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

Varshney, Rajeev K.; Song, Chi; Saxena, Rachit K.; Azam, Sarwar; Yu, Shanlin; Sharpe, Andrew; Cannon, Steven B.; Baek, Jong‐Min; Rosen, Benjamin D.; Tar’an, Bunyamin; Millán, Teresa; Zhang, Xudong; Ramsay, Larissa; Iwata, Akihisa; Wang, Ying; Nelson, William M.; Farmer, Andrew; Gaur, Pooran M.; Soderlund, Carol; Penmetsa, R. Varma; Xu, Chunyan; Bharti, Arvind K.; He, Weiming; Winter, Peter; Zhao, Shancen; Hane, James K.; Carrasquilla‐Garcia, Noelia; Condie, Janet; Upadhyaya, Hari D.; Luo, Ming‐Cheng; Thudi, Mahendar; Gowda, C. L. L.; Singh, Narendra Pratap; Lichtenzveig, Judith; Gali, Krishna Kishore; Rubio, J.; Nadarajan, N.; Doležel, Jaroslav; Bansal, Kailash C.; Xu, Xun; Edwards, David; Zhang, Gengyun; Kahl, G.; Gil, J.; Singh, Karam B.; Datta, Swapan K.; Jackson, Scott A.; Wang, Jun; Cook, Douglas R.

doi:10.1038/nbt.2491

Cited by 1,092 publications

(1,165 citation statements)

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“…This draft A. duranensis genome provides rich new information about an important branch of the legume clade, building on the genomes of Lotus (11), Medicago (14), soybean (35), pigeonpea (36), chickpea (37), and common bean (38). The Arachis genome sequences presented here provide new insights and new resources for evolution and polyploidization research.…”

Section: Discussionmentioning

confidence: 99%

Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens

Chen

Li²,

Pandey

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

214

222

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Peanut or groundnut (Arachis hypogaea L.), a legume of South American origin, has high seed oil content (45-56%) and is a staple crop in semiarid tropical and subtropical regions, partially because of drought tolerance conferred by its geocarpic reproductive strategy. We present a draft genome of the peanut A-genome progenitor, Arachis duranensis, and 50,324 protein-coding gene models. Patterns of gene duplication suggest the peanut lineage has been affected by at least three polyploidizations since the origin of eudicots. Resequencing of synthetic Arachis tetraploids reveals extensive gene conversion in only three seed-to-seed generations since their formation by human hands, indicating that this process begins virtually immediately following polyploid formation. Expansion of some specific gene families suggests roles in the unusual subterranean fructification of Arachis. For example, the S1Fa-like transcription factor family has 126 Arachis members, in contrast to no more than five members in other examined plant species, and is more highly expressed in roots and etiolated seedlings than green leaves. The A. duranensis genome provides a major source of candidate genes for fructification, oil biosynthesis, and allergens, expanding knowledge of understudied areas of plant biology and human health impacts of plants, informing peanut genetic improvement and aiding deeper sequencing of Arachis diversity.

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Section: Discussionmentioning

confidence: 99%

Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens

Chen

Li²,

Pandey

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

214

222

View full text Add to dashboard Cite

show abstract

“…Genome sequences for most of the grain legumes are now available, for instance soybean (Schmutz et al, 2010), groundnut progenitors (Bertioli et al, 2016;Chen et al, 2016), chickpea (Varshney et al, 2013d;Parween et al, 2015), pigeonpea (Varshney et al, 2012a), common bean (Schmutz et al, 2014;Yang et al, 2015), and adzuki bean (Kang et al, 2015;Yang et al, 2015) (Table 1). Efforts are underway to sequence the remaining legume genomes.…”

Section: Sequencing and Genotypingmentioning

confidence: 99%

Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy

Varshney

Thudi

Pandey

et al. 2018

Journal of Experimental Botany

Self Cite

101

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Grain legumes form an important component of the human diet, provide feed for livestock, and replenish soil fertility through biological nitrogen fixation. Globally, the demand for food legumes is increasing as they complement cereals in protein requirements and possess a high percentage of digestible protein. Climate change has enhanced the frequency and intensity of drought stress, posing serious production constraints, especially in rainfed regions where most legumes are produced. Genetic improvement of legumes, like other crops, is mostly based on pedigree and performance-based selection over the past half century. To achieve faster genetic gains in legumes in rainfed conditions, this review proposes the integration of modern genomics approaches, high throughput phenomics, and simulation modelling in support of crop improvement that leads to improved varieties that perform with appropriate agronomy. Selection intensity, generation interval, and improved operational efficiencies in breeding are expected to further enhance the genetic gain in experimental plots. Improved seed access to farmers, combined with appropriate agronomic packages in farmers' fields, will deliver higher genetic gains. Enhanced genetic gains, including not only productivity but also nutritional and market traits, will increase the profitability of farming and the availability of affordable nutritious food especially in developing countries.

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“…Under such conditions, comparative genomics emerged as a viable attempt, which enables assessment of data from one species to investigate other incongruent species, which has already been achieved in case of annotating wheat sequences using information from E. coli, human, A. thaliana and rice. 39 However, in the recent past, the unravelling of genome information of a few species like the chickpea, 40 mulberry, 41 soybean, [42][43] Medicago, 44 pigeon pea [45][46] and peanut (www.peanutbioscience.com) 47 has provided tremendous potential for targeted way of addressing various crop improvement issues. Over the years, technology advancement has led to a great leap in gene discovery from the mid 20th century to the late 2000s and till date (Fig.…”

Section: Prospecting the Trait Regulatory Genesmentioning

confidence: 99%

Emerging tools, concepts and ideas to track the modulator genes underlying plant drought adaptive traits: An overview

Nataraja

2016

Plant Signaling & Behavior

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Crop vulnerability to multiple abiotic stresses is increasing at an alarming rate in the current global climate change scenario, especially drought. Crop improvement for adaptive adjustments to accomplish stress tolerance requires a comprehensive understanding of the key contributory processes. This requires the identification and careful analysis of the critical morpho-physiological plant attributes and their genetic control. In this review we try to discuss the crucial traits underlying drought tolerance and the various modes followed to understand their molecular level regulation. Plant stress biology is progressing into new dimensions and a conscious attempt has been made to traverse through the various approaches and checkpoints that would be relevant to tackle drought stress limitations for sustainable crop production.

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

Cited by 1,092 publications

References 54 publications

Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens

Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens

Accelerating genetic gains in legumes for the development of prosperous smallholder agriculture: integrating genomics, phenotyping, systems modelling and agronomy

Emerging tools, concepts and ideas to track the modulator genes underlying plant drought adaptive traits: An overview

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