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

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 domesticate
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.
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Author:Spurthi N. Nayak, Hongyan Zhu, Nicy Varghese, Subhojit Datta, Hong-Kyu Choi, Ralf Horres, Ruth Jüngling, Jagbir Singh, P. B. Kavi Kishor, S. Sivaramakrishnan, Dave A. Hoisington, Günter Kahl, Peter Winter, Douglas R. Cook, Rajeev K. Varshney
URN:urn:nbn:de:hebis:30:3-263382
DOI:http://dx.doi.org/10.1007/s00122-010-1265-1
ISSN:0040-5752
ISSN:1432-2242
Pubmed Id:http://www.ncbi.nlm.nih.gov/pubmed?term=20098978
Parent Title (English):Theoretical and applied genetics : TAG
Publisher:Springer
Place of publication:Berlin ; Heidelberg
Document Type:Article
Language:English
Date of Publication (online):2010/01/23
Date of first Publication:2010/01/23
Publishing Institution:Univ.-Bibliothek Frankfurt am Main
Release Date:2012/09/19
Volume:120
Issue:7
Pagenumber:27
First Page:1415
Last Page:1441
Note:
Open Access This article is distributed under the terms of the Creative
Commons Attribution Noncommercial License which permits any
noncommercial use, distribution, and reproduction in any medium,
provided the original author(s) and source are credited.
Note:
The online version of this
article (doi:10.1007/s00122-010-1265-1) contains supplementary
material, which is available to authorized users.
Institutes:Biowissenschaften
Dewey Decimal Classification:570 Biowissenschaften; Biologie
Sammlungen:Universitätspublikationen
Sondersammelgebiets-Volltexte
Licence (German):License LogoCreative Commons - Namensnennung-Nicht kommerziell 3.0

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