Multiple post‐domestication origins ofkabulichickpea through allelic variation in a diversification‐associated transcription factor

Abstract

SummaryChickpea (Cicer arietinum) is among the founder crops domesticated in the Fertile Crescent. One of two major forms of chickpea, the so-called kabuli type, has white flowers and light-colored seed coats, properties not known to exist in the wild progenitor. The origin of the kabuli form has been enigmatic.We genotyped a collection of wild and cultivated chickpea genotypes with 538 single nucleotide polymorphisms (SNPs) and examined patterns of molecular diversity relative to geographical sources and market types. In addition, we examined sequence and expression variation in candidate anthocyanin biosynthetic pathway genes.A reduction in genetic diversity and extensive genetic admixture distinguish cultivated chickpea from its wild progenitor species. Among germplasm, the kabuli form is polyphyletic. We identified a basic helix-loop-helix (bHLH) transcription factor at chickpea's B locus that conditions flower and seed colors, orthologous to Mendel's A gene of garden pea, whose loss of function is associated invariantly with the kabuli type of chickpea.From the polyphyletic distribution of the kabuli form in germplasm, an absence of nested variation within the bHLH gene and invariant association of loss of function of bHLH among the kabuli type, we conclude that the kabuli form arose multiple times during the phase of phenotypic diversification after initial domestication of cultivated chickpea.

Genomic and phenotypic analysis of Vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits

“…1b). The resulting tree topology underscores the origin of Ethiopian genotypes as derived from the blue Turkish clade, while the dispersion of Kabuli forms among the green and blue Turkish clades supports our earlier conclusion that the Kabuli form is polyphyletic 16 .…”

“…The history of chickpea domestication and breeding involved differentiation of the crop into two market classes based on a suite of traits, typified by differences in seed size, seed coat tannins and flower colour 12–16 . Desi genotypes generally have smaller, dark seeds and coloured flowers, while Kabuli genotypes are characterized by larger, light coloured seed and white flowers.…”

Genetic variation of a global germplasm collection of chickpea (Cicer arietinum L.) including Italian accessions at risk of genetic erosion

“…Notably, the work of Penmetsa et al (2016), published during the revision of this manuscript, clearly distinguishes between chickpea gene pools from Ethiopia and the Indian subcontinent. Although, the 103 accessions genotyped in this study might not be representative of the whole genetic variation in cultivated chickpea, another relevant finding is that European desi accessions seem to be closer to the Fig.…”

“…For example, following the SSR analysis of a chickpea composite collection, Upadhyaya et al (2008) generated a Neighbour-Joining tree in which a small cluster of desi was included in major branch containing kabuli accessions and vice versa. In addition, the recent work of Penmetsa et al (2016), evaluating the genetic structure of a representative set of cultivated chickpea, also questioned the strict dichotomy of a desi and kabuli genetic subdivision within cultivated chickpea.…”

Analysis of the Chickpea genome using next generation sequencing data

“…The kabuli form has developed from the phase of phenotypic diversification after the initial domestication of cultivated chickpea (Varma Penmetsa et al, 2016). The greater similarity of desi seed with wild type (C.reticulatum) seed represents the early domesticated form (Ladizinsky G, 1976) and kabuli as subsequently derived type.…”