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

Submitted to: Plant Biotechnology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 16, 2011
Publication Date: May 25, 2011
Citation: Hiremath, P.J., Farmer, A., Woodward, J., Cannon, S.B., Kudapa, H., Tuteja, R., Kumar, A., 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. 9:922-931.

Interpretive Summary: Chickpea (or "garbanzo bean") is an important seed crop worldwide, with protein-rich seeds used for grain and flour. The crop can often be grown on (and be used to improve) marginal land, requiring few inputs other than labor and seed. Chickpea is also suitable for production in a wide variety of areas, from tropical through temperate regions-from India and Africa to the U.S. and Canada. The crop has, however, received relatively little attention using modern breeding methods. Strong breeding programs could help make varieties that will be more productive in many different environments, from drought-prone tropical regions to frost-prone northern areas. This study reports the sequencing of most of the genes of this crop, and comparison of gene changes in response to drought- and salt-stressed plants. The study also provides thousands of new genetic markers which breeders can now use in new breeding efforts. These results will be important to breeders working to produce higher-yielding, more stress-tolerant chickpea varieties. Stress-response mechanisms found in chickpea will help also scientists and breeders working on other closely related crops such as faba bean, pea, and lentil, as well as more distantly related legumes such as common bean and soybean.

Technical Abstract: 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 due to biotic and abiotic stresses. To help enhance crop productivity using molecular breeding techniques, next generation sequencing (NGS) technologies (Roche/454 and Illumina) 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 transcript assemblies (TAs) have been produced from 435,018 Roche/454 reads and 21,491 Sanger ESTs. Putative functions were determined for 49,437 (47.8 %) of the TAs, and gene ontology (GO) assignments were determined for 20,634 (41.7%) of the TAs. Comparison of the chickpea TAs with the Medicago genome assembly (Mt 3.5.1 build) resulted in ~5,608 putative gene structures and 22,848 intron-spanning junctions in 10,964 TAs. Alignment of ~37 million Illumina/Solexa tags generated from drought-challenged root tissues of two chickpea genotypes against the TAs identified 44,639 differentially expressed TAs. The TAs were also used to identify a diverse set of markers, including 728 SSRs, 495 SNPs, 387 conserved orthologous sequence markers, and 1,496 intron-spanning markers. This resource will be useful for basic and applied research for genome analysis and crop improvement in chickpea.