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; Peng Qi; He Zhang; Yusheng Zhao; Xiyin Wang; Abhishek Rathore; Rakesh K. Srivastava; Annapurna Chitikineni; Guangyi Fan; Prasad Bajaj; Somashekhar Punnuri; S. K. Gupta; Hao Wang; Yong Jiang; Marie Couderc; 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 Ardo Kane; Joann A. Conner; Arindam Ghatak; Palak Chaturvedi; Sabarinath Subramaniam; Om Parkash Yadav; Cécile Berthouly-Salazar; Falalou Hamidou; Jianping Wang; Xinming Liang; Jérémy Clotault; Hari D. Upadhyaya; Philippe Cubry; Bénédicte Rhoné; Mame Codou Gueye; Ramanjulu Sunkar; Christian Dupuy; Francesca Sparvoli; Shifeng Cheng; R. S. Mahala; Bharat Singh; Rattan S. 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; Trilochan Mohapatra; Wolfram Weckwerth; Jochen C. Reif; Xin Liu; Yves Vigouroux; Xun Xu

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, Peng Qi, He Zhang, Yusheng Zhao, Xiyin Wang, Abhishek Rathore, Rakesh K. Srivastava, Annapurna Chitikineni, Guangyi Fan, Prasad Bajaj, Somashekhar Punnuri, S. K. Gupta, Hao Wang, Yong Jiang, Marie Couderc, Mohan A.V.S.K. KattaDev R. Paudel, K. D. Mungra, Wenbin Chen, Karen R. Harris-Shultz, Vanika Garg, Neetin Desai, Dadakhalandar Doddamani, Ndjido Ardo Kane, Joann A. Conner, Arindam Ghatak, Palak Chaturvedi, Sabarinath Subramaniam, Om Parkash Yadav, Cécile Berthouly-Salazar, Falalou Hamidou, Jianping Wang, Xinming Liang, Jérémy Clotault, Hari D. Upadhyaya, Philippe Cubry, Bénédicte Rhoné, Mame Codou Gueye, Ramanjulu Sunkar, Christian Dupuy, Francesca Sparvoli, Shifeng Cheng, R. S. Mahala, Bharat Singh, Rattan S. 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, Trilochan Mohapatra, Wolfram Weckwerth, Jochen C. Reif, Xin Liu, Yves Vigouroux, Xun Xu

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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 â 1/41.79 Gb draft whole genome sequence of reference genotype Tift 23D 2 B 1-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 (US)
Pages (from-to)	969-976
Number of pages	8
Journal	Nature biotechnology
Volume	35
Issue number	10
DOIs	https://doi.org/10.1038/nbt.3943
State	Published - Oct 1 2017

ASJC Scopus subject areas

Applied Microbiology and Biotechnology
Bioengineering
Molecular Medicine
Biotechnology
Biomedical Engineering

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10.1038/nbt.3943

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Varshney, R. K., Shi, C., Thudi, M., Mariac, C., Wallace, J., Qi, P., Zhang, H., Zhao, Y., Wang, X., Rathore, A., Srivastava, R. K., Chitikineni, A., Fan, G., Bajaj, P., Punnuri, S., Gupta, S. K., Wang, H., Jiang, Y., Couderc, M., ... Xu, X. (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

Varshney, RK, Shi, C, Thudi, M, Mariac, C, Wallace, J, Qi, P, Zhang, H, Zhao, Y, Wang, X, Rathore, A, Srivastava, RK, Chitikineni, A, Fan, G, Bajaj, P, Punnuri, S, Gupta, SK, Wang, H, Jiang, Y, Couderc, M, Katta, MAVSK, Paudel, DR, Mungra, KD, Chen, W, Harris-Shultz, KR, Garg, V, Desai, N, Doddamani, D, Kane, NA, Conner, JA, Ghatak, A, Chaturvedi, P, Subramaniam, S, Yadav, OP, Berthouly-Salazar, C, Hamidou, F, Wang, J, Liang, X, Clotault, J, Upadhyaya, HD, Cubry, P, Rhoné, B, Gueye, MC, Sunkar, R, Dupuy, C, Sparvoli, F, Cheng, S, Mahala, RS, Singh, B, Yadav, RS, Lyons, E, Datta, SK, Tom Hash, C, Devos, KM, Buckler, E, Bennetzen, JL, Paterson, AH, Ozias-Akins, P, Grando, S, Wang, J, Mohapatra, T, Weckwerth, W, Reif, JC, Liu, X, Vigouroux, Y & Xu, X 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

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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 {\^a} 1/41.79 Gb draft whole genome sequence of reference genotype Tift 23D 2 B 1-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.",

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

year = "2017",

month = oct,

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doi = "10.1038/nbt.3943",

language = "English (US)",

volume = "35",

pages = "969--976",

journal = "Nature biotechnology",

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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 - Qi, Peng

AU - Zhang, He

AU - Zhao, Yusheng

AU - Wang, Xiyin

AU - Rathore, Abhishek

AU - Srivastava, Rakesh K.

AU - Chitikineni, Annapurna

AU - Fan, Guangyi

AU - Bajaj, Prasad

AU - Punnuri, Somashekhar

AU - Gupta, S. K.

AU - Wang, Hao

AU - Jiang, Yong

AU - Couderc, Marie

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

AU - Paudel, Dev R.

AU - Mungra, K. D.

AU - Chen, Wenbin

AU - Harris-Shultz, Karen R.

AU - Garg, Vanika

AU - Desai, Neetin

AU - Doddamani, Dadakhalandar

AU - Kane, Ndjido Ardo

AU - Conner, Joann A.

AU - Ghatak, Arindam

AU - Chaturvedi, Palak

AU - Subramaniam, Sabarinath

AU - Yadav, Om Parkash

AU - Berthouly-Salazar, Cécile

AU - Hamidou, Falalou

AU - Wang, Jianping

AU - Liang, Xinming

AU - Clotault, Jérémy

AU - Upadhyaya, Hari D.

AU - Cubry, Philippe

AU - Rhoné, Bénédicte

AU - Gueye, Mame Codou

AU - Sunkar, Ramanjulu

AU - Dupuy, Christian

AU - Sparvoli, Francesca

AU - Cheng, Shifeng

AU - Mahala, R. S.

AU - Singh, Bharat

AU - Yadav, Rattan S.

AU - Lyons, Eric

AU - Datta, Swapan K.

AU - Tom Hash, C.

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 - Mohapatra, Trilochan

AU - Weckwerth, Wolfram

AU - Reif, Jochen C.

AU - Liu, Xin

AU - Vigouroux, Yves

AU - Xu, Xun

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 â 1/41.79 Gb draft whole genome sequence of reference genotype Tift 23D 2 B 1-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 â 1/41.79 Gb draft whole genome sequence of reference genotype Tift 23D 2 B 1-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.

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JO - Nature biotechnology

JF - Nature biotechnology

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ER -

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

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