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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #358197

Research Project: Improving Crop Efficiency Using Genomic Diversity and Computational Modeling

Location: Plant, Soil and Nutrition Research

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

Author
item Varshney, Rajeev - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item Shi, Chengcheng - Bgi Shenzhen
item Thudi, Mahendar - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item Mariac, Cedric - Institute For Research And Development (IRD)
item Wallace, Jason - University Of Georgia
item Qi, Peng - University Of Georgia
item Zhang, He - Bgi Shenzhen
item Zhao, Yusheng - Leibniz Institute Of Plant Genetics And Crop Plant Research
item Wang, Xiyin - University Of Georgia
item Rathore, Abhishek - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item Srivastava, Rakesh K. - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item Chitikineni, Annapurna - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item Fan, Guangyi - Bgi Shenzhen
item Bajaj, Prasad - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item Punnuri, Somashekhar - Fort Valley State University
item Gupta, Sk - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item Wang, Hao - Cornell University - New York
item Jiang, Yong - Leibniz Institute Of Plant Genetics And Crop Plant Research
item Couderc, Marie - Institute For Research And Development In Agri-Environment(IRDA)
item Katta, Mohan Avsk - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item Paudel, Dev R - University Of Florida
item Mungra, K D - Junagadh Agricultural University
item Chen, Wenbin - Bgi Shenzhen
item Harris-shultz, Karen
item Garg, Vanika - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item Desai, Neetin - University Of Vienna
item Doddamani, Dadakhalandar - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item Kane, Ndjido Ardo - Institut Senegalais De Recherches Agricoles
item Conner, Joann A - University Of Georgia
item Ghatak, Arindam - University Of Vienna
item Chaturvedi, Palak - University Of Vienna
item Subramaniam, Sabarinath - University Of Arizona
item Yadav, Om Parkash - Central Arid Zone Research Institute
item Berthouly-salazar, Cécile - Institute For Research And Development In Agri-Environment(IRDA)
item Hamidou, Falalou - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - Nigeria
item Wang, Jianping - University Of Florida
item Liang, Xinming - Bgi Shenzhen
item Clotault, Jérémy - Institute For Research And Development In Agri-Environment(IRDA)
item Upadhyaya, Hari D - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item Cubry, Philippe - Fort Valley State University
item Rhoné, Bénédicte - Institute For Research And Development In Agri-Environment(IRDA)
item Gueye, Mame Codou - Institut Senegalais De Recherches Agricoles
item Sunkar, Ramanjulu - Oklahoma State University
item Dupuy, Christian - African Center For Health
item Sparvoli, Francesca - Consiglio Nazionale Delle Ricerche
item Cheng, Shifeng - Bgi Shenzhen
item Mahala, R S - Pioneer Hi-Bred, Inc
item Singh, Bharat - Fort Valley State University
item Yadav, Rattan S - Aberystwyth University
item Lyons, Eric - University Of Arizona
item Datta, Swapan K - Jadavpur University
item Hash, C Tom - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - Nigeria
item Devos, Katrien M - University Of Georgia
item Buckler, Edward - Ed
item Bennetzen, Jeffrey L - University Of Georgia
item Paterson, Andrew - University Of Georgia
item Ozias-akins, Peggy - University Of Georgia
item Grando, Stefania - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item Wang, Jun - Bgi Shenzhen
item Mohapatra, Trilochan - Indian Council Of Agricultural Research (ICAR)
item Weckwerth, Wolfram - University Of Vienna
item Reif, Jochen - Leibniz Institute Of Plant Genetics And Crop Plant Research
item Liu, Xin - University Of Georgia
item Vigouroux, Yves - Institute For Research And Development In Agri-Environment(IRDA)
item Xu, Xun - Bgi Shenzhen

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/17/2017
Publication Date: 9/18/2017
Citation: Varshney, R., Shi, C., Thudi, M., Mariac, C., Wallace, J., Qi, P., Zhang, H., Zhao, Y., Wang, X., Rathore, A., Srivastava, R., Chitikineni, A., Fan, G., Bajaj, P., Punnuri, S., Gupta, S., Wang, H., Jiang, Y., Couderc, M., Katta, M., Paudel, D., Mungra, K., Chen, W., Harris-Shultz, K.R., Garg, V., Desai, N., Doddamani, D., Kane, N., Conner, J., Ghatak, A., Chaturvedi, P., Subramaniam, S., Yadav, O., Berthouly-Salazar, C., Hamidou, F., Wang, J., Liang, X., Clotault, J., Upadhyaya, H., Cubry, P., Rhoné, B., Gueye, M., Sunkar, R., Dupuy, C., Sparvoli, F., Cheng, S., Mahala, R., Singh, B., Yadav, R., Lyons, E., Datta, S., Hash, C., Devos, K., Buckler IV, E.S., Bennetzen, J., Paterson, A.H., Ozias-Akins, P., Grando, S., Wang, J., Mohapatra, T., Weckwerth, W., Reif, J.C., Liu, X., Vigouroux, Y., Xu, X. 2017. Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nature Communications. 35(10):969.

Interpretive Summary: With global temperatures on the rise, something needs to be done to ensure the food security for the global population. Because of this crisis, there could be serious consequences for agriculture in the future. Consequently we need crops that are adaptable to these predicted environmental changes. Pearl millet has excellent photosynthetic efficiency as well as biomass production potential and has been found to be highly nutritious. While other crops may fail to grow or survive in harsh conditions, pearl millet is well suited for growing in severe conditions. Sadly the crop is grown in a marginal production environment and with minimal use of commercial inputs making the yield considerably low. Due to the limited genomic tools available, improvement in pearl millet crop yields has been slow. To increase understanding of the pearl millet population structure, genetic diversity, and domestication, we sequenced the whole genome of the reference genotype. We then carried out a genome-wide association study (GWAS) to predict yield-associated traits in both irrigated and drought conditions. We hope with this research to accelerate breeding and enhancement for genetic gains in pearl millet.

Technical 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.