title: 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.
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.
authors.affiliation: Centre of Excellence in Genomics (CEG), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, Andhra Pradesh, India.
authors.forename: Spurthi N
authors.initials: SN
authors.lastname: Nayak
authors.forename: Hongyan
authors.initials: H
authors.lastname: Zhu
authors.forename: Nicy
authors.initials: N
authors.lastname: Varghese
authors.forename: Subhojit
authors.initials: S
authors.lastname: Datta
authors.forename: Hong-Kyu
authors.initials: HK
authors.lastname: Choi
authors.forename: Ralf
authors.initials: R
authors.lastname: Horres
authors.forename: Ruth
authors.initials: R
authors.lastname: Jüngling
authors.forename: Jagbir
authors.initials: J
authors.lastname: Singh
authors.forename: P B Kavi
authors.initials: PB
authors.lastname: Kishor
authors.forename: S
authors.initials: S
authors.lastname: Sivaramakrishnan
authors.forename: Dave A
authors.initials: DA
authors.lastname: Hoisington
authors.forename: Günter
authors.initials: G
authors.lastname: Kahl
authors.forename: Peter
authors.initials: P
authors.lastname: Winter
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Cook
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D029863:Cicer / Q000235:genetics*; D020224:Expressed Sequence Tags; D015723:Gene Library; D017343:Genes, Plant / Q000235:genetics*; D008040:Genetic Linkage; D056426:Genetic Loci / Q000235:genetics*; D005819:Genetic Markers; D005838:Genotype; D046913:Medicago truncatula / Q000235:genetics*; D018895:Microsatellite Repeats / Q000235:genetics; D018598:Minisatellite Repeats / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid
chemical_list: D005819:Genetic Markers