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ARS Home » Pacific West Area » Pullman, Washington » Plant Germplasm Introduction and Testing Research » Research » Publications at this Location » Publication #403491
Research Project: Management of Priority Legume, Oilseed, Vegetable, Forage Grass, Sugar, Ornamental, and Medicinal Plant Genetic Resources and Associated Information

Location: Plant Germplasm Introduction and Testing Research

Title: Kabuli chickpea seed quality diversity and preliminary genome-wide association study identifies markers and potential candidate genes

Author
item MUGABE, DEUS - University Of Guelph
item FRIESZELL, CRISTEN - Washington State University
item Warburton, Marilyn
item Coyne, Clarice - Clare
item SARI, HATICE - Washington State University
item UHDRE, RENAN - Washington State University
item Wallace, Lyle
item MA, YU - Washington State University
item ZHENG, PING - Washington State University
item McGee, Rebecca
item GANJYAL, GIRISH - Washington State University

Submitted to: Agrosystems, Geosciences & Environment
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/19/2023
Publication Date: 10/18/2023
Citation: Mugabe, D., Frieszell, C., Warburton, M.L., Coyne, C.J., Sari, H., Uhdre, R., Wallace, L.T., Ma, Y., Zheng, P., McGee, R.J., Ganjyal, G. 2023. Kabuli chickpea seed quality diversity and preliminary genome-wide association study identifies markers and potential candidate genes. Agrosystems, Geosciences & Environment. 6(4):e20437. https://doi.org/10.1002/agg2.20437.
DOI: https://doi.org/10.1002/agg2.20437

Interpretive Summary: Malnutrition due to macro and micro- nutrient deficiencies is one of the major global health concerns, especially in developing countries. Chickpea can be an important component of diet that can improve human health due to high and economical nutritional value. Genetics tools including special populations of chickpeas and molecular genetic markers developed from known DNA sequences can help speed the development of new chickpea cultivars by breeders. These new cultivars may have higher nutritional content than those currently grown by farmers.

Technical Abstract: Malnutrition due to macro and micro- nutrient deficiencies is one of the major global health concerns, especially in developing countries. Using genomic-assisted breeding to enhance the nutritional value of important crops such as chickpea can help to address the problem. In this study, we conducted GWAS to identify genes that are associated with protein, starch, oil and fiber in chickpea. The USDA kabuli chickpea mini-core of 88 accessions was genotyped-by-sequencing and 174K SNP polymorphisms were identified. The SNPs were filtered for no missing data criteria for the 88 kabuli lines resulting in a complete set of 36,645 markers across the eight chromosomes of the chickpea genome. A genome-wide marker-trait analysis using FarmCPU model was conducted to identify SNP markers for breeding for protein, fiber, oil, and starch percent concentrations in the seed. The most significantly associated markers for seed protein concentration (P=8.82E-12), starch (P= 2.79E-12), fiber (P=7.65E-12) and oil (P=1.37E-08) were found on chromosomes 1, 2, 6 and 7 controlling 11, 12, 20, 16% of the phenotypic variation, respectively. Validation of the SNP markers in a broader set of plant genetic resources and environments will be needed to determine their usefulness in breeding for end use characteristics.