Open AccessTranscriptome sequencing of wild chickpea as a rich resource for marker development
Author(s) -
Jhanwar Shalu,
Priya Pushp,
Garg Rohini,
Parida Swarup K.,
Tyagi Akhilesh K.,
Jain Mukesh
Publication year - 2012
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1111/j.1467-7652.2012.00712.x
Subject(s) - biology , transcriptome , single nucleotide polymorphism , microsatellite , pyrosequencing , genetics , gene , deep sequencing , illumina dye sequencing , expressed sequence tag , dna sequencing , allele , genotype , genome , gene expression
Summary 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.