Location: Plant Science Research
Project Number: 5062-21500-001-034-R
Project Type: Reimbursable Cooperative Agreement
Start Date: Jan 1, 2026
End Date: Dec 31, 2027
Objective:
1. Characterize the genetic diversity and population structure of alfalfa breeding populations to assess genotype redundancy and interconnections among alfalfa projects.
2. Conduct allele mining to identify rare (private) alleles within specific breeding populations and associate them with each population's breeding objectives.
3. Develop an integrated genomic prediction model that incorporates population structure, QTL effects, and genotype-by-environment interactions across more than 10,000 alfalfa genotypes.
4. Generate estimated breeding values for at least 10 agronomic traits across 10,000 existing North American alfalfa genotypes and newly developed materials.
Approach:
The project will begin with the compilation and curation of genotypic and phenotypic data from 14 completed studies of alfalfa populations genotyped using the 3K DArTag marker array. The populations will be assessed for genetic diversity then private allele identification across breeding populations will be carried out using microhaplotypes. Next, a robust genomic prediction model will be developed that integrates population structure, QTL effects, and genotype-by-environment (G×E) interactions across all available alfalfa projects. This phase will require extensive data curation and complex genetic modeling. Finally, the training population system will be validated using new testing populations to determine its effectiveness in predicting genomic performance based on average allele effects or breeding values.