title: Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L.).
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.
authors.affiliation: Grain Legumes Research Program, International Crops Research Institute for the Semi-Arid Tropics-ICRISAT, Hyderabad, India.
authors.forename: Mahendar
authors.initials: M
authors.lastname: Thudi
authors.forename: Abhishek
authors.initials: A
authors.lastname: Bohra
authors.forename: Spurthi N
authors.initials: SN
authors.lastname: Nayak
authors.forename: Nicy
authors.initials: N
authors.lastname: Varghese
authors.forename: Trushar M
authors.initials: TM
authors.lastname: Shah
authors.forename: R Varma
authors.initials: RV
authors.lastname: Penmetsa
authors.forename: Nepolean
authors.initials: N
authors.lastname: Thirunavukkarasu
authors.forename: Srivani
authors.initials: S
authors.lastname: Gudipati
authors.forename: Pooran M
authors.initials: PM
authors.lastname: Gaur
authors.forename: Pawan L
authors.initials: PL
authors.lastname: Kulwal
authors.forename: Hari D
authors.initials: HD
authors.lastname: Upadhyaya
authors.forename: Polavarapu B
authors.initials: PB
authors.lastname: Kavikishor
authors.forename: Peter
authors.initials: P
authors.lastname: Winter
authors.forename: Günter
authors.initials: G
authors.lastname: Kahl
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Town
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kilian
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Cook
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
mesh_terms: D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D032461:Chromosomes, Plant / Q000235:genetics; D029863:Cicer / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D008040:Genetic Linkage; D005819:Genetic Markers / Q000235:genetics*; D018745:Genome, Plant; D018895:Microsatellite Repeats / Q000235:genetics*; D011110:Polymorphism, Genetic / Q000235:genetics; D040641:Quantitative Trait Loci
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers
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