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.
Highlights
Chickpea (Cicer arietinum L.) is a self-pollinated, diploid (2n = 2x = 16), grain legume crop with a genome size of 740 Mb [1]
A total of 46,270 high quality BAC-end sequences (BESs) were generated. These sequence data are available in the form of genome survey sequences (GSS) at National Center for Biotechnology Information (NCBI) with GenBank accession numbers EI846478.1 to GS878115.1 and GenBank gi numbers 14645554 to 270242271
Novel simple sequence repeat (SSR) markers from BESs A new 10X bacterial artificial chromosome (BAC) library and 46,270 BESs have been generated for the reference genotype ICC 4958 in the present study
Summary
Chickpea (Cicer arietinum L.) is a self-pollinated, diploid (2n = 2x = 16), grain legume crop with a genome size of 740 Mb [1]. The kabuli types are generally grown in the Mediterranean region including Southern Europe, Western Asia and Northern Africa and the desi types are grown mainly in Ethiopia and Indian subcontinent. It is cultivated mostly on lowinput and residual moisture from monsoon rains on the Indian subcontinent and semi-arid regions of Sub-Saharan Africa. Despite the growing demands and high yield potential, chickpea yields are stable and productivity has remained almost stagnant at unacceptably low levels [3,4]
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