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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Available from: Yang Zhang, Aug 12, 2015
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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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    ABSTRACT: Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.49 Mb per contig and 3,256 singletons represent 407 Mb genome. The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. This allowed locating some of the BACs in the vicinity of some important quantitative trait loci (QTLs) for drought tolerance and reistance to Fusarium wilt and Ascochyta blight. In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (~54 Mb) of the draft genome. Comprehensive analysis of markers in abiotic and biotic stress tolerance QTL regions led to identification of 654, 306 and 23 genes in drought tolerance “QTL-hotspot” region, Ascochyta blight resistance QTL region and Fusarium wilt resistance QTL region, respectively. Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement. Electronic supplementary material The online version of this article (doi:10.1007/s10142-014-0363-6) contains supplementary material, which is available to authorized users.
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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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