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

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 as...

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Bibliographic Details
Published in:Plant biotechnology journal 2012-08, Vol.10 (6), p.690-702
Main Authors: Jhanwar, Shalu, Priya, Pushp, Garg, Rohini, Parida, Swarup K., Tyagi, Akhilesh K., Jain, Mukesh
Format: Article
Language:English
Subjects:
Chickpeas
Cicer - genetics
Cicer - metabolism
Cicer arietinum
Divergence
Evolution, Molecular
Flowers & plants
Genes
Genetic diversity
Genetic Speciation
Genomes
Genomics
Legumes
Microsatellite Repeats
Nucleotides
Phylogenetics
Polymorphism
Polymorphism, Single Nucleotide
Rice
Sequence Analysis, RNA
simple sequence repeat
Simple sequence repeats
Single-nucleotide polymorphism
Soybeans
Speciation
Transcriptome
Transcriptomes
wild chickpea
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Summary: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.
ISSN:1467-7644
1467-7652
DOI:10.1111/j.1467-7652.2012.00712.x