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ARS Home » Southeast Area » Raleigh, North Carolina » Plant Science Research » Research » Research Project #441591

Research Project: NIFA CAP for Innovation in Genomic Technology to Accelerate Breeding: Leveraging high-throughput genotyping and phenotyping technologies

Location: Plant Science Research

Project Number: 6070-22000-019-010-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. Overall hypothesis or goal: The overall goals for this project are the acceleration of gains in wheat grain yield and the training of a new generation of plant breeders. The specific objectives of the project are to: 1) Develop cost-effective medium-density SNP assays incorporating both functional and haplotype-tagging SNPs for effective genome-wide imputation and link these assays with PHG to establish a centralized automated platform for GS in public wheat breeding programs 2) Implement a centralized BRAPI-compliant pipeline for UAS-HTP data processing, analysis and management aimed at accelerating the adoption of this technology in public wheat breeding programs and the deposit of UAS data in T3. 3) Develop improved tools for T3/BreedBase to accelerate the automatic deposit of genotypic and agronomic data from public breeding programs into T3, and actively promote the exchange of data and analyses tools with equivalent public wheat databases in CIMMYT and the UK. 4) Develop a public genomic resource including the characterized natural and induced genetic variants that regulate gene expression in wheat, assess the role of regulatory diversity in controlling pathways underlying variation in growth and grain yield, and integrate information about regulatory variants into the T3/BreedBase database. 5) Train a new cohort of 20 plant breeders within an active Community of Practice in plant breeding, by integrating them into active wheat breeding programs that combine field research, UAS-HTP, and GS to accelerate the development of improved wheat varieties.

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 (