Journal article
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
Theoretical and Applied Genetics, Vol.120(7), pp.1415-1441
2010
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 × 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.
Details
- 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
- Authors/Creators
- S.N. Nayak (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsH. Zhu (Author/Creator) - University of KentuckyN. Varghese (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsS. Datta (Author/Creator) - Indian Institute of Pulses ResearchH-K Choi (Author/Creator) - Dong-A UniversityR. Horres (Author/Creator) - Goethe University FrankfurtR. Jüngling (Author/Creator) - Goethe University FrankfurtJ. Singh (Author/Creator) - Acharya N. G. Ranga Agricultural UniversityP.B. Kavi Kishore (Author/Creator)S. Sivaramakrishnan (Author/Creator) - Acharya N. G. Ranga Agricultural UniversityD.A. Hoisington (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsG. Kahl (Author/Creator) - European University ViadrinaP. Winter (Author/Creator) - GenXPro (Germany)D.R. Cook (Author/Creator) - University of CaliforniaR.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
- Publication Details
- Theoretical and Applied Genetics, Vol.120(7), pp.1415-1441
- Publisher
- Springer Verlag
- Identifiers
- 991005544030107891
- Copyright
- © 2010 The Authors.
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.96 QTL
- Web Of Science research areas
- Agronomy
- Genetics & Heredity
- Horticulture
- Plant Sciences
- ESI research areas
- Agricultural Sciences