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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

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Relation http://oar.icrisat.org/77/
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
Khal, 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-speciWc 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 interspeciWc
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 arehighly 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 cc_by_nc
 
Identifier http://oar.icrisat.org/77/1/vars2010-5.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 Khal, 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. TAG Theoretical and Applied Genetics, 120 (7). pp. 1415-1441.