Dissecting the genetic basis of seed-iron content in Chickpea using a combinatorial approach of QTL-Seq and molecular...

In order to map the QTL(s) and genes regulating the complex seed-iron content (SFC) trait in chickpea, the quantitative trait locus (QTL)-seq approach was used. Whole genome re-sequencing of DNA bulks derived from a mapping population (ICC8261 × 1CC4958) contrasting for SFC led to the identification of three QTLs, [CaqFe4.1 (0.10 Mb), CaqFe4.2 (0.54 Mb) and CaqFe7.1 (0.83 Mb)] in chickpea. In-silico expression analysis of genes underlying the QTLs revealed their varied levels during stages of seed development. Moreover, estimation of G' values of the SNPs identified in the QTL region revealed a SNP that generated synonymous variant of the MAIN-like-2 gene. Haplotype analysis of MAIN-like-2 in a diverse panel of chickpea germplasm varying for SFC further exemplified its haplotypes that displayed strong association to this trait. Homology-based protein interaction analysis coupled with quantitative-real time PCR based-expression analysis revealed several co-expressing co-chaperone and heat shock proteins including P23-1, HSP 90.5 and HSP90.6, having well established roles in seed development as protein components of MAIN-like-2 proteins in chickpea. The functional loci as well as the molecular signatures defined in this study have potential to expedite marker assisted breeding of iron-rich chickpea varieties.

The online version contains supplementary material available at 10.1007/s11032-026-01644-x.