Article

A BAC/BIBAC-based physical map of chickpea, Cicer arietinum L

Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843-2474, USA.
BMC Genomics (Impact Factor: 4.04). 09/2010; 11:501. DOI: 10.1186/1471-2164-11-501
Source: PubMed

ABSTRACT Chickpea (Cicer arietinum L.) is the third most important pulse crop worldwide. Despite its importance, relatively little is known about its genome. The availability of a genome-wide physical map allows rapid fine mapping of QTL, development of high-density genome maps, and sequencing of the entire genome. However, no such a physical map has been developed in chickpea.
We present a genome-wide, BAC/BIBAC-based physical map of chickpea developed by fingerprint analysis. Four chickpea BAC and BIBAC libraries, two of which were constructed in this study, were used. A total of 67,584 clones were fingerprinted, and 64,211 (~11.7 x) of the fingerprints validated and used in the physical map assembly. The physical map consists of 1,945 BAC/BIBAC contigs, with each containing an average of 28.3 clones and having an average physical length of 559 kb. The contigs collectively span approximately 1,088 Mb. By using the physical map, we identified the BAC/BIBAC contigs containing or closely linked to QTL4.1 for resistance to Didymella rabiei (RDR) and QTL8 for days to first flower (DTF), thus further verifying the physical map and confirming its utility in fine mapping and cloning of QTL.
The physical map represents the first genome-wide, BAC/BIBAC-based physical map of chickpea. This map, along with other genomic resources previously developed in the species and the genome sequences of related species (soybean, Medicago and Lotus), will provide a foundation necessary for many areas of advanced genomics research in chickpea and other legume species. The inclusion of transformation-ready BIBACs in the map greatly facilitates its utility in functional analysis of the legume genomes.

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    • " The existence of more overlap than the expected between the contigs will reduce the overall size of contigs and , hence , the physical map assembly . Discrepancies in genome size of chickpea was also reported in an earlier study of the development of physical map in chickpea ; how - ever , they reported more genome size than the expected 738 Mb ( Zhang et al . 2010 ) . Despite the genome size estima - tion discrepancy , the quality of the chickpea physical map developed in the present study was found to be sufficiently high for use in various applications of genomics research ."
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    • "However, despite its agricultural value and continuous demand, no major breakthrough for yield enhancement has occurred mainly due to low genome variability and susceptibility of the crop to several biotic and abiotic stresses (Ryan 1997; Ahmad et al. 2005; Millan et al. 2006). Recently with the development of modern tools, chickpea genomics research has significantly progressed as evidenced by the availability of genomic resources such as molecular markers and linkage maps (Nayak et al. 2010; Gaur et al. 2011; Gujaria et al. 2011), bacterial artificial chromosome (BAC) libraries (Rajesh et al. 2004; Lichtenzveig et al. 2005; Zhang et al. 2010), and cDNA libraries (Buhariwalla et al. 2005; Coram and Pang 2005; Varshney et al. 2009; Ashraf et al. 2009; Deokar et al. 2011) from which approx. 40,000 ESTs are available in the NCBI EST database. "
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