Integrated genomic approaches delineate the novel role of ROP1 ENHANCER1 in regulating seed protein content of chickpea.

Utilizing a combinatorial approach of QTL-Seq and candidate gene-based association mapping, the QTLs and genes responsible for seed protein content (SPC), a major quality trait in chickpea were identified. Whole Genome Re-sequencing based QTL-Seq analysis of bulked RILs from a mapping population contrasting for SPC led to identification of two QTLs (0.94 Mb on Linkage Group (LG)5 and 1.16 Mb on LG6) encompassing three SNPs displaying the highest ΔSNP-index. These highly significant SNPs and their associated genes were validated in 211 chickpea mini-core accessions varying in SPC that revealed a tightly associated marker affecting CaREN1 (ROP1 ENHANCER1) with phenotypic variation explained of 23%. This SNP was subsequently converted into a cost effective allele specific PCR based marker that could be utilized for rapid screening of SPC during marker assisted breeding. Further, in planta functional validation via knockdown of CaREN1 led to significant reduction in SPC of chickpea. This decrease in seed protein is likely due to disruption in the formation of CaREN1 protein complexes comprising of chaperones, phosphopeptide-binding proteins and GTPases that mediate folding, transport and accumulation of seed storage proteins as indicated through AP-MS. Taken together, the information generated would expedite tailoring of chickpea cultivars with augmented SPC.