Journal article
Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.)
Functional & Integrative Genomics, Vol.14(1), pp.59-73
2014
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.
Details
- Title
- Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.)
- Authors/Creators
- R.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsR.R. Mir (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsS. Bhatia (Author/Creator) - National Institute of Plant Genome ResearchM. Thudi (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsY. Hu (Author/Creator) - University of CaliforniaS. Azam (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsY. Zhang (Author/Creator) - University of CaliforniaD. Jaganathan (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsF.M. You (Author/Creator) - Agriculture and Agri-Food CanadaJ. Gao (Author/Creator) - University of CaliforniaO. Riera-Lizarazu (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsM-C Luo (Author/Creator) - University of California
- Publication Details
- Functional & Integrative Genomics, Vol.14(1), pp.59-73
- Publisher
- Springer Verlag
- Identifiers
- 991005542707507891
- Copyright
- © 2014 The Authors.
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.96 QTL
- Web Of Science research areas
- Genetics & Heredity
- ESI research areas
- Molecular Biology & Genetics