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

Summary Chickpea (Cicer arietinum L.) is an important legume crop in the semi-arid regions of Asiaand Africa. Gains in crop productivity have been low however, particularly because of bioticand abiotic stresses. To help enhance crop productivity using molecular breeding techniques,next generation sequencing technologies such as Roche ⁄454 and Illumina Solexa were usedto determine the sequence of most gene transcripts and to identify drought-responsive genesand 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 sequencetags (ESTs). Putative functions were determined for 49 437 (47.8%) of the TUSs, and geneontology assignments were determined for 20 634 (41.7%) of the TUSs. Comparison of thechickpea TUSs with the Medicago truncatula genome assembly (Mt 3.5.1 build) resulted in42 141 aligned TUSs with putative gene structures (including 39 281 predicted intron⁄splicejunctions). Alignment of 37 million Illumina⁄Solexa tags generated from drought-challengedroot tissues of two chickpea genotypes against the TUSs identified 44 639 differentiallyexpressed TUSs. The TUSs were also used to identify a diverse set of markers, including 728simple sequence repeats (SSRs), 495 single nucleotide polymorphisms (SNPs), 387 conservedorthologous sequence (COS) markers, and 2088 intron-spanning region (ISR) markers. Thisresource will be useful for basic and applied research for genome analysis and cropimprovement in chickpea.