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

Hiremath, P J and Farmer, A and Cannon, S B and Woodward, J and Kudapa, H and Tuteja, R and Kumar, Ashish and Bhanuprakash, A and Mulaosmanovic, B and Gujaria, N and Krishnamurthy, L and Gaur, P M and Kavikishor, P B and Shah, Tushar and Srinivasan, R and Lohse, M and Xiao, Y and Town, C D and Cook, D R and May, G D and Varshney, R K (2011) Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. Plant Biotechnology Journal, 9. pp. 922-931.

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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 103 215 tentative unique sequences (TUSs) have been produced from 435 018 Roche/454 reads and 21 491 Sanger expressed sequence tags (ESTs). Putative functions were determined for 49 437 (47.8%) of the TUSs, and gene ontology assignments were determined for 20 634 (41.7%) of the TUSs. Comparison of the chickpea TUSs with the Medicago truncatula genome assembly (Mt 3.5.1 build) resulted in 42 141 aligned TUSs with putative gene structures (including 39 281 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 44 639 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.

Item Type: Article
Uncontrolled Keywords: chickpea, next generation sequencing, transcriptome, drought-responsive genes, markers
Subjects: Mandate crops > Chickpea
Depositing User: Ms Sandhya Gir
Date Deposited: 12 Sep 2011 04:12
Last Modified: 04 Sep 2013 13:04
Official URL:
Funders: Generation Challenge Programme, Bill and Melinda Gates Foundation, Indian Council of Agricultural Research, Government of India - Department of Biotechnology
Acknowledgement: The authors are thankful to the CGIAR Generation Challenge Programme (GCP), Mexico; the Bill and Melinda Gates Foundation (BMGF), USA; the National Fund of Indian Council of Agricultural Research (ICAR) and the Department of Biotechnology (DBT) of Government of India for financial support of the study. Thanks are also due to Spurthi Nayak and Mahendar Thudi of ICRISAT and Nathan Weeks of USDA-ARS for their help while carrying out this study.

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