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ARS Home » Plains Area » Manhattan, Kansas » Center for Grain and Animal Health Research » Hard Winter Wheat Genetics Research » Research » Research Project #441596

Research Project: NIFA CAP for Innovation in Genomic Technology to Accelerate Breeding

Location: Hard Winter Wheat Genetics Research

Project Number: 3020-21000-012-011-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Jan 1, 2022
End Date: Dec 31, 2024

This project will establish a nationally coordinated consortium of public wheat breeders, molecular geneticists, high-throughput genotyping and phenotyping laboratories, database experts and educators focused on sustainable increases in wheat productivity. It will accelerate breeding cycles by implementing high-throughput genotyping and phenotyping technologies across public US wheat breeding programs and by integrating the information in a centralized database. Our project addresses the integrated education and research CAP priorities of Program Area Code A1141. In the education area, this project will address the need for plant breeders by training a cohort of 20 PhD students in the multiple disciplines required for modern plant breeding. In the research area, this project will harness new genomic and phenotyping tools and strong international collaborations to accelerate sustainable improvements in wheat productivity. This project addresses the following focus areas: i) integration between genotyping and high-throughput phenotyping for source- and sink- related traits, ii) implementation of genomic selection approaches into active public breeding programs and cultivar production, and iii) functional genomic studies to identify pathways affecting plant productivity and incorporation of this information into genomic selection.

The project will implement cost-effective a medium-throughput SNP platform incorporating functional SNPs. These SNPs will be used in a centralized Genomic Selection (GS) data analyses pipeline. The Practical Haplotype Graph (PHG) will be applied for imputation and data analyses. The project will implement a centralized Unmanned Aircraft System (UAS) high-throughput phenotyping (HTP) data analysis pipeline. Breeders and graduate students will be trained in the use of this UAS-HTP pipeline. The pipeline will be compatible with the ARS T3/wheat database. T3/Wheat and BreedBase will be integrated to provide a data management platform. Graduate students will be trained in these tools. Decision-support tools will be implemented in T3/Wheat. This project will provide support and integrated training in plant breeding to a minimum of 20 PhD students. The WheatCAP has a good track record of training diverse cohorts of students that included approximately equal number of female and male students from different ethnicities and nationalities. The more diverse group of coPIs in this proposal will contribute to maintaining this diversity. In addition to their research (see D.5.7.), WheatCAP students will also be involved in the wheat breeding activities to gain hands-on experience in managing a breeding program. Students will also interact with stakeholders through participation in field days, grain grower meetings and conferences. WheatCAP students will participate in implementing the GS and UAS-HTP platforms and in integrating field trial data into BreedBase. Students will be formally trained in experimental design, marker-assisted selection, genomic selection and basic bioinformatics, all important skills for modern plant breeders. Students will receive soft skill training to learn about their strengths, improve interpersonal communication skills, team work, mentorship and to manage people. Students will organize workshops and symposiums as in previous WheatCAP (