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Transcriptome sequencing of wild chickpea as a rich resource for marker development

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Title Transcriptome sequencing of wild chickpea as a rich resource for marker development
 
Creator Jhanwar, Shalu
Priya, Pushp
Garg, Rohini
Parida, Swarup K.
Tyagi, Akhilesh K.
Jain, Mukesh
 
Subject wild chickpea
transcriptome
polymorphism
simple sequence repeat
single-nucleotide polymorphism
 
Description The transcriptome of cultivated chickpea (Cicer arietinum L.), an important crop legume, has recently been sequenced. Here, we report sequencing of the transcriptome of wild chickpea, C. reticulatum (PI489777), the progenitor of cultivated chickpea, by GS-FLX 454 technology. The optimized assembly of C. reticulatum transcriptome generated 37 265 transcripts in total with an average length of 946 bp. A total of 4072 simple sequence repeats (SSRs) could be identified in these transcript sequences, of which at least 561 SSRs were polymorphic between C. arietinum and C. reticulatum. In addition, a total of 36 446 single-nucleotide polymorphisms (SNPs) were identified after optimization of probability score, quality score, read depth and consensus base ratio. Several of these SSRs and SNPs could be associated with tissue-specific and transcription factor encoding transcripts. A high proportion (92-94%) of polymorphic SSRs and SNPs identified between the two chickpea species were validated successfully. Further, the estimation of synonymous substitution rates of orthologous transcript pairs suggested that the speciation event for divergence of C. arietinum and C. reticulatum may have happened approximately 0.53 million years ago. The results of our study provide a rich resource for exploiting genetic variations in chickpea for breeding programmes.
We acknowledge the financial support from the Department of
Biotechnology, Government of India, New Delhi, under the Next
Generation Challenge Programme on Chickpea Genomics.
 
Date 2014-05-15T06:16:55Z
2014-05-15T06:16:55Z
2012
20 April 2012
 
Type Article
 
Identifier Plant Biotechnol. Journal, 10(6): 690-702
http://hdl.handle.net/123456789/241
 
Language en
 
Publisher Wiley-Blackwell