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

Title 
Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. 
Publication Type 
Journal Article 
Authors 
Hiremath PJ, Farmer A, Cannon SB, Woodward J, Kudapa H, Tuteja R, Kumar A, Bhanuprakash A, Mulaosmanovic B, Gujaria N, Krishnamurthy L, Gaur PM, Kavi Kishor PB, Shah T, Srinivasan R, Lohse M, Xiao Y, Town CD, Cook DR, May GD, Varshney RK 
Year of Publication 
2011 
Volume 
Journal 
Plant biotechnology journal 
Issue 
Pagination 
922-31 
Date Published 
2011 Oct 
ISSN 
1467-7652 
Keywords 
Africa, Asia, Chickpea, Chromosome Mapping, Cicer, Droughts, Energy Metabolism, expressed sequence tags, Gene Expression Profiling, Gene Expression Regulation, Plant, Gene Library, Genetic Markers, Genome, Plant, genotype, Introns, Medicago truncatula, Microsatellite Repeats, Plant Roots, Polymorphism, Single Nucleotide, Sequence Alignment, Stress, Physiological, Transcription Factors 
DOI 
10.1111/j.1467-7652.2011.00625.x 
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 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.

 
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