Genome-wide association study in Chickpea (Cicer arietinum L.) for yield and nutritional components

Abstract

The increase in the global human population and the accompanying challenges in meeting nutritional needs amidst climate change are a worldwide concern. Widespread protein and micronutrient deficiencies contribute to a significant number of individuals experiencing malnutrition, leading to severe health repercussions. This issue can be addressed through genomics-assisted breeding, particularly in enhancing the nutritional profile of vital staple crops like chickpea (Cicer arietinum L.). Chickpea, beyond being a rich source of protein, provides a diverse nutritional spectrum encompassing carbohydrates, fats, and minerals. To explore and improve the genetic basis of nutritional traits in chickpea, a study was conducted using 93 kabuli-type single plant derived lines and five cultivars in 2018, 2022, and 2023. Genotyping by sequencing revealed a total of 165K single nucleotide polymorphisms (SNPs) within this kabuli chickpea mini-core collection. After filtering for a minor allele frequency greater than 5%, 113,512 SNPs were utilized, distributed across eight chromosomes of the chickpea genome. Marker-trait associations were analyzed using genome wide association study, leading to the identification of 27 significantly associated SNPs from across all eight chromosomes linked to three seed nutritional concentrations and 100-seed weight. To unravel the molecular mechanisms governing seed protein, fiber, fat concentrations, and 100-seed weight, 31 candidate genes were determined within a 30 kb window size. This comprehensive approach holds promise for advancing crop breeding strategies to combat malnutrition and improve global food security.