Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.)

Varshney, R K and Mir, R R and Bhatia, S and Thudi, M and Hu, Yukin and Azam, S and Zang, Y and Jaganathan, D and You, F M and Gao, J and Riera-Lizarazu, O and Luo, M (2014) Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.). Functional & Integrative Genomics, 14 (1). pp. 59-73. ISSN 1438-7948

[img]
Preview
PDF (Author-pay open access) - Published Version
Download (1MB) | Preview

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.

Item Type: Article
Divisions: RP-Grain Legumes
CRPS: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Chickpea, genetic map, genome map
Subjects: Mandate crops > Chickpea
Depositing User: Siva Shankar
Date Deposited: 11 Mar 2014 04:57
Last Modified: 19 Aug 2016 09:36
URI: http://oar.icrisat.org/id/eprint/7604
Official URL: http://dx.doi.org/10.1007/s10142-014-0363-6
Projects: Tropical Legumes I
Funders: Bill and Melinda Gates Foundation
Acknowledgement: The authors are thankful to Douglas R. Cook, University of California, Davis, USA, and Aamir W. Khan for their help during analysis and interpretation of data. This study was supported as a part of the Tropical Legumes I (TLI- Objective 4: Chickpea) project funded by Bill & Melinda Gates Foundation (BMGF) through CGIAR Generation Challenge Programme (RKV) and National Institute of Plant Genome Research (NIPGR), Department of Biotechnology, Government of India (SB). This work has been undertaken as part of the CGIAR Research Program on Grain Legumes. ICRISAT is a member of CGIAR Consortium
Links:

Actions (login required)

View Item View Item