Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa.
Pavana J Hiremath,Andrew Farmer,Steven B. Cannon,Steven B. Cannon,Jimmy E. Woodward,Himabindu Kudapa,Reetu Tuteja,Ashok Kumar,Amindala BhanuPrakash,Benjamin Mulaosmanovic,Neha Gujaria,L. Krishnamurthy,Pooran M. Gaur,P. B. KaviKishor,Trushar Shah,Ramamurthy Srinivasan,Marc Lohse,Yongli Xiao,Christopher D. Town,Douglas R. Cook,Gregory D. May,Rajeev K. Varshney,Rajeev K. Varshney +22 more
TLDR
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 in chickpea.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.read more
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Draft genome sequence of chickpea ( Cicer arietinum ) provides a resource for trait improvement
Rajeev K. Varshney,Rajeev K. Varshney,Chi Song,Rachit K. Saxena,Sarwar Azam,Sheng Yu,Andrew G. Sharpe,Steven B. Cannon,Jong-Min Baek,Benjamin D. Rosen,Bunyamin Tar’an,Teresa Millán,Xudong Zhang,Larissa Ramsay,Aiko Iwata,Ying Wang,William Nelson,Andrew Farmer,Pooran M. Gaur,Carol Soderlund,R. Varma Penmetsa,Chunyan Xu,Arvind K. Bharti,Weiming He,Peter Winter,Shancen Zhao,James K. Hane,Noelia Carrasquilla-Garcia,Janet A. Condie,Hari D. Upadhyaya,Ming-Cheng Luo,Mahendar Thudi,C. L. L. Gowda,Narendra Singh,Judith Lichtenzveig,Krishna K. Gali,Josefa Rubio,N. Nadarajan,Jaroslav Dolezel,Kailash C. Bansal,Xun Xu,David Edwards,Gengyun Zhang,Guenter Kahl,Juan Gil,Karam B. Singh,Karam B. Singh,Swapan K. Datta,Scott A. Jackson,Jun Wang,Jun Wang,Douglas R. Cook +51 more
TL;DR: This work reports the ∼738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes, and identifies targets of both breeding-associated genetic sweeps and breeding- associated balancing selection.
Journal ArticleDOI
Phenotyping for drought tolerance of crops in the genomics era.
TL;DR: This review provides basic principles and a broad set of references useful for the management of phenotyping practices for the study and genetic dissection of drought tolerance and, ultimately, for the release of drought-tolerant cultivars.
Journal ArticleDOI
Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences
Juan Zalapa,Juan Zalapa,Hugo E. Cuevas,Huayu Zhu,Shawn A. Steffan,Douglas Senalik,Douglas Senalik,Eric L. Zeldin,Brent H. McCown,Rebecca Harbut,Philipp W. Simon,Philipp W. Simon +11 more
TL;DR: In the future, NGS technologies will massively increase the number of SSRs and other genetic markers available to conduct genetic research in understudied but economically important crops such as cranberry.
Journal ArticleDOI
Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops.
Reyazul Rouf Mir,Reyazul Rouf Mir,Mainassara Zaman-Allah,Nese Sreenivasulu,Richard Trethowan,Rajeev K. Varshney,Rajeev K. Varshney,Rajeev K. Varshney +7 more
TL;DR: The most recent advances in plant physiology for precision phenotyping of drought response are discussed, a vital step before implementing the genetic and molecular-physiological strategies to unravel the complex multilayered drought tolerance mechanism and further exploration using molecular breeding approaches for crop improvement.
Journal ArticleDOI
Legume phylogeny and classification in the 21st century: Progress, prospects and lessons for other species-rich clades
Anne Bruneau,Jeff J. Doyle,Patrick S. Herendeen,Colin E. Hughes,Gregory Kenicer,Gwilym P. Lewis,Barbara A. Mackinder,R.T. Pennington,Michael J. Sanderson,Martin F. Wojciechowski,S. Boatwright,Gillian K. Brown,Domingos Cardoso,M. Crips,Ashley N. Egan,R. Fortunato,Julie A. Hawkins,T. Kajita,Bente B. Klitgaard,Erik J. M. Koenen,Matt Lavin,M. Luckow,Brigitte Marazzi,Michelle M. McMahon,Joseph T. Miller,Daniel J. Murphy,H. Ohashi,L. P. de Queiroz,L. Rico,Tiina Särkinen,B. Schrire,Marcelo F. Simon,Edivan Rodrigues de Souza,Kelly P. Steele,B.M. Torke,Jan J. Wieringa,B.E. Wijk +36 more
TL;DR: This work examines how the legume systematic research community might join forces to produce a comprehensive phylogenetic estimate for the Leguminosae, and examines how morphology can be incorporated into legume phylogeny to address issues in comparative biology and classification.
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