Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

Rajeev K. Varshney; Chengcheng  Shi; Mahendar Thudi; Cedric Mariac; Jason Wallace; He  Zhang; Arindam Ghatak; Palak Chaturvedi; Yusheng Zhao; Xiyin Wang; Abhishek Rathore; Jianping  Wang; Rakesh Srivastava; Annapurna Chitikineni; Guangyi Fan; Somashekhar Punnuri; S.K. Gupta; Yong Jiang; Marie Couderc; Prasad Bajaj; Mohan A.V.S.K. Katta; Dev R Paudel; K.D. Mungra; Wenbin Chen; Karen R. Harris-Shultz; Vanika Garg; Neetin Desai; Dadakhalandar  Doddamani; Ndjido Kane; Joann A.  Conner; Sabarinath  Subramaniam; Om Prakash  Yadav; Cécile Berthouly-Salazard; Falalou Hamidu; Xinming Liang; Jeremy  Clotault; Mame Codou Gueye; Ramanujulu Sunkar; Christian Dupuy; Francesca Sparvoli; Shifeng Cheng; R.S. Mahala; Bharat Singh; Rattan Yadav; Eric Lyons; Swapan K. Datta; C.Tom Hash; Katrien M. Devos; Edward Buckler; Jeffrey L. Bennetzen; Andrew H. Paterson; Peggy Ozias-Akins; Stefania Grando; Jun Wang; Jochen C.  Reif; Wolfram Weckwerth; Xin Liu; Yves Vigouroux; Xun Xu; Trilochan Mohapatra; Bénédicte Rhoné; Philippe Cubry; Peng Qi; Hao Wang; Hari D. Upadhyaya

doi:10.1038/nbt.3943

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

Rajeev K. Varshney, Chengcheng Shi, Mahendar Thudi, Cedric Mariac, Jason Wallace , He Zhang, Arindam Ghatak, Palak Chaturvedi, Yusheng Zhao, Xiyin Wang, Abhishek Rathore, Jianping Wang, Rakesh Srivastava, Annapurna Chitikineni, Guangyi Fan, Somashekhar Punnuri, S.K. Gupta, Yong Jiang, Marie Couderc, Prasad BajajMohan A.V.S.K. Katta, Dev R Paudel, K.D. Mungra, Wenbin Chen, Karen R. Harris-Shultz, Vanika Garg, Neetin Desai, Dadakhalandar Doddamani, Ndjido Kane, Joann A. Conner, Sabarinath Subramaniam, Om Prakash Yadav, Cécile Berthouly-Salazard, Falalou Hamidu, Xinming Liang, Jeremy Clotault, Mame Codou Gueye, Ramanujulu Sunkar, Christian Dupuy, Francesca Sparvoli, Shifeng Cheng, R.S. Mahala, Bharat Singh, Rattan Yadav, Eric Lyons, Swapan K. Datta, C.Tom Hash, Katrien M. Devos, Edward Buckler, Jeffrey L. Bennetzen, Andrew H. Paterson, Peggy Ozias-Akins, Stefania Grando, Jun Wang, Jochen C. Reif, Wolfram Weckwerth, Xin Liu, Yves Vigouroux, Xun Xu, Trilochan Mohapatra, Bénédicte Rhoné, Philippe Cubry, Peng Qi, Hao Wang, Hari D. Upadhyaya

Department of Life Sciences

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Abstract

Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.

Original language	English
Pages (from-to)	969-976
Number of pages	8
Journal	Nature Biotechnology
Volume	35
Issue number	10
Early online date	18 Sept 2017
DOIs	https://doi.org/10.1038/nbt.3943
Publication status	Published - 01 Oct 2017

Keywords

Agriculture
Base Sequence
Conserved Sequence
Desert Climate
Genes, Plant
Genetic Variation
Genome, Plant
Genome-Wide Association Study
Hybridization, Genetic
Molecular Sequence Annotation
Pennisetum/genetics
Quantitative Trait, Heritable

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Varshney, R. K., Shi, C., Thudi, M., Mariac, C., Wallace , J., Zhang, H., Ghatak, A., Chaturvedi, P., Zhao, Y., Wang, X., Rathore, A., Wang, J., Srivastava, R., Chitikineni, A., Fan, G., Punnuri, S., Gupta, S. K., Jiang, Y., Couderc, M., ... Upadhyaya, H. D. (2017). Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nature Biotechnology, 35(10), 969-976. https://doi.org/10.1038/nbt.3943

@article{eb3c7c5cdb0a48f88df4652ede283a03,

title = "Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments",

abstract = "Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.",

keywords = "Agriculture, Base Sequence, Conserved Sequence, Desert Climate, Genes, Plant, Genetic Variation, Genome, Plant, Genome-Wide Association Study, Hybridization, Genetic, Molecular Sequence Annotation, Pennisetum/genetics, Quantitative Trait, Heritable",

author = "Varshney, {Rajeev K.} and Chengcheng Shi and Mahendar Thudi and Cedric Mariac and Jason Wallace and He Zhang and Arindam Ghatak and Palak Chaturvedi and Yusheng Zhao and Xiyin Wang and Abhishek Rathore and Jianping Wang and Rakesh Srivastava and Annapurna Chitikineni and Guangyi Fan and Somashekhar Punnuri and S.K. Gupta and Yong Jiang and Marie Couderc and Prasad Bajaj and {A.V.S.K. Katta}, Mohan and {R Paudel}, Dev and K.D. Mungra and Wenbin Chen and {R. Harris-Shultz}, Karen and Vanika Garg and Neetin Desai and Dadakhalandar Doddamani and Ndjido Kane and Conner, {Joann A.} and Sabarinath Subramaniam and Yadav, {Om Prakash} and C{\'e}cile Berthouly-Salazard and Falalou Hamidu and Xinming Liang and Jeremy Clotault and {Codou Gueye}, Mame and Ramanujulu Sunkar and Christian Dupuy and Francesca Sparvoli and Shifeng Cheng and R.S. Mahala and Bharat Singh and Rattan Yadav and Eric Lyons and {K. Datta}, Swapan and C.Tom Hash and Devos, {Katrien M.} and Edward Buckler and Bennetzen, {Jeffrey L.} and Paterson, {Andrew H.} and Peggy Ozias-Akins and Stefania Grando and Jun Wang and Reif, {Jochen C.} and Wolfram Weckwerth and Xin Liu and Yves Vigouroux and Xun Xu and Trilochan Mohapatra and B{\'e}n{\'e}dicte Rhon{\'e} and Philippe Cubry and Peng Qi and Hao Wang and Upadhyaya, {Hari D.}",

year = "2017",

month = oct,

day = "1",

doi = "10.1038/nbt.3943",

language = "English",

volume = "35",

pages = "969--976",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "Springer Nature",

number = "10",

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Varshney, RK, Shi, C, Thudi, M, Mariac, C, Wallace , J, Zhang, H, Ghatak, A, Chaturvedi, P, Zhao, Y, Wang, X, Rathore, A, Wang, J, Srivastava, R, Chitikineni, A, Fan, G, Punnuri, S, Gupta, SK, Jiang, Y, Couderc, M, Bajaj, P, A.V.S.K. Katta, M, R Paudel, D, Mungra, KD, Chen, W, R. Harris-Shultz, K, Garg, V, Desai, N, Doddamani, D, Kane, N, Conner, JA, Subramaniam, S, Yadav, OP, Berthouly-Salazard, C, Hamidu, F, Liang, X, Clotault, J, Codou Gueye, M, Sunkar, R, Dupuy, C, Sparvoli, F, Cheng, S, Mahala, RS, Singh, B, Yadav, R, Lyons, E, K. Datta, S, Hash, CT, Devos, KM, Buckler, E, Bennetzen, JL, Paterson, AH, Ozias-Akins, P, Grando, S, Wang, J, Reif, JC, Weckwerth, W, Liu, X, Vigouroux, Y, Xu, X, Mohapatra, T, Rhoné, B, Cubry, P, Qi, P, Wang, H & Upadhyaya, HD 2017, 'Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments', Nature Biotechnology, vol. 35, no. 10, pp. 969-976. https://doi.org/10.1038/nbt.3943

TY - JOUR

T1 - Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

AU - Varshney, Rajeev K.

AU - Shi, Chengcheng

AU - Thudi, Mahendar

AU - Mariac, Cedric

AU - Wallace , Jason

AU - Zhang, He

AU - Ghatak, Arindam

AU - Chaturvedi, Palak

AU - Zhao, Yusheng

AU - Wang, Xiyin

AU - Rathore, Abhishek

AU - Wang, Jianping

AU - Srivastava, Rakesh

AU - Chitikineni, Annapurna

AU - Fan, Guangyi

AU - Punnuri, Somashekhar

AU - Gupta, S.K.

AU - Jiang, Yong

AU - Couderc, Marie

AU - Bajaj, Prasad

AU - A.V.S.K. Katta, Mohan

AU - R Paudel, Dev

AU - Mungra, K.D.

AU - Chen, Wenbin

AU - R. Harris-Shultz, Karen

AU - Garg, Vanika

AU - Desai, Neetin

AU - Doddamani, Dadakhalandar

AU - Kane, Ndjido

AU - Conner, Joann A.

AU - Subramaniam, Sabarinath

AU - Yadav, Om Prakash

AU - Berthouly-Salazard, Cécile

AU - Hamidu, Falalou

AU - Liang, Xinming

AU - Clotault, Jeremy

AU - Codou Gueye, Mame

AU - Sunkar, Ramanujulu

AU - Dupuy, Christian

AU - Sparvoli, Francesca

AU - Cheng, Shifeng

AU - Mahala, R.S.

AU - Singh, Bharat

AU - Yadav, Rattan

AU - Lyons, Eric

AU - K. Datta, Swapan

AU - Hash, C.Tom

AU - Devos, Katrien M.

AU - Buckler, Edward

AU - Bennetzen, Jeffrey L.

AU - Paterson, Andrew H.

AU - Ozias-Akins, Peggy

AU - Grando, Stefania

AU - Wang, Jun

AU - Reif, Jochen C.

AU - Weckwerth, Wolfram

AU - Liu, Xin

AU - Vigouroux, Yves

AU - Xu, Xun

AU - Mohapatra, Trilochan

AU - Rhoné, Bénédicte

AU - Cubry, Philippe

AU - Qi, Peng

AU - Wang, Hao

AU - Upadhyaya, Hari D.

PY - 2017/10/1

Y1 - 2017/10/1

N2 - Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.

AB - Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.

KW - Agriculture

KW - Base Sequence

KW - Conserved Sequence

KW - Desert Climate

KW - Genes, Plant

KW - Genetic Variation

KW - Genome, Plant

KW - Genome-Wide Association Study

KW - Hybridization, Genetic

KW - Molecular Sequence Annotation

KW - Pennisetum/genetics

KW - Quantitative Trait, Heritable

UR - http://www.scopus.com/inward/record.url?scp=85031113085&partnerID=8YFLogxK

U2 - 10.1038/nbt.3943

DO - 10.1038/nbt.3943

M3 - Article

C2 - 28922347

SN - 1087-0156

VL - 35

SP - 969

EP - 976

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 10

ER -

Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

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Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments

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