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

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.

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

“…Using a combination of ab initio modeling, and homology-based searches with gene sets from six plant species, including legumes, and the CaTA transcript sequences 8 , we predicted a nonredundant set of 28,269 gene models, with average transcript and coding sequence sizes of 3,055 bp and 1,166 bp, respectively (Supplementary Table 7). Most of these genes have homology with gene models in TrEMBL 9 (89.58%) and Interpro 10 (70.03%) databases.…”

“…The chickpea genome assembly contained 81,845 SSRs, of which 48,298 SSRs were suitable for PCR primer design for use as genetic markers (Supplementary Tables 16 and 17). SNP discovery using 1,073 million Illumina transcript reads and 15 million 454-sequencer transcript reads generated in an earlier study 8 from four desi genotypes of chickpea (ICC 506, ICC 1882, ICC 4958, ICCC 37) and one accession (PI 489777) of the progenitor species C. reticulatum Table 18 and Supplementary Fig. 7).…”

Genomics-assisted breeding for drought tolerance in chickpea

“…However, in another comprehensive study, after aligning 37 million Illumina short sequence tags generated from drought-challenged root tissues of the same genotypes as used in the transcriptome assembly, Hiremath et al (2011) identified 2974 TUSs with significant expression changes, 2823 of which could be associated with gene ontology annotations. Furthermore, the expression patterns of many genes suggested that their role in various pathways of secondary metabolism.…”

Translational Genomics in Agriculture: Some Examples in Grain Legumes

“…Among legume crop species, several versions of transcriptome assemblies were generated by different research groups (Table 2). For instance, in the case of chickpea, several transcriptome assemblies based on different sequencing platforms have been developed (Garg et al, 2011a;2011b;Hiremath et al, 2011). These assemblies together with unpublished data from the University of Saskatchewan have been used for defining a comprehensive trasncriptome assembly (Lam et al, 2010) comprising of 46,369 contigs with an average N50 of 1,726 bp (Kudapa et al, 2014).…”

“…Flowering time/maturation Homology based (Kim et al, 2012) GmDGAT2C/ GmDGAR1B Seed yield Homology based (Eskandari et al, 2013) conserved orthologous sequence (COS) and intron spanning region (ISR) markers Hiremath et al, 2011;Jhanwar et al, 2012;Kudapa et al, 2012). Using the Roche 454-FLX platform, a transcriptome assembly in M. truncatula was generated with a total of 184,599 contigs (Cheung et al, 2006) and this assembly was found to contain 610 SSRs.…”