Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome. uri icon

abstract

  • This study presents the development and mapping of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in chickpea. The mapping population is based on an inter-specific cross between domesticated and non-domesticated genotypes of chickpea (Cicer arietinum ICC 4958 x C. reticulatum PI 489777). This same population has been the focus of previous studies, permitting integration of new and legacy genetic markers into a single genetic map. We report a set of 311 novel SSR markers (designated ICCM-ICRISAT chickpea microsatellite), obtained from an SSR-enriched genomic library of ICC 4958. Screening of these SSR markers on a diverse panel of 48 chickpea accessions provided 147 polymorphic markers with 2-21 alleles and polymorphic information content value 0.04-0.92. Fifty-two of these markers were polymorphic between parental genotypes of the inter-specific population. We also analyzed 233 previously published (H-series) SSR markers that provided another set of 52 polymorphic markers. An additional 71 gene-based SNP markers were developed from transcript sequences that are highly conserved between chickpea and its near relative Medicago truncatula. By using these three approaches, 175 new marker loci along with 407 previously reported marker loci were integrated to yield an improved genetic map of chickpea. The integrated map contains 521 loci organized into eight linkage groups that span 2,602 cM, with an average inter-marker distance of 4.99 cM. Gene-based markers provide anchor points for comparing the genomes of Medicago and chickpea, and reveal extended synteny between these two species. The combined set of genetic markers and their integration into an improved genetic map should facilitate chickpea genetics and breeding, as well as translational studies between chickpea and Medicago.
  • This study presents the development and mappingof simple sequence repeat (SSR) and single nucleotidepolymorphism (SNP) markers in chickpea. The mappingpopulation is based on an inter-speciWc cross betweendomesticated and non-domesticated genotypes of chickpea(Cicer arietinum ICC 4958 £ C. reticulatum PI 489777).This same population has been the focus of previous studies,permitting integration of new and legacy genetic markersinto a single genetic map. We report a set of 311 novelSSR markers (designated ICCM?ICRISAT chickpeamicrosatellite), obtained from an SSR-enriched genomiclibrary of ICC 4958. Screening of these SSR markers on adiverse panel of 48 chickpea accessions provided 147 polymorphicmarkers with 2?21 alleles and polymorphic informationcontent value 0.04?0.92. Fifty-two of these markerswere polymorphic between parental genotypes of the interspeciWcpopulation. We also analyzed 233 previously published(H-series) SSR markers that provided another set of52 polymorphic markers. An additional 71 gene-based SNPmarkers were developed from transcript sequences that arehighly conserved between chickpea and its near relativeMedicago truncatula. By using these three approaches, 175new marker loci along with 407 previously reported markerloci were integrated to yield an improved genetic map ofchickpea. The integrated map contains 521 loci organizedinto eight linkage groups that span 2,602 cM, with an averageinter-marker distance of 4.99 cM. Gene-based markersprovide anchor points for comparing the genomes of Medicagoand chickpea, and reveal extended synteny betweenthese two species. The combined set of genetic markers andtheir integration into an improved genetic map should facilitatechickpea genetics and breeding, as well as translationalstudies between chickpea and Medicago

publication date

  • 2010
  • 2010
  • 2010

has subject area