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Open Access Research article

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

Xiaojun Zhang16, Chantel F Scheuring1, Meiping Zhang12, Jennifer J Dong1, Yang Zhang1, James J Huang1, Mi-Kyung Lee1, Shahal Abbo3, Amir Sherman4, Dani Shtienberg4, Weidong Chen5, Fred Muehlbauer5 and Hong-Bin Zhang1*

Author affiliations

1 Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843-2474, USA

2 College of Life Science, Jilin Agricultural University, Changchun, Jilin 130118, China

3 Institute of Plant Science and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, 76100, Israel

4 The Volcani Center, P.O. Box 6, Bet-Dagan, 50250, Israel

5 USDA-ARS and Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6434, USA

6 The Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China

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Citation and License

BMC Genomics 2010, 11:501  doi:10.1186/1471-2164-11-501

Published: 17 September 2010

Abstract

Background

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.

Results

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 ×) 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.

Conclusion

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.