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

Malnutrition due to macro- and micro-nutrient deficiencies is one of the major global health concerns, especially in developing countries. Using genomics-assisted breeding to enhance the nutritional value of important crops such as chickpea (Cicer arietinum L.) can help to address the problem. In this study, we conducted genome-wide association studies to identify genes associated with protein, starch, oil, and fiber in chickpea to create resources to speed the breeding process. The USDA kabuli chickpea mini-core of 88 accessions was genotyped using genotyped-by-sequencing, and 36,645 single nucleotide polymorphisms (SNPs) were identified across the eight chromosomes of the chickpea genome. A genome-wide marker-trait analysis using the FarmCPU model was conducted to identify SNP markers that can enable marker-assisted breeding for seed protein, fiber, oil, and starch concentrations. 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%, and 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.