<b>Dissecting the genetic basis of seed-iron content in chickpea using a combinatorial approach of QTL-Seq and molecular haplotyping</b>

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 x 1CC4958) contrasting for SFC led to the identification of three QTLs, [<i>CaqFe4.1 </i>(0.10 Mb<i>), CaqFe4.2 </i>(0.54Mb) and <i>CaqFe7.1</i><i> </i>(0.83Mb)] in chickpea<i>. In-silico</i> expression analysis of genes underlying the QTLs revealed their varied levels during different stages of seed development<i>. </i>Moreover, estimation of Gʹ values of the SNPs identified in the QTL region revealed a SNP that generated synonymous variant of the <i>MAIN-like-2 </i>gene. Haplotype analysis of <i>MAIN</i>-<i>like-2</i> in a diverse panel of chickpea germplasm varying for SFC further exemplified its superior haplotype that displayed strong association to this trait. Homology-based protein interaction analysis coupled with<i> </i>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<i> </i>proteins in chickpea.<i> </i>The functional loci as well as the molecular signatures defined in the study have potential to expedite marker assisted breeding of iron-rich chickpea varieties.