The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication

Authors: ZHUANG, WEIJIAN - Fujian Agricultural & Forestry University; CHEN, HUA - Fujian Agricultural & Forestry University; YANG, MENG - Nextomics Biosciences Co, Ltd; WANG, JIANPING - University Of Florida; PANDEY, MANISH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; ZHANG, CHONG - Fujian Agricultural & Forestry University; CHANG, WEN-CHI - Cheng Kung University; ZHANG, LIANGSHENG - Fujian Agricultural & Forestry University; ZHANG, XINGTAN - Fujian Agricultural & Forestry University; TANG, RONGHUA - Guangxi Academy Of Agricultural Sciences; Guo, Baozhu; PATERSON, ANDREW - University Of Georgia; WANG, XIYIN - North China University Of Science And Technology; MING, RAY - Fujian Agricultural & Forestry University; VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/22/2019
Publication Date: 5/1/2019
Citation: Zhuang, W., Chen, H., Yang, M., Wang, J., Pandey, M.K., Zhang, C., Chang, W., Zhang, L., Zhang, X., Tang, R., Garg, V., Wang, X., Tang, H., Chow, C., Wang, J., Deng, Y., Wang, D., Khan, A.W., Yang, Q., Cai, T., Bajaj, P., Wu, K., Guo, B., Zhang, X., Li, J., Liang, F., Hu, J., Liao, B., Liu, S., Chitikineni, A., Yan, H., Zheng, Y., Shan, S., Liu, Q., Xie, D., Wang, Z., Khan, S.A., Ali, N., Zhao, C., Li, X., Luo, Z., Zhang, S., Zhuang, R., Peng, Z., Wang, S., Mamadou, G., Zhuang, Y., Zhao, Z., Yu, W., Xiong, F., Quan, W., Yuan, M., Li, Y., Zou, H., Xia, H., Zha, L., Fan, J., Yu, J., Xie, W., Yuan, J., Chen, K., Zhao, S., Chu, W., Chen, Y., Sun, P., Meng, F., Zhuo, T., Zhao, Y., Li, C., He, G., Zhao, Y, Wang, C., Kavikishor, P.B., Pan, R., Paterson, A.H., Wang, X., Ming, R., Varshney, R.K. 2019. The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication. Nature Genetics. 51:865-876. https://doi.org/10.1038/s41588-019-0402-2.
DOI: https://doi.org/10.1038/s41588-019-0402-2

Interpretive Summary: Cultivated peanut is one of the most important oil and food legume crops, grown on 25 million ha. In China, peanut accounts for over 46% of total output of all oil crops, ranking fourth after rice, wheat and corn in market value. As a nitrogen fixing plant with geocarpy, peanut can grow on arid and marginal land as a pioneer crop. The multilayered genome complexity resulting from allotetraploidy with closely related subgenomes, high content of repetitive sequences and large genome size (2.7 Gb) pose significant challenges in developing a high-quality peanut genome assembly in support of functional genomics studies and molecular marker accelerated improvement. We present here a high-quality reference genome sequence for cultivated allotetraploid peanut to facilitate understanding of genome architecture and accelerate peanut improvement. We also sequenced another 30 allotetraploid accessions of various ecotypes, 18 wild species and four synthetic tetraploids, gaining insights into peanut genome architecture, trait biology, evolution, and domestication. The peanut genome aids trait mapping such as seed features and foliar disease resistance, expediting validation and deployment in breeding.

Technical Abstract: High oil and protein content make tetraploid peanut/groundnut a leading oil and food legume. Here, we report a high-quality genome sequence for peanut variety Shitoqi, comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models. Patterns of retention/loss implicate particular gene functional groups in seed size evolution, seed oil content, disease resistance and symbiotic nitrogen fixation. The peanut B subgenome has more genes and general expression dominance – the A subgenome is surprisingly divergent from diploid A. duranensis, implying rapid changes from and/or uncertainty about the A-genome progenitor. Following tetraploidy ~59 mya doubling chromosome number, karyotype restructuring restored the original number to peanut. Resequencing of 52 diverse accessions suggests independent domestications evolving Peruvian, Valencia and Spanish peanut ecotypes. While 0.42-0.47 mya polyploidy constrains genetic variation, the peanut genome aids trait mapping such as seed features and foliar disease resistance, expediting validation and deployment in breeding. Sequences of four synthetic tetraploids illustrate opportunities to diversify the peanut gene pool.