Identification of candidate genes for dissecting complex branchnumber trait in chickpea

Abstract

tThe present study exploited integrated genomics-assisted breeding strategy for genetic dissection ofcomplex branch number quantitative trait in chickpea. Candidate gene-based association analysis in abranch number association panel was performed by utilizing the genotyping data of 401 SNP allelicvariants mined from 27 known cloned branch number gene orthologs of chickpea. The genome-wideassociation study (GWAS) integrating both genome-wide GBS- (4556 SNPs) and candidate gene-basedgenotyping information of 4957 SNPs in a structured population of 60 sequenced desi and kabuli acces-sions (with 350–400 kb LD decay), detected 11 significant genomic loci (genes) associated (41% combinedPVE) with branch number in chickpea. Of these, seven branch number-associated genes were furthervalidated successfully in two inter (ICC 4958×ICC 17160)- and intra (ICC 12299×ICC 8261)-specificmapping populations. The axillary meristem and shoot apical meristem-specific expression, includingdifferential up- and down-regulation (4–5 fold) of the validated seven branch number-associated genesespecially in high branch number as compared to the low branch number-containing parental accessionsand homozygous individuals of two aforesaid mapping populations was apparent. Collectively, this com-binatorial genomic approach delineated diverse naturally occurring novel functional SNP allelic variantsin seven potential known/candidate genes [PIN1 (PIN-FORMED protein 1), TB1 (teosinte branched 1),BA1/LAX1 (BARREN STALK1/LIKE AUXIN1), GRAS8 (gibberellic acid insensitive/GAI, Repressor of ga13/RGAand Scarecrow8/SCR8), ERF (ethylene-responsive element-binding factor), MAX2 (more axillary growth2) and lipase] governing chickpea branch number. The useful information generated from this study havepotential to expedite marker-assisted genetic enhancement by developing high-yielding cultivars withmore number of productive (pods and seeds) branches in chickpea.