A chickpea WIP2 gene underlying a major QTL contributes to lateral root development.

Lateral root is a major component of root system architecture and lateral root count (LRC) positively contributes to yield under drought in chickpea. To understand the genetic regulation of LRC, a biparental mapping population derived from two chickpea accessions having contrasting LRC was genotyped by sequencing and phenotyped to map four major quantitative trait loci (QTLs) contributing to 13 to 32% of the LRC trait variation. A SNP tightly linked to the locus contributing to highest trait variation was located on the coding region of a gene (CaWIP2) orthologous to WIP2 gene of Arabidopsis thaliana. A polymorphic simple sequence repeat (SSR) in the CaWIP2 promoter showed differentiation between low vs. high LRC parents and mapping individuals suggesting its utility for marker-assisted selection. CaWIP2 promoter showed strong activities in chickpea apical root meristem and lateral root primordia. Expression of CaWIP2 under its native promoter in Arabidopsis wip2wip4wip5 mutant rescued its root-less phenotype to produce more lateral root than the wild type plants and led to formation of amyloplasts in the columella. CaWIP2 expression also induced expression of genes that regulate lateral root emergence. Our study identified a gene-based marker for LRC which will be useful to develop drought tolerant high-yielding chickpea.