A meta‐analysis of quantitative trait loci (QTLs), associated with agronomic traits, fertility restoration, disease resistance, and seed quality traits was conducted for the first time in pigeonpea (Cajanus cajan L.). Data on 498 QTLs was collected from 9 linkage mapping studies (involving 21 biparental populations). Of these 498, 203 QTLs were projected onto “PigeonPea_ConsensusMap_2022,” saturated with 10,522 markers, which resulted in the prediction of 34 meta‐QTLs (MQTLs). The average confidence interval (CI) of these MQTLs (2.54 cM) was 3.37 times lower than the CI of the initial QTLs (8.56 cM). Of the 34 MQTLs, 12 high‐confidence MQTLs with CI (≤5 cM) and a greater number of initial QTLs (≥5) were utilized to extract 2255 gene models, of which 105 were believed to be associated with different traits under study. Furthermore, eight of these MQTLs were observed to overlap with several marker‐trait associations or significant SNPs identified in previous genome‐wide association studies. Furthermore, synteny and ortho‐MQTL analyses among pigeonpea and four related legumes crops, such as chickpea, pea, cowpea, and French bean, led to the identification of 117 orthologous genes from 20 MQTL regions. Markers associated with MQTLs can be employed for MQTL‐assisted breeding as well as to improve the prediction accuracy of genomic selection in pigeonpea. Additionally, MQTLs may be subjected to fine mapping, and some of the promising candidate genes may serve as potential targets for positional cloning and functional analysis to elucidate the molecular mechanisms underlying the target traits.

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Chickpea is the most important nutrient rich grain legume crop in the world. A diverse core set of 147 chickpea genotypes was genotyped with 50K Cicer SNP array and trait phenotyped in two different environments for four seed micro-nutrients (Cu, Fe, Mn, and Zn). The trait data and high-throughput 50K SNP genotypic data was used for genome-wide association study (GWAS) that led the discovery of gene/QTLs for seed Cu, Fe, Mn, and Zn concentrations in chickpea. The analysis of seed micronutrient data revealed significant differences for all the four micronutrient concentrations (P ≤ 0.05). The mean concentration of seed Fe, Zn, Cu, and Mn pooled over two-year data was 146.1 ppm, 45.9 ppm, 63.8 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 MTAs, 5 were stable (consistently identified in different environments), 6 were major (explain more than 15% phenotypic variation for an individual trait) and 3 were both major and stable MTAs. The stable and major MTAs identified during the present study shall prove useful in molecular breeding programs aimed at enhancing seed nutrient density of chickpea.

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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.