Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L.)

Publication Overview
TitleNovel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L.)
AuthorsThudi M, Bohra A, Nayak SN, Varghese N, Shah TM, Penmetsa RV, Thirunavukkarasu N, Gudipati S, Gaur PM, Kulwal PL, Upadhyaya HD, Kavikishor PB, Winter P, Kahl G, Town CD, Kilian A, Cook DR, Varshney RK
TypeJournal Article
Journal NamePloS one
Volume6
Issue11
Year2011
Page(s)e27275
CitationThudi M, Bohra A, Nayak SN, Varghese N, Shah TM, Penmetsa RV, Thirunavukkarasu N, Gudipati S, Gaur PM, Kulwal PL, Upadhyaya HD, Kavikishor PB, Winter P, Kahl G, Town CD, Kilian A, Cook DR, Varshney RK. Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L.). PloS one. 2011; 6(11):e27275.

Abstract

Chickpea (Cicer arietinum L.) is the third most important cool season food legume, cultivated in arid and semi-arid regions of the world. The goal of this study was to develop novel molecular markers such as microsatellite or simple sequence repeat (SSR) markers from bacterial artificial chromosome (BAC)-end sequences (BESs) and diversity arrays technology (DArT) markers, and to construct a high-density genetic map based on recombinant inbred line (RIL) population ICC 4958 (C. arietinum)×PI 489777 (C. reticulatum). A BAC-library comprising 55,680 clones was constructed and 46,270 BESs were generated. Mining of these BESs provided 6,845 SSRs, and primer pairs were designed for 1,344 SSRs. In parallel, DArT arrays with ca. 15,000 clones were developed, and 5,397 clones were found polymorphic among 94 genotypes tested. Screening of newly developed BES-SSR markers and DArT arrays on the parental genotypes of the RIL mapping population showed polymorphism with 253 BES-SSR markers and 675 DArT markers. Segregation data obtained for these polymorphic markers and 494 markers data compiled from published reports or collaborators were used for constructing the genetic map. As a result, a comprehensive genetic map comprising 1,291 markers on eight linkage groups (LGs) spanning a total of 845.56 cM distance was developed (http://cmap.icrisat.ac.in/cmap/sm/cp/thudi/). The number of markers per linkage group ranged from 68 (LG 8) to 218 (LG 3) with an average inter-marker distance of 0.65 cM. While the developed resource of molecular markers will be useful for genetic diversity, genetic mapping and molecular breeding applications, the comprehensive genetic map with integrated BES-SSR markers will facilitate its anchoring to the physical map (under construction) to accelerate map-based cloning of genes in chickpea and comparative genome evolution studies in legumes.

Features
This publication contains information about 7,093 features:
Feature NameUniquenameType
cpPb-682393cpPb-682393genetic_marker
cpPb-682395cpPb-682395genetic_marker
cpPb-682398cpPb-682398genetic_marker
cpPb-682399cpPb-682399genetic_marker
cpPb-682401cpPb-682401genetic_marker
cpPb-682403cpPb-682403genetic_marker
cpPb-682405cpPb-682405genetic_marker
cpPb-682410cpPb-682410genetic_marker
cpPb-682413cpPb-682413genetic_marker
cpPb-682415cpPb-682415genetic_marker
cpPb-682420cpPb-682420genetic_marker
cpPb-682421cpPb-682421genetic_marker
cpPb-682425cpPb-682425genetic_marker
cpPb-682426cpPb-682426genetic_marker
cpPb-682428cpPb-682428genetic_marker
cpPb-682429cpPb-682429genetic_marker
cpPb-682430cpPb-682430genetic_marker
cpPb-682431cpPb-682431genetic_marker
cpPb-682432cpPb-682432genetic_marker
cpPb-682441cpPb-682441genetic_marker
cpPb-682444cpPb-682444genetic_marker
cpPb-682445cpPb-682445genetic_marker
cpPb-682446cpPb-682446genetic_marker
cpPb-682448cpPb-682448genetic_marker
cpPb-682450cpPb-682450genetic_marker

Pages

Featuremaps
This publication contains information about 1 maps:
Map Name
chickpea-ICC4958xPI489777-RIL-F10
Properties
Additional details for this publication include:
Property NameValue
Publication ModelPrint-Electronic
ISSN1932-6203
eISSN1932-6203
Publication Date2011
Journal AbbreviationPLoS ONE
DOI10.1371/journal.pone.0027275
LanguageEnglish
Language Abbreng
Publication TypeJournal Article
Elocation10.1371/journal.pone.0027275
Journal CountryUnited States
Publication TypeResearch Support, Non-U.S. Gov't