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Natural allelic diversity, genetic structure and linkage disequilibrium pattern in wild chickpea

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Title Natural allelic diversity, genetic structure and linkage disequilibrium pattern in wild chickpea
 
Creator Saxena, Maneesha S.
Bajaj, Deepak
Kujur, Alice
Das, Shouvik
Badoni, Saurabh
Kumar, Vinod
Singh, Mohar
Bansal, Kailash C.
Tyagi, Akhilesh K.
Parida, Swarup K.
 
Subject Wild Chickpea
Chickpea
natural allelic diversity
 
Description Accepted date: August 11, 2014
Characterization of natural allelic diversity and understanding the genetic structure and linkage disequilibrium (LD) pattern in wild germplasm accessions by large-scale genotyping of informative microsatellite and single nucleotide polymorphism (SNP) markers is requisite to facilitate chickpea genetic improvement. Large-scale validation and high-throughput genotyping of genome-wide physically mapped 478 genic and genomic microsatellite markers and 380 transcription factor gene-derived SNP markers using gel-based assay, fluorescent dye-labelled automated fragment analyser and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass array have been performed. Outcome revealed their high genotyping success rate (97.5%) and existence of a high level of natural allelic diversity among 94 wild and cultivated Cicer accessions. High intra- and inter-specific polymorphic potential and wider molecular diversity (11-94%) along with a broader genetic base (13-78%) specifically in the functional genic regions of wild accessions was assayed by mapped markers. It suggested their utility in monitoring introgression and transferring target trait-specific genomic (gene) regions from wild to cultivated gene pool for the genetic enhancement. Distinct species/gene pool-wise differentiation, admixed domestication pattern, and differential genome-wide recombination and LD estimates/decay observed in a six structured population of wild and cultivated accessions using mapped markers further signifies their usefulness in chickpea genetics, genomics and breeding.
The authors gratefully acknowledge the financial support by the Department of Biotechnology (DBT), Government of India, through their research grant (102/IFD/SAN/2161/2013-14) for this research work. Alice Kujur and Shouvik Das acknowledges the Council of Scientific and Industrial Research (CSIR) and Department of Biotechnology (DBT) for the award of Junior/Senior Research Fellowships. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
 
Date 2015-12-23T06:59:05Z
2015-12-23T06:59:05Z
2014
 
Type Article
 
Identifier PLoS One, 9(9): e107484
1932-6203
http://172.16.0.77:8080/jspui/handle/123456789/451
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0107484
10.1371/journal.pone.0107484
 
Language en_US
 
Publisher PLOS