Record Details

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

OAR@ICRISAT

View Archive Info
 
 
Field Value
 
Relation http://oar.icrisat.org/6425/
http://dx.doi.org/10.1007/s00122-010-1265-1
 
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
 
Creator Nayak, S N
Zhu, H
Varghese, N
Datta, S
Choi, H K
Horres, R
Jüngling, R
Singh, J
Kavi Kishor, P B
Sivaramakrishnan, S
Hoisington, D A
Kahl, G
Winter, P
Cook, D R
Varshney, R K
 
Subject Chickpea
 
Description 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
 
Publisher Springer Verlag
 
Date 2010
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights —
 
Identifier http://oar.icrisat.org/6425/1/TAG_120_7_1415-1441_2010.pdf
Nayak, S N and Zhu, H and Varghese, N and Datta, S and Choi, H K and Horres, R and Jüngling, R and Singh, J and Kavi Kishor, P B and Sivaramakrishnan, S and Hoisington, D A and Kahl, G and Winter, P and Cook, D R and Varshney, R K (2010) 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, 120 (7). pp. 1415-1441. ISSN 0040-5752