title: Multiple post-domestication origins of kabuli chickpea through allelic variation in a diversification-associated transcription factor.
abstract: Chickpea (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.
authors.affiliation: Department of Plant Pathology, University of California, One Shields Ave, Davis, CA, 95616, USA.
authors.forename: R
authors.initials: R
authors.lastname: Varma Penmetsa
authors.affiliation: Department of Plant Pathology, University of California, One Shields Ave, Davis, CA, 95616, USA.
authors.forename: Noelia
authors.initials: N
authors.lastname: Carrasquilla-Garcia
authors.affiliation: Department of Plant Pathology, University of California, One Shields Ave, Davis, CA, 95616, USA.
authors.forename: Emily M
authors.initials: EM
authors.lastname: Bergmann
authors.affiliation: Department of Plant Pathology, University of California, One Shields Ave, Davis, CA, 95616, USA.
authors.forename: Lisa
authors.initials: L
authors.lastname: Vance
authors.affiliation: Department of Plant Pathology, University of California, One Shields Ave, Davis, CA, 95616, USA.
authors.forename: Brenna
authors.initials: B
authors.lastname: Castro
authors.affiliation: Department of Plant Pathology, University of California, One Shields Ave, Davis, CA, 95616, USA.
authors.forename: Mulualem T
authors.initials: MT
authors.lastname: Kassa
authors.affiliation: Department of Plant Pathology, University of California, One Shields Ave, Davis, CA, 95616, USA.|Department of Mycology and Plant Pathology, Banaras Hindu University, Pandit Madan Mohan Malviya Road, Varanasi, Uttar Pradesh, 221005, India.
authors.forename: Birinchi K
authors.initials: BK
authors.lastname: Sarma
authors.affiliation: Department of Plant Pathology, University of California, One Shields Ave, Davis, CA, 95616, USA.|Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, 208024, India.
authors.forename: Subhojit
authors.initials: S
authors.lastname: Datta
authors.affiliation: National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM, 87505, USA.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Farmer
authors.affiliation: Department of Plant Pathology, University of California, One Shields Ave, Davis, CA, 95616, USA.
authors.forename: Jong-Min
authors.initials: JM
authors.lastname: Baek
authors.affiliation: USDA-ARS, Western Regional Plant Introduction Station, Washington State University, 59 Johnson Hall, Pullman, WA, 99164-6402, USA.
authors.forename: Clarice J
authors.initials: CJ
authors.lastname: Coyne
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics, Center of Excellence in Genomics, Patancheru, Andhra Pradesh, 502324, India.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
authors.affiliation: Department of Biological Sciences, Florida International University, 11200 SW 8th Street, Miami, FL, 33199, USA.|Kushlan Institute for Tropical Science, Fairchild Tropical Botanic Garden, 10901 Old Cutter Road, Coral Gables, FL, 33156, USA.
authors.forename: Eric J B
authors.initials: EJ
authors.lastname: von Wettberg
authors.affiliation: Department of Plant Pathology, University of California, One Shields Ave, Davis, CA, 95616, USA.
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Cook
mesh_terms: D000483:Alleles; D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors / Q000235:genetics* / Q000378:metabolism; D029863:Cicer / Q000033:anatomy & histology / Q000235:genetics*; D018556:Crops, Agricultural / Q000235:genetics; D000071278:Domestication; D060146:Ecotype; D035264:Flowers / Q000033:anatomy & histology / Q000502:physiology; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D006239:Haplotypes / Q000235:genetics; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D025341:Principal Component Analysis; D012639:Seeds / Q000033:anatomy & histology
chemical_list: D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors
keywords: Cicer arietinum; Mendel's A locus; basic helix-loop-helix (bHLH) transcription factor; chickpea B locus; diversification; domestication; legume ortholog