Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.)

Publication Overview
TitleDevelopment and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.)
AuthorsGujaria N, Kumar A, Dauthal P, Dubey A, Hiremath P, Bhanu Prakash A, Farmer A, Bhide M, Shah T, Gaur PM, Upadhyaya HD, Bhatia S, Cook DR, May GD, Varshney RK
TypeJournal Article
Journal NameTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Volume122
Issue8
Year2011
Page(s)1577-89
CitationGujaria N, Kumar A, Dauthal P, Dubey A, Hiremath P, Bhanu Prakash A, Farmer A, Bhide M, Shah T, Gaur PM, Upadhyaya HD, Bhatia S, Cook DR, May GD, Varshney RK. Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.). TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 2011 May; 122(8):1577-89.

Abstract

A transcript map has been constructed by the development and integration of genic molecular markers (GMMs) including single nucleotide polymorphism (SNP), genic microsatellite or simple sequence repeat (SSR) and intron spanning region (ISR)-based markers, on an inter-specific mapping population of chickpea, the third food legume crop of the world and the first food legume crop of India. For SNP discovery through allele re-sequencing, primer pairs were designed for 688 genes/expressed sequence tags (ESTs) of chickpea and 657 genes/ESTs of closely related species of chickpea. High-quality sequence data obtained for 220 candidate genic regions on 2-20 genotypes representing 9 Cicer species provided 1,893 SNPs with an average frequency of 1/35.83 bp and 0.34 PIC (polymorphism information content) value. On an average 2.9 haplotypes were present in 220 candidate genic regions with an average haplotype diversity of 0.6326. SNP2CAPS analysis of 220 sequence alignments, as mentioned above, provided a total of 192 CAPS candidates. Experimental analysis of these 192 CAPS candidates together with 87 CAPS candidates identified earlier through in silico mining of ESTs provided scorable amplification in 173 (62.01%) cases of which predicted assays were validated in 143 (82.66%) cases (CGMM). Alignments of chickpea unigenes with Medicago truncatula genome were used to develop 121 intron spanning region (CISR) markers of which 87 yielded scorable products. In addition, optimization of 77 EST-derived SSR (ICCeM) markers provided 51 scorable markers. Screening of easily assayable 281 markers including 143 CGMMs, 87 CISRs and 51 ICCeMs on 5 parental genotypes of three mapping populations identified 104 polymorphic markers including 90 markers on the inter-specific mapping population. Sixty-two of these GMMs together with 218 earlier published markers (including 64 GMM loci) and 20 other unpublished markers could be integrated into this genetic map. A genetic map developed here, therefore, has a total of 300 loci including 126 GMM loci and spans 766.56 cM, with an average inter-marker distance of 2.55 cM. In summary, this is the first report on the development of large-scale genic markers including development of easily assayable markers and a transcript map of chickpea. These resources should be useful not only for genome analysis and genetics and breeding applications of chickpea, but also for comparative legume genomics.

Features
This publication contains information about 253 features:
Feature NameUniquenameType
CISR089CISR089genetic_marker
CISR090CISR090genetic_marker
CISR091CISR091genetic_marker
CISR092CISR092genetic_marker
CISR093CISR093genetic_marker
CISR094CISR094genetic_marker
CISR095CISR095genetic_marker
CISR096CISR096genetic_marker
CISR097CISR097genetic_marker
CISR098CISR098genetic_marker
CISR099CISR099genetic_marker
CISR100CISR100genetic_marker
CISR101CISR101genetic_marker
CISR102CISR102genetic_marker
CISR103CISR103genetic_marker
CISR104CISR104genetic_marker
CISR105CISR105genetic_marker
CISR106CISR106genetic_marker
CISR107CISR107genetic_marker
CISR108CISR108genetic_marker
CISR109CISR109genetic_marker
CISR110CISR110genetic_marker
CISR111CISR111genetic_marker
CISR112CISR112genetic_marker
CISR113CISR113genetic_marker

Pages

Featuremaps
This publication contains information about 1 maps:
Map Name
chickpea-ICC4958xPI489777-RIL-2011
Properties
Additional details for this publication include:
Property NameValue
Journal CountryGermany
Publication ModelPrint-Electronic
ISSN1432-2242
eISSN1432-2242
Publication Date2011 May
Journal AbbreviationTheor. Appl. Genet.
DOI10.1007/s00122-011-1556-1
Elocation10.1007/s00122-011-1556-1
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Publication TypeResearch Support, Non-U.S. Gov't