Genome-wide association analysis to delineate high-quality SNPs for seed micronutrient density in chickpea (Cicer arietinum L.)

Abstract

Chickpea is the most important nutrient-rich grain legume crop in the world. A diverse core set of 147 chickpea genotypes was genotyped with a Axiom(®)50K CicerSNP array and trait phenotyped in two different environments for four seed micronutrients (Zn, Cu, Fe and Mn). The trait data and high-throughput 50K SNP genotypic data were used for the genome-wide association study (GWAS). The study led to the discovery of genes/QTLs for seed Zn, Cu, Fe and Mn, concentrations in chickpea. The analysis of seed micronutrient data revealed significant differences for all four micronutrient concentrations (P ≤ 0.05). The mean concentrations of seed Zn, Cu, Fe and Mn pooled over the 2 years were 45.9 ppm, 63.8 ppm 146.1 ppm, and 27.0 ppm, respectively. The analysis of results led to the identification of 35 SNPs significantly associated with seed Zn, Cu, Fe and Mn concentrations. Among these 35 marker-trait associations (MTAs), 5 were stable (consistently identified in different environments), 6 were major (explaining more than 15% of the phenotypic variation for an individual trait) and 3 were both major and stable MTAs. A set of 6 MTAs, MTAs (3 for Mn, 2 for Fe, and 1 for Cu) reported by us during the present study have been also reported in the same/almost same genomic regions in earlier studies and therefore declared as validated MTAs. The stable, major and validated MTAs identified during the present study will prove useful in future chickpea molecular breeding programs aimed at enhancing the seed nutrient density of chickpea.

Fatty acid composition and genome-wide associations of a chickpea (Cicer arietinum L.) diversity panel for biofortification efforts

“…Numerous GWAS have been conducted in chickpea to identify SNPs significantly associated with agronomic traits 48 – 51 , stress tolerance 52 , 53 , and nutritional traits 20 , 50 , 54 , 55 . However, no GWAS have been reported for fatty acids in chickpea to date.…”

“…3 a), which follows previous studies in chickpea 67 . However, some studies reported two or three subpopulations in chickpea 20 , 50 , 54 , 55 . These seven subpopulations represent the diverse ancestral background of chickpea.…”

Unlocking the nutritional potential of chickpea: strategies for biofortification and enhanced multinutrient quality

“…(2022) reported significant genetic variation in 258 chickpea accessions for various nutritional components: Fe (2.26–7.25 mg 100 g –1 , mean: 4.36), Ca (60.7–176.5 mg 100 g –1 , mean: 108.6), Mg (64.08–134.57 mg 100 g –1 , mean: 100.35), Mn (0.67–3.73 mg 100 g –1 , mean: 1.78), phytic acid (2.07–19.38 mg g –1 , mean: 10.68), and Zn (1.15–4.59 mg 100 g –1 , mean: 2.76. Similarly, Fayaz et al. (2022) reported significant genetic variation in various micronutrients in 147 chickpea genotypes over a two-year evaluation: Zn (1.45–20.49 and 0.936–20.58 mg 100 g –1 , Fe (7.93–19.82 and 10.36–12.72 mg 100 g –1 ), Cu (0.42–18.54 and 0.366–19.03 mg 100 g –1 ), and Mn (0.907–5.43 and 0.48–12.28 mg 100 g –1 ) and Farida Traore et al.…”

“…Furthermore, genotyping 92 sequenced desi and kabuli accessions with 24,620 SNPs identified 16 genomic loci/genes contributing to seed Fe and Zn, accounting for a combined 29% PVE ( Upadhyaya et al., 2016a ). Subsequently, a GWAS on a diverse panel of 147 chickpea genotypes phenotyped for two years and genotyped with an “Axiom ® 50K CicerSNP array” identified 35 significant marker-trait associations (MTAs) contributing to grain Zn, Fe, Cu, and Mn, with five MTAs consistently identified in different environments (stable), six explaining more than 15% of the phenotypic variation (major), and three both stable and major MTAs ( Fayaz et al., 2022 ). Likewise, over two years, SNP204 on LG1 and SNP9478 on LG5 showed significant MTAs for Fe content at Sanliurfa, and SNP8254 and SNP8255 on LG4 showed significant MTAs for Fe content at Bornova ( Karaca et al., 2020 ).…”