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

被引：184

作者：

Hiremath, Pavana J. ^{[1
,2
]}

Farmer, Andrew ^{[3
]}

Cannon, Steven B. ^{[4
,5
]}

Woodward, Jimmy ^{[3
]}

Kudapa, Himabindu ^{[1
]}

Tuteja, Reetu ^{[1
]}

Kumar, Ashish ^{[1
]}

BhanuPrakash, Amindala ^{[1
]}

Mulaosmanovic, Benjamin ^{[5
]}

Gujaria, Neha ^{[1
]}

Krishnamurthy, Laxmanan ^{[1
]}

Gaur, Pooran M. ^{[1
]}

KaviKishor, Polavarapu B. ^{[2
]}

Shah, Trushar ^{[1
]}

Srinivasan, Ramamurthy ^{[6
]}

Lohse, Marc ^{[7
]}

Xiao, Yongli ^{[8
]}

Town, Christopher D. ^{[8
]}

Cook, Douglas R. ^{[9
]}

May, Gregory D. ^{[3
]}

Varshney, Rajeev K. ^{[1
,10
]}

机构：

[1] Int Crops Res Inst Semi Arid Trop, Patancheru 502324, Andhra Pradesh, India

[2] Osmania Univ, Hyderabad 500007, Andhra Pradesh, India

[3] NCGR, Santa Fe, NM USA

[4] ARS, USDA, Corn Insects & Crop Genet Res Unit, Ames, IA USA

[5] Iowa State Univ, Dept Agron, Ames, IA USA

[6] NRCPB, New Delhi, India

[7] MPIMPP, Potsdam, Germany

[8] JCVI, Rockville, MD USA

[9] Univ Calif Davis, Davis, CA 95616 USA

[10] CIMMYT, GCP, Mexico City 06600, DF, Mexico

来源：

PLANT BIOTECHNOLOGY JOURNAL | 2011年 / 9卷 / 08期

关键词：

chickpea; next generation sequencing; transcriptome; drought-responsive genes; markers; MEDICAGO-TRUNCATULA; GENE-EXPRESSION; MICROSATELLITE MARKERS; GENOME ANALYSIS; SSR-MARKERS; STRESS; GENERATION; DATABASE; CONSTRUCTION; INTEGRATION;

D O I：

10.1111/j.1467-7652.2011.00625.x

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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 similar to 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.

引用

页码：922 / 931

页数：10

共 52 条

[1] A PROTEIN ALIGNMENT SCORING SYSTEM SENSITIVE AT ALL EVOLUTIONARY DISTANCES [J].