-2020 (120 plots experiment). For the hexaploid lines, UCD will send to CIMMYT the four GW2 x ELF3 homozygous combinations in two genetic backgrounds: Kingbird BC4F3 and Patwin BC3F3. Depending on the amount of seed harvested at Tulelake in September 2019, the seeds will be used for a field increase or preliminary yield trials. CIMMYT will increase the seeds of the new materials generated by Wheat CAP during 2020. Plans for the cloning projects for the 4th year: All cloning projects will continue to narrow down their 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 the narrowed candidate gene region using the exome capture data. Projects that have identified good candidate genes will shift their focus 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.Loss-of-function mutations in the A and B genome homeologs 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. For the two projects that have already validated their candidate genes the focus will be on the molecular mechanisms and in the identification of interacting genes.

Impacts
What was accomplished under these goals? ?WheatCAP overall productivity: During the third year, the members of the WheatCAP published 54 peer-reviewed papers acknowledging USDA-NIFA support. WheatCAP breeders released 24 improved commercial varieties in all wheat market classes, 3 improved germplasm, and 5 mapping populations. Nine of the varieties released in 2018 received PVP in 2019 (see https://www.triticeaecap.org/publications-and-germplasm/). Education: WheatCAP is currently training 23 graduate students and six additional students have graduated. Student progress is being tracked with an annual survey (https://www.triticeaecap.org/2019-graduate-student-survey/). More detailed description of the educational activities is provided in a following section: "Training Opportunities" T3 database: T3 participated in the development of a wheat Practical Haplotype Graph (PHG) and worked on the development of statistical methods that leverage homeology between wheat genes inferred from the wheat reference genome sequence. A total of 1,153 phenotype trials were added to T3. Practical Farmers of Iowa and T3 are developing a variety selection tool to be used by growers to predict the top-yielding varieties for their local environment. T3 data is being loaded into the BreedBase platform. The benefit of transitioning to the new BreedBase platform is that it has more functionality for applied breeding and is more broadly used by breeding programs. Once existing T3 datasets transition to BreedBase, all these functions will be available to small grains breeders. The T3 report pages from "GWAS Report" and "Gene Annotations" have been enhanced with links to KnetMiner pages. KnetMiner helps scientists search across large biological databases and literature to find links between genes, traits, diseases and many other information types. The PolyMarker program was used to design KASP primers for all the SNPs in the WheatCAP exome capture experiment. New tutorials were added for PolyMarker, KnetMiner, and for translating gene names from previous assemblies. A Uniprot database was added to the WheatIS search tool at https://urgi.versailles.inra.fr/wheatis/. A new section on the T3 website was created for searching gene, protein, and molecular pathway information contained in the Ensembl Plant BioMart. Lastly, T3 added genotype data from the 1000 wheat exome project led by Eduard Akhunov. Because of the large dataset, T3 developed a specialized search page that allows researchers and students to download a subset of this data by specifying the desired chromosome intervals. Genomics resources: WheatCAP has re-mapped more than 10,000,000 mutations in the coding regions of the wheat genome to Chinese Spring RefSeq v1.1, and mutation effects on all genes were annotated. The data was made available through ENSEMBL and the Dubcovsky lab website https://dubcovskylab.ucdavis.edu/wheat_blast. WheatCAP sequenced the promoters of the 38 US Breeding lines used in the mapping projects and 200 additional diverse wheat lines. This was done using a new regulatory element capture assay developed in collaboration with A. Hall in the UK and the NovaSeq platform. WheatCAP is also using the same regulatory capture to sequence the promoters of the tetraploid TILLING populations. Whole exome re-sequencing data generated for a diverse collection of wheat landraces, cultivars and breeding lines was analyzed resulting in discovery of 8.8 million SNPs (8.8 billion genotype calls). All SNPs were uploaded to the T3 database and the study was published in Nature Genetics. The data was successfully used to investigate the origin and evolutionary history of two yield component genes identified by WheatCAP teams. These data, together with 195 lines from the US breeding programs are being used to develop a PHG for wheat. The same SNPs are being used to develop a low-cost genotyping platform for the US breeding programs. The new assay was updated to include a total of 3,000 SNPs with high minor allele frequency (MAF) not only in the 1000 wheat exome dataset, but also in the population of ~200 US wheat cultivars re-sequenced by exome capture. The assay will be used for cost-effective genomic selection in breeding programs. Finally, analysis on differential digestion of MNase libraries has been completed and the paper has been submitted. Genotyping Laboratories: During the third year of the grant, the genotyping labs provided KASP and other marker genotyping services for QTL analysis and high-resolution mapping of candidate genes for yield-related QTL. The genotyping labs made substantial contributions to the recent isolation of the first two genes controlling grain yield components. The Raleigh group developed a tool for computer-generated KASP designs for the WheatCAP parent exome capture data set to facilitate fine-mapping of QTL http://tcapg.ag.cornell.edu/primer_filter/.A total of fifty-one markers based on exome capture data were developed and evaluated on 480 fine-mapping samples for the NCSU cloning projects. The Fargo lab provided services for processing Illumina 90K SNP arrays for 13 projects consisting of over 3,000 samples and generating 275 million data points. The Fargo and the Manhattan lab assisted WheatCAP researchers in screening populations with SNP and SSR markers to identify critical recombinants near the target QTLs. In conjunction with researchers at KSU, exome capture was done on more than 200 winter and spring wheats from the Great Plains and the eastern growing region. The Pullman lab performed exome capture on 127 western wheat lines. Finally, the genotyping labs continued development of sequencing based platforms for genotyping with genome-wide markers and with markers targeted to traits. CIMMYT HUB: During the 2018-2019 growing season a factorial experiment was performed combining the Elf-A3 (T. aestivum) and Elf-Am3 (T. monococcum) alleles for increased grain number with the Gw2 wild-type and mutant allele for increased grain size. The presence of the gw-A2 mutant allele was associated with a 4.2 % increase in TKW relative to the wild type, and the Elf-Am3 allele from T. monococcum was associated with a 2.6% increase in plant height (P = 0.004), 10.8% increase in biomass (P = 0.025) and 10.9% increase in total grain yield (P = 0.0243). This last result is encouraging because a 2018 preliminary experiment using the same lines also showed an 8.6% increase in total grain yield associated with the Elf-Am3 allele from T. monococcum. In 2019, CIMMYT completed experiments in Kronos combining loss-of-function mutations and WT alleles in both the gw-A2 and gw-B2 loci. These experiments detected significant increases in grain weight associated with the gw-A2 and gw-B2 loci, with the largest effects observed in the double mutants. Grain protein content was also significantly higher for gw-A2 and gw-B2, with the largest increase in the double mutant. Although the introduction of these two mutations did not result in a significant increase in grain yield, they produced a significant increase in protein yield. QTL cloning projects: Three WheatCAP groups identified the candidate genes underlying their targeted QTL for grain yield components and published their results (WAPO-A1, B1 and GW7). All QTL cloning projects advanced their projects by identifying recombination events within their candidate gene regions and are evaluating these critical recombinant lines in greenhouse and field experiments. Using the data, most projects defined the QTL candidate regions more precisely within the reference wheat genome. Candidate genes have been identified for several QTL cloning projects and validation experiments of the candidate genes have been initiated using mutant lines.

Publications

  • Type: Journal Articles Status: Published Year Published: 2019 Citation: 39. Sarinelli, J.M., J.P. Murphy, P. Tyagi, J.B. Holland, J.W. Johnson, M. Mergoum, R.E. Mason, A. Babar, S. Harrison, R. Sutton, C.A. Griffey, and G. Brown?Guedira. 2019. Training population selection and use of fixed effects to optimize genomic predictions in a historical USA winter wheat panel. Theor. Appl. Genet. 132: 12471261
  • 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. 131:16831697.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Wang R., Y. Liu, K. Isham, W. Zhao, J. Wheeler, N. Klassen, Y. Hu, J.M. Bonman, J. Chen. 2018. QTL identification and KASP marker development for productive tiller and fertile spikelet numbers in two high-yielding hard white spring wheat cultivars. Mol. Bred. 38:135
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Wang, R., T. Gordon, D. Hole, W. Zhao, K. Isham, J. M. Bonman, B. Goates, and J. Chen. 2019. Identification and assessment of two major QTL for dwarf bunt resistance in winter wheat line IDO835. Theor. Appl. Genet. doi.org/10.1007/s00122-019-03385-2.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Wang W., Q. Pan, B. Tian, F. He, Y. Chen, G. Bai, A. Akhunova, H.N. Trick, E. Akhunov. 2019. Gene editing of the wheat homologs of TONNEAU1recruiting motif encoding gene affects grain shape and weight in wheat. Plant J. doi.org/10.1111/tpj.14440.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Ward, B.P., G.L. Brown-Guedira, F.L. Kolb, D.A. Van Sanford, P. Tyagi, C.H. Sneller and C.A. Griffey. 2019. Genome-wide association studies for yield-related traits in soft red winter wheat grown in Virginia. PLoS ONE, 14, p.e0208217
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Ward, B.P., G.L. Brown-Guedira, P. Tyagi, F.L. Kolb, D.A. Van Sanford, C.H. Sneller and C.A. Griffey 2019. Multi-environment and multi-trait genomic selection models in unbalanced early-generation wheat yield trials. Crop Science. 59:491-507.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Yang, Y., B.R. Basnet, A.M.H. Ibrahim, J.C. Rudd, X. Chen, R.L. Bowden, Q. Xue, R.D. Devkota, S. Wang, C.D. Johnson, R. Metz, R.E. Mason, D.B. Hays and S-Y. Liu. 2019. Developing KASP markers on a major stripe rust resistance QTL in a popular wheat TAM 111 using 90K array and genotyping-by-sequencing SNPs. Crop Sci. 59:165-175.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Zhao, J., N.R. Mohamed, L. Khalaf, W. Chuang, L. Zhao, C.M. Smith, B. Carver, G. Bai. 2019. Development of single nucleotide polymorphism markers for the wheat curl mite resistance gene Cmc4. Crop Sci. 59: 1567-1575.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Hayat, H., Mason, R.E., Lozada, D.N., Acuna, A., Holder, A., Larkin, D.L., Winn, Z., Murry, J., Murphy, P., Moon, D.E., Miller, R.G. 2019. Effects of allelic variation at Rht-B1 and Rht-D1 on grain yield and agronomic traits of southern US soft red winter wheat. Euphytica. DOI: 10.1007/s10681-019-2478-2
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Alipour, H., G. Bai, G. Zhang, M.R. Bihamta, V. Mohammadi, S.A. Peyghambari. 2019. Imputation accuracy of wheat GBS data using barley and wheat genome references. PloS One PLoS ONE 14: e0208614
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Anderson, J.A., J.J. Wiersma, S.K. Reynolds, G.L. Linkert, R. Caspers, J.A. Kolmer, Y. Jin, M.N. Rouse, R. Dill-Macky, M.J. Smith, L. Dykes, and J.-B. Ohm. 2019. Registration of 'Shelly' hard red spring wheat. J. Plant Registrations, doi:10.3198/jpr2018.07.0049crc.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Bernardo, A., P.St. Amand, H.Q. Le, Z. Su, and G. Bai. 2019. Multiplex restriction amplicon sequencing: a novel next-generation sequencing-based marker platform for high-throughput genotyping. Plant Biotechnol. J., https://doi.org/10.1111/pbi.13192
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Blake, N. K., M. Pumphrey, K. Glover, S. Chao, K. Jordan, J.-L. Jannick, E. A. Akhunov, J. Dubcovsky, H. Bockelman, L. E. Talbert. 2019. Registration of the Triticeae-CAP Spring Wheat Nested Association Mapping Population. J. Plant Reg. 13:294-297.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Cai, J., S. Wang, Z. Su, T. Li, X. Zhang, G. Bai. 2019. Meta-analysis of QTL for Fusarium head blight resistance in Chinese wheat landraces. The Crop Journal. doi.org/10.1016/j.cj.2019.05.003
  • Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Chen, S., M. N. Rouse, W. Zhang, X. Zhang, Y. Guo, J. Briggs, J. Dubcovsky. 2019. Wheat gene Sr60 encodes a protein with two putative kinase domains that confers resistance to stem rust. New Phytologists. DOI:10.1111/nph.16169
  • Type: Journal Articles Status: Published 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 Sci. 58: 2470-2483.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Cobo, N., H. Wanjugi, E. Lagudah, J. Dubcovsky. 2019. High-resolution map of wheat QYr.ucw-1BL, an adult-plant stripe rust resistance locus in the same chromosomal region as Yr29. The Plant Genome. 12:180055.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Cook, J. P., D. K. Weaver, A. C. Varella, J. D. Sherman, M. L. Hofland, H.-Y. Heo, C. Caron, P. F. Lamb, N. K. Blake, L. E. Talbert. 2019. Comparison of three alleles at a major solid stem QTL for wheat stem sawfly resistance and agronomic performance in hexaploid wheat. Crop Sci. 59:16391647.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: DeWitt, N., M. Guedira, E. Lauer, M. Sarinelli, P. Tyagi, D. Fu, Q. Hao, J.P. Murphy, D. Marshall, A. Akhunova, K. Jordan, E. Akhunov, and G. Brown-Guedira. 2019. Sequence based mapping identifies AWNS1, a candidate transcription repressor underlying awn suppression at the B1 locus in wheat. New Phytologist. doi: 10.1111/nph.16152
  • Type: Journal Articles Status: Published 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. 2018. Mapping and KASP marker development for wheat curl mite resistance in TAM 112 wheat using linkage and association analysis. Mol. Breed. 38: 119
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Gao, L., E.M. Babiker, I.C. Nava, J. Nirmala, Z. Bedo, L. Lang, S. Chao, S. Gale, Y. Jin, J.A. Anderson, U. Bansal, R.F. Park, M.N. Rouse, J.M. Bonman, and H. Bariana. 2018. Temperature-sensitive wheat stem rust resistance gene Sr15 is effective against Puccinia graminis f. sp. tritici race TTKSK. Plant Pathol. 68:143151.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Gill H.S., C. Li, J.S. Sidhu, W. Liu, D. Wilson, G. Bai, G.S. Gill, S.K. Sehgal. 2019. Fine mapping of the wheat leaf rust resistance gene Lr42. Int. J. Mol. Sci. 20, 2445; doi.org/10.3390/ijms20102445
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Gizaw S.A., J.G. Godoy, M.O. Pumphrey, and A.H. Carter. 2018. Spectral reflectance for indirect selection and genome-wide association analysis of grain yield and drought tolerance in North American spring wheat (Triticum aestivum L.). Crop Sci. 58: 2289-2301
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Gizaw, S.A., J. Godoy, K. Garland-Campbell, and A.H. Carter. 2018. Genome-wide association study of yield and component traits in Pacific Northwest winter wheat (Triticum aestivum L.). Crop Sci. 58: 2315-2330.
  • 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 58:1838-1852
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Djanaguiraman, M., P.V.V. Prasad, J. Kumari, S.K. Sehgal, B. Friebe, I. Djalovic, Y. Chen, K.H.M. Siddique, B.S. Gill. 2019. Alien chromosome segment from Aegilops speltoides and Dasypyrum villosum increases drought tolerance in wheat via profuse and deep root system. BMC Plant Biology201919:242 doi.org/10.1186/s12870-019-1833-8.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Gaire, R, M. Huang, C. Sneller, C. Griffey, G. Brown-Guedira, M. Mohammadi. 2019. Association analysis of baking and milling quality traits in elite soft red winter wheat population. Crop Sci. 59:1085-1094
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: He F., R. Pasam, F. Shi, S. Kant, G. Keeble-Gagnere, P. Kay, K. Forrest, A. Fritz, P. Hucl, K. Wiebe, R. Knox, R. Cuthbert, C. Pozniak, A. Akhunova, P.L. Morrell, J.P. Davies, S.R. Webb, G. Spangenberg, B. Hayes, H. Daetwyler, J. Tibbits, M. Hayden, E. Akhunov. 2019. Exome sequencing highlights the role of wild relative introgression in shaping the adaptive landscape of the wheat genome. Nat Genet. 51:896904.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Howell T, J.I. Moriconi, X. Zhao, T. Fahima, G. E. Santa-Maria, and J. Dubcovsky. 2019. A wheat/rye polymorphism affects seminal root length and is associated with drought and waterlogging tolerance. J Exp. Bot. 70:4027-4037.
  • Type: Journal Articles Status: Published 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. 58: 2274-2288.
  • Type: Journal Articles Status: Published 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. Front. Pl. Sci. 9:271. doi.org/10.3389/fpls.2018.00271
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Kandel, J.S., M. Huang, Z. Zhang, D.Z. Skinner, D.R. See. 2018. Genetic diversity of clinal freezing tolerance variation in winter wheat landraces. Agronomy 8, 95
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Krause, M.R., L. Gonza?lez-Pe?rez, J. Crossa, P. Pe?rez-Rodri?guez, O. Montesinos-Lo?pez, R.P. Singh, S. Dreisigacker, J. Poland, J. Rutkoski, M.E. Sorrells, M.A. Gore, and S. Mondal. 2019. Hyperspectral reflectance-derived relationship matrices for genomic prediction of grain yield in wheat. Genes Genomes Genetics. 9:1231-1247.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Kuzay, S., Y. Xu, J. Zhang, A. Katz, S. Pearce, Z. Su, M. Fraser, J. A. Anderson, G. Brown-Guedira, N. DeWitt, A. Peters Haugrud, J.D. Faris, E. Akhunov, G. Bai, J. Dubcovsky. 2019. Identification of a candidate gene for a QTL for spikelet number per spike on wheat chromosome arm 7AL by high-resolution genetic mapping. Theor. Appl. Genet. 132:26892705.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Larkin, D.L., D.N. Lozada, and R.E Mason. 2019. Genomic selection  considerations for successful implementation in wheat breeding programs. Agronomy. doi:10.3390/agronomy9090479
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Li, C., H. Lin, A. Chen, M. Lau, J. Jernstedt, and J. Dubcovsky. 2019. Wheat VRN1, FUL2 and FUL3 play critical and redundant roles in spikelet meristem identity and spike determinacy. Development. 146: On line first. doi:10.1242/dev.175398
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Lin, M., S. Liu, G. Zhang, and G. Bai. 2018. Effects of TaPHS1 and TaMKK3-A genes on wheat pre-harvest sprouting resistance. Agronomy 8, doi:10.3390/agronomy8100210
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Liu, W., J. Kolmer, S. Rynearson, X. Chen, L. Gao, J.A. Anderson, M.K. Turner, M. Pumphrey. 2019. Identifying loci conferring resistance to leaf and stripe rusts in a spring wheat population (Triticum aestivum L.) via genome-wide association mapping. Phytopathology. doi.org/10.1094/PHYTO-04-19-0143-R.
  • Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Lozada, D.L., R.E. Mason, J.M. Sarinelli, and G. Brown-Guedira. 2019 Accuracy of genomic selection for grain yield and agronomic traits in soft red winter wheat. BMC Genetics. In press.
  • Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Maulana F., K-S. Kim, J.D. Anderson, M.E. Sorrells, T. J. Butler, S. Liu, P. S. Baenziger, P.F. Byrne, and X-F. Ma. 2019. Genomic selection of forage quality traits in winter wheat. Crop Sci. In press.
  • Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Muleta, K.T., X. Chen and M. Pumphrey. 2019. Genome-wide mapping of resistance to stripe rust caused by Puccinia striiformis f. sp. tritici in hexaploid winter wheat. Crop Science. In press.
  • Type: Journal Articles Status: Published Year Published: 2018 Citation: Nyine, M., S. Wang, K. Kiani, K. Jordan, S.Y. Liu, P. Byrne, S. Haley, S. Baenziger, S. Chao, R. Bowden, E. Akhunov. 2018. Genotype imputation in winter wheat using first-generation haplotype map SNPs improves genome-wide association mapping and genomic predictions of traits. G3 9:125-133. G3/2018/200664
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Ramakrishnan S.M., J.S. Sidhu, S. Ali, N. Kaur, J. Wu, and S.K. Sehgal. 2019. Molecular characterization of bacterial leaf streak resistance in hard winter wheat. PeerJ 7:e7276
  • Type: Journal Articles Status: Accepted Year Published: 2019 Citation: Rudd, J. C., R.N. Devkota, A.M.H. Ibrahim, J. A. Baker, S. Baker, R. Sutton, B. Simoneaux, G. Ope�a, L.W. Rooney, J.M. Awika, S.-Y. Liu, Q. Xue, B. Bean, C.B. Neely, R.W. Duncan, Y. Jin, B.W. Seabourn, R.L. Bowden, Y. Jin, M.-S. Chen, and R.A. Graybosch. 2019. TAM 204 wheat, adapted to grazing, grain, and graze-out production systems in the southern High Plains. J. Plant Reg. In press.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Santantonio, N., J.L. Jannink, and M.E. Sorrells. 2019. Homeologous epistasis in wheat: the search for an immortal hybrid. Genetics. doi.org/10.1534/genetics.118.301851
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Santantonio, N., J.L. Jannink and M.E. Sorrells. 2019. Prediction of subgenome additive and interaction effects in allohexaploid wheat. G3: Genes, Genomes, Genetics. doi.org/10.1534/g3.118.200613.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Santantonio, N., J.L. Jannink and M.E. Sorrells. 2019. A low resolution epistasis mapping approach to identify chromosome arm interactions in allohexaploid wheat. G3: Genes, Genomes, Genetics. Early Online: doi.org/10.1534/g3.118.200646.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Sidhu, J.S., S.M. Ramakrishnan, S. Ali, A. Bernardo, G. Bai, S. Abdullah G. Ayana, and S.K. Sehgal. 2019. Assessing the genetic diversity and characterizing genomic regions conferring tan spot resistance in rye. PLoS One 14: e0214519 doi.org/10.1371/journal.pone.0214519
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Su, Z., A. Bernardo, B. Tian, H. Chen, S. Wang, H. Ma, S. Cai, D. Liu, D. Zhang, T. Li, H. Trick, P.St. Amand, J. Yu, Z. Zhang, and G. Bai. 2019. A deletion mutation in TaHRC confers Fhb1 resistance to Fusarium Head Blight in wheat. Nat. Genet. 51: 1099-1105.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Sun J., J.A. Poland, S. Mondal, J. Crossa, P. Juliana, R.P. Singh, J.E. Rutkoski, J-L. Jannink, L. Crespo-Herrera, G. Velu, J. Huerta-Espino, M.E. Sorrells. 2019. High-throughput phenotyping platforms enhance genomic selection for wheat grain yield across populations and cycles in early stage. Theor Appl Genet. 132:1705-1720.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Shaw, L. B. Lyu, R. Turner, C. Li, F. Chen, X. Han, D. Fu, and J. Dubcovsky. 2019. FLOWERING LOCUS T2 (FT2) regulates spike development and fertility in temperate cereals. J. of Exp. Bot. 70: 193-204.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Varella, A. C., H. Zhang, D. K. Weaver, J. P. Cook, M. L. Hofland, P. Lamb, S. Chao, J. M. Martin, N. K. Blake, L. E. Talbert. 2019. A novel QTL in durum wheat for resistance to the wheat stem sawfly associated with early expression of stem solidness. G3: Genes, Genomes and Genetics 9:1999-2006.
  • Type: Journal Articles Status: Published Year Published: 2019 Citation: Varella, A. C., D. K. Weaver, N. K. Blake, M. L. Hofland, H.-Y. Heo, J. P. Cook, P. F. Lamb, K. W. Jordan, E. Akhunov, S. Chao, and L. E. Talbert. 2019. Analysis of recombinant inbred line populations derived from wheat landraces to identify new genes for wheat stem sawfly resistance. Theor. Appl. Genet. 132: 21952207


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.
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