Unraveling Chickpea Transcriptome for Gene Discovery and Marker Development Using Next Generation Sequencing Technologies

Chickpea ranks third among the food legume crop production in the world. However, the genomic resources available for chickpea are still very limited. The generation of large-scale ESTs/transcripts is a very useful approach for the identification of gene-rich regions in a genome, gene identification and genome annotation. Next generation sequencing technologies provide a rapid and cost-effective means of sequencing and characterization of the transcriptome of an organism. We sequenced the transcriptome of cultivated chickpea using short-read Illumina and long-read Roche 454 platforms. The optimization of de novo assembly clearly indicated that hybrid assembly of long-read and short-read primary assemblies gave better results. The hybrid assembly generated a set of 34,760 transcripts with an average length of 1,020 bp representing about 4.8% (35.5 Mb) of the total chickpea genome. We identified more than 4,000 simple sequence repeats (SSRs) in the transcriptome, which could be developed as functional molecular markers in chickpea. Putative function and gene ontology terms were assigned to at least 73% and 71% of chickpea transcripts, respectively. Several chickpea transcripts showing tissue-specific expression were also identified and the results were validated using real-time PCR analysis. We have also sequenced the transcriptome of wild chickpea and generated 37265 transcripts. A total of 561 polymorhic SSRs and 36446 single nucleotide polymorphisms (SNPs) were identified among the cultivated and wild chickpea species. Many of these SSRs and SNPs were detected in the transcripts expressed in tissue-specific manner and those encoding for transcription factors. A web resource, Chickpea Transcriptome Database (http://www.nipgr.res.in/ctdb.html), which provides public access to the chickpea transcriptome data, has also been developed. The set of chickpea transcripts generated provides a resource for gene discovery and development of functional molecular markers. It is anticipated that this study is a significant contribution towards development of genomic resources for chickpea and will accelerate functional genomic studies and breeding programmes.