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Cicer arietinum Transcriptome or Gene expression

Identifiers: SRA: SRP006045
BioProject: PRJNA80015
Study Type: 
Abstract: Although chickpea (Cicer arietinum L.) is an important legume crop in the semi-arid tropic (SAT) regions of Africa and Asia, the crop productivity remained very low for several decades mainly due to its exposure to abiotic stresses like drought. With an objective to initiate molecular breeding to enhance crop productivity, next generation sequencing technologies (e.g. Roche/454 and Illumina/Solexa) have been used to develop a comprehensive transcriptomic resource for identification of drought-responsive candidate genes and gene-based molecular markers. In this context, 103,215 tentative unique sequences (TUSs) have been assembled by using 435,018 short transcript reads with an average size 216 bp generated by Roche/454 sequencing and 21,491 Sanger ESTs. Sequence similarity of TUSs showed maximum similarity with Medicago truncatula (35.8%) and least with Oryza sativa (2.7%). Functional analysis provided a putative function for 49,437 (47.8 %) TUSs of which 20,634 (41.7%) were assigned to gene ontology categories. Analysis of chickpea TUSs with Medicago genome assembly (Mt 3.0 build) predicted ~6,714 gene structures and 22,848 putative intron-spanning splice junctions in 10,964 TUSs. Alignment of 37.75 million Illumina tags generated from drought challenged roots tissues of two chickpea genotypes with TUSs provided 44,639 differentially expressed TUSs. Of this, 2,974 TUSs were mapped onto different metabolic pathways. qRT-PCR analysis of 20 selected drought-responsive genes provided high-confidence for 8 genes. In addition, a novel set of 728 SSR, 495 high-confidence SNP, 387 COS and 1,496 intron-spanning region markers have been developed. In summary, this resource should be useful for undertaking basic and applied research for genome analysis and crop improvement in chickpea.

Related SRA data

6 ( 6 samples )
18 (7.0Gbp; 4.3Gb)
Additional objects:
File type count
fastq 47
srf 2