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Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers

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Title Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers
 
Creator Agarwal, Gaurav
Jhanwar, Shalu
Priya, Pushp
Singh, Vikash K.
Saxena, Maneesha S.
Parida, Swarup K.
Garg, Rohini
Tyagi, Akhilesh K.
Jain, Mukesh
 
Subject Chickpea
Functional Markers
Kabuli Chickpea
Transcriptome
 
Description Chickpea (Cicer arietinum L.) is an important crop legume plant with high nutritional value. The transcriptomes of desi and wild chickpea have already been sequenced. In this study, we sequenced the transcriptome of kabuli chickpea, C. arietinum (genotype ICCV2), having higher commercial value, using GS-FLX Roche 454 and Illumina technologies. The assemblies of both Roche 454 and Illumina datasets were optimized using various assembly programs and parameters. The final optimized hybrid assembly generated 43,389 transcripts with an average length of 1065 bp and N50 length of 1653 bp representing 46.2 Mb of kabuli chickpea transcriptome. We identified a total of 5409 simple sequence repeats (SSRs) in these transcript sequences. Among these, at least 130 and 493 SSRs were polymorphic with desi (ICC4958) and wild (PI489777) chickpea, respectively. In addition, a total of 1986 and 37,954 single nucleotide polymorphisms (SNPs) were predicted in kabuli/desi and kabuli/wild genotypes, respectively. The SNP frequency was 0.043 SNP per kb for kabuli/desi and 0.821 SNP per kb for kabuli/wild, reflecting very low genetic diversity in chickpea. Further, SSRs and SNPs present in tissue-specific and transcription factor encoding transcripts have been identified. The experimental validation of a selected set of polymorphic SSRs and SNPs exhibited high intra-specific polymorphism potential between desi and kabuli chickpea, suggesting their utility in large-scale genotyping applications. The kabuli chickpea gene index assembled, and SSRs and SNPs identified in this study will serve as useful genomic resource for genetic improvement of chickpea.
This work was funded by the Department of Biotechnology, Government of India, under the Next Generation Challenge Programme on Chickpea
Genomics (grant number BT/PR12919/AGR/02/676/2009 from 2009–2014). The funders had no role in study design, data collection and analysis, decision to
publish, or preparation of the manuscript.
 
Date 2014-05-01T09:04:00Z
2014-05-01T09:04:00Z
2012
13 November 2012
 
Type Article
 
Identifier PLoS One, 7(12): e52443
http://hdl.handle.net/123456789/219
 
Language en
 
Publisher Public Library of Science