Location: Cereal Crops Research
Project Number: 3060-21000-038-012-R
Project Type: Reimbursable Cooperative Agreement
Start Date: Dec 15, 2016
End Date: Nov 14, 2021
Objective:
The overall goals of this project are to validate, characterize, and deploy QTL for yield components in wheat and to train the next generation of plant breeders. The specific objectives are 1) Validation of QTL for grain yield components identified in previous studies. 2) Dissection of QTL by map-based cloning. 3) Validations of candidate genes using mutant and transgenic approaches. 4) Deployment of useful QTL in public wheat breeding programs. 5) Training a new cohort of 15 plant breeders.
Approach:
Approaches for objective 1: QTL for grain yield components identified in the wheat AM panels will be evaluated in different environments using previously genotyped populations. Wheat includes different market classes and is grown in diverse environments, so this project will provide the rare opportunity to characterize genotype by environment interactions in great detail. All information will be deposited in the T3 database and integrated with GrainGenes. Selection of QTL targets will be coordinated at a national level.
Approaches for objective 2: Once a QTL is validated in a bi-parental population, lines heterozygous for the target regions will be selected from advanced generations to develop heterogeneous inbred families or HIFs (Barrero et al. 2015, Genome Biol 16:93). We will use exome capture to identify polymorphisms in HIFs coding regions. In collaboration with the genotyping labs, KASP markers flanking the target QTL region will be developed to characterize >2,000 segregating progeny from each HIF. Informative recombinants will be tested in highly replicated field trials. This information will be used to delimit the QTL region in the current draft wheat genome and to identify candidate genes. To prioritize these genes for validation we will integrate genomic information from model species, wheat gene expression databases, and whole-genome imputation methods based on the massive genotypic and phenotypic data accumulated during the previous T-CAP project.
Approaches for objective 3: Candidate genes will be validated using mutagenesis and transgenic approaches. We have developed a sequenced TILLING population carrying 4 million mutations in tetraploid wheat and 7 million mutations in hexaploid wheat. Mutants in different homoeologs will be combined to study the effects of loss-of-function mutations on yield components. CRISPR-CAS9 genome editing will be used for winter wheats and in spring wheat if no mutations are found in the TILLING populations. T3 will develop tools to facilitate the integration of phenotypic and genomics data.
Approaches for objective 4: PhD students will be assigned a QTL or mutant to study and deploy in his/her home breeding program using backcross and forward breeding. Regional genotyping labs will facilitate deployment across regions and breeding programs. Genomic selection approaches will be explored to combine multiple QTL. We established collaboration with CIMMYT to test and distribute worldwide the beneficial alleles identified in this study.
Approaches for objective 5: We will provide an integrated training to 15 PhD students including field breeding, experimental design, genomics, bioinformatics and plant physiology. All students will have a field-based component in their projects. We will emphasize training in bioinformatics and statistics through online conferences and courses, short workshops, student seminars, and support for travel to conferences. Students will be encouraged to participate in the development of germplasm including the new QTLs.
