Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa

Chickpea (Cicer arietinum L.) is an important legume crop in the semi-arid regions of Asia and Africa. Gains in crop productivity have been low however, particularly because of biotic and abiotic stresses. To help enhance crop productivity using molecular breeding techniques, next generation sequencing technologies such as Roche/454 and Illumina/Solexa were used to determine the sequence of most gene transcripts and to identify drought-responsive genes and gene-based molecular markers. A total of 103215 tentative unique sequences (TUSs) have been produced from 435018 Roche/454 reads and 21491 Sanger expressed sequence tags (ESTs). Putative functions were determined for 49437 (47.8%) of the TUSs, and gene ontology assignments were determined for 20634 (41.7%) of the TUSs. Comparison of the chickpea TUSs with the Medicago truncatula genome assembly (Mt 3.5.1 build) resulted in 42141 aligned TUSs with putative gene structures (including 39281 predicted intron/splice junctions). Alignment of ∼37 million Illumina/Solexa tags generated from drought-challenged root tissues of two chickpea genotypes against the TUSs identified 44639 differentially expressed TUSs. The TUSs were also used to identify a diverse set of markers, including 728 simple sequence repeats (SSRs), 495 single nucleotide polymorphisms (SNPs), 387 conserved orthologous sequence (COS) markers, and 2088 intron-spanning region (ISR) markers. This resource will be useful for basic and applied research for genome analysis and crop improvement in chickpea.

Bibliographic Details

Main Authors:	Hiremath, P.J., Farmer, A., Cannon, S.B., Woodward, J., Kudapa, H., Tuteja, R., Kumar, A., Bhanuprakash, A., Mulaosmanovic, B., Gujaria, N., Krishnamurthy, L., Pooran M. Gaur, Kavikishor, P.B., Shah, T., Srinivasan, R., Lohse, M., Yongli Xiao, Town, C.D., Cook, D., May, G.D., Varshney, R.K.
Format:	Article biblioteca
Language:	English
Published:	Wiley 2011
Subjects:	AGRICULTURAL SCIENCES AND BIOTECHNOLOGY, Next Generation Sequencing, Drought-Responsive Genes, CHICKPEAS, TRANSCRIPTION, GENES, DROUGHT TOLERANCE, GENETIC MARKERS,
Online Access:	https://hdl.handle.net/10883/21094
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