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ARS Home » Southeast Area » Griffin, Georgia » Plant Genetic Resources Conservation Unit » Research » Research Project #444059

Research Project: Genome-wide Association Analysis and Genomic Prediction of Seed Mineral Concentration in the USDA Cowpea Germplasm

Location: Plant Genetic Resources Conservation Unit

Project Number: 6046-21000-013-037-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 1, 2023
End Date: Nov 30, 2024

Cowpea is a significant source of seed minerals and provides many essential elements for human health. The main goal of this proposal is to identify and develop cowpea germplasm with high seed mineral concentration. Such germplasm will be a good source of high seed mineral trait that will have practical breeding applications. However, conventional breeding for high seed mineral cowpea is time consuming and expensive. Therefore, developing molecular markers will be the most affordable and faster way to screen germplasm with high seed mineral concentration.

Objective 1. To evaluate seed mineral concentrations in the USDA cowpea germplasm: A total of 250 USDA cowpea accessions obtained from the Plant Genetic Resources Conservation Unit, Griffin, GA were used for this project. Our preliminary data showed a large variation in all seed mineral concentrations among the 250 cowpea accessions indicating natural variations exists within this cowpea germplasm. The development of molecular markers associated with these minerals will further increase the efficiency of the breeding process aimed to improve these seed minerals. Objective 2. To conduct a genome-wide association study for seed mineral concentration in cowpea: Cowpea germplasm is the same as in obj 1. Whole genome resequencing of 250 cowpea genotypes was conducted by cooperator. Least square means (LS Means) for cowpea seed mineral concentration from Objective 1 will be used to conduct the Genome-Wide Association Study (GWAS). Objective 3. To develop genomic selection models that will predict seed mineral concentration in cowpea: Cowpea germplasm is the same as in obj 1. Genomic selection will be conducted using the significant SNPs from the genome-wide association study. The sum of the effects of each SNP/markers on the trait of interest, known as Genomic Estimated Breeding Value (GEBV), will be estimated . The accuracy of genomic selection will be evaluated by computing the Pearson’s correlation coefficient between the true phenotypic data and the predicted GEBVs in the testing population.