Location: Plant, Soil and Nutrition Research
Project Number: 8062-21000-045-03-R
Project Type: Reimbursable Cooperative Agreement
Start Date: Dec 15, 2016
End Date: Dec 14, 2019
Overall grant 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. Specific objectives: 1) Validation and characterization of QTL for grain yield and identification of the underlying genes using a combination of map-based cloning. 2) Identification and validation of candidate genes using sequenced mutants and transgenic approaches 3) Deployment of useful QTL in public wheat breeding programs. 4) Development of new genomics and informatics tools to accelerate candidate gene identification and validation. 5) Training of a new cohort of 15 plant breeders. USDA-ARS-Ithaca objective: Bioinformatic integration of multiple sources of genomic information from model systems research, previous wheat-specific genomic resources such as gene expression atlases, and finally from whole-genome imputation enabled meta-analysis of the massive trove of wheat phenotypic data deposited to the triticeae toolbox by the current TCAP grant. Output from QTL discovery and validation will feedback into the framework as underlying characteristics of true QTL are observed and can serve to train statistical prioritization models.
The cloning of a QTL using a map-based approach requires a precise mapping of the QTL effect, which can be achieved by reducing the genetic and environmental variability in segregating populations. To reduce the genetic variability among lines we will use heterogeneous inbred families. To reduce environmental variability we will use an appropriate number of replications. Recombinants to identify the precise QTL position will be generated in two stages. To saturate the target regions with markers we will use the exon capture platform. Each of 15 programs will target one QTL for cloning. 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. PhD students will be assigned a QTL or wheat mutant and will be responsible for its incorporation into his/her home breeding program using backcross to the top yielding lines and forward breeding. Genomics tools to assist in these activities will include exome Capture of regulatory regions, Micrococcal Nuclease (MNase) Analysis of Wheat Chromatin Structure, CRISPR-Cas9 transformation technologies to support candidate gene validation, as well as new informatics tools to be developed and incorporated into the Triticeae Toolbox (T3) by USDA-ARS, Ithaca. Finally, this project will provide support and integrated training to 15 PhD students in plant breeding. PhD students in this project will have a field-based component and will be trained in experimental design and bioinformatics through online conferences and courses, short face-to-face workshops, student seminars, and student discussion workshops. USDA-ARS-Ithaca approach: Phenotype warehousing for the project will be maintained through the ARS-Ithaca efforts. Ongoing integration of genomic information through indexing to the wheat reference genome will be performed. Specifically, information from analysis of phenotypes previously deposited to T3, from gene expression analysis, and from evolutionary conservation of loci sequenced will be collated, enabling researchers to fine-tune hypotheses on the functions of candidate polymorphisms discovered in QTL fine-mapping efforts.