The genome sequence of segmental allotetraploid peanut Arachis hypogaea

Bertioli, D J and Jenkins, J and Clevenger, J and Dudchenko, O and Gao, D and Seijo, G and Leal-Bertioli, S C M and Ren, L and Farmer, A D and Pandey, M K and Samoluk, S S and Abernathy, B and Agarwal, G and Ballén-Taborda, C and Cameron, C and Campbell, J and Chavarro, C and Chitikineni, A and Chu, Y and Dash, S and El Baidouri, M and Guo, B and Huang, W and Kim, K D and Korani, W and Lanciano, S and Lui, C G and Mirouze, M and Moretzsohn, M C and Pham, M and Shin, J H and Shirasawa, K and Sinharoy, S and Sreedasyam, A and Weeks, N and Zhang, X and Zheng, Z and Sun, Z and Froenicke, L and Aiden, E L and Michelmore, R and Varshney, R K and Holbrook, C C and Cannon, E K S and Scheffler, B E and Grimwood, J and Ozias-Akins, P and Cannon, S B and Jackson, S A and Schmutz, J (2019) The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nature Genetics (TSI), 51 (5). pp. 877-884. ISSN 1061-4036

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Abstract

Like many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has evolved through mobile-element activity, deletions and by the flow of genetic information between corresponding ancestral chromosomes (that is, homeologous recombination). Uniformity of patterns of homeologous recombination at the ends of chromosomes favors a single origin for cultivated peanut and its wild counterpart A. monticola. However, through much of the genome, homeologous recombination has created diversity. Using new polyploid hybrids made from the ancestral species, we show how this can generate phenotypic changes such as spontaneous changes in the color of the flowers. We suggest that diversity generated by these genetic mechanisms helped to favor the domestication of the polyploid A. hypogaea over other diploid Arachis species cultivated by humans.

Item Type:	Article
Divisions:	Research Program : Genetic Gains
CRP:	CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC)
Uncontrolled Keywords:	genome sequence, groundnut, genetics, genomics
Subjects:	Others > Genetic Engineering Mandate crops > Groundnut Others > Genetics and Genomics
Depositing User:	Mr Ramesh K
Date Deposited:	23 Jul 2019 08:43
Last Modified:	26 Aug 2019 05:14
URI:	http://oar.icrisat.org/id/eprint/11183
Official URL:	https://doi.org/10.1038/s41588-019-0405-z
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	We thank G. Birdsong, V. Nwosu, J. Elder, D. Smyth, H. Valentine, F. Luo, D. Hoisington, H. Shapiro, D. Ward, S. Knapp, R. Wilson and S. Brown for their support of, and work for, the Peanut Genome Initiative. Major financial contributors for this work were from Mars-Wrigley Confectionary, US peanut sheller associations, the National Peanut Board and other industry groups. A full list can be downloaded at https://peanutbase.org/IPGI. D.J.B. thanks the Georgia Peanut Commission and the Georgia Research Alliance for support. The genome sequencing was funded from grant 04-852-14 from The Peanut Foundation to J.S. and B.E.S., characterization of diverse genotypes was funded from grant 04-805-17 to D.J.B. The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under contract number DE-AC02-05CH11231. The work done at the DNA Technologies and Expression Analysis Cores at the UC Davis Genome Center was supported by NIH Shared Instrumentation Grant 1S10OD010786-01. We thank the US National Science Foundation for support from grant number 1339194 to S.A.J. This research was funded in part by the US Department of Agriculture Agricultural Research Service, projects 5030-21000-069-00-D, 6048-21000-028-00-D, 6048-21000-029-00-D, 6066-21310-005-00-D and NIFA Award no. 2018-67013-28139. We also grateful for funding granted to X.Z. and Z.Z. from the Henan Province Open Cooperation Project of Science and Technology (172106000007), the Henan Science and Technology Major Project of the Ministry of Science and Technology of China (161100111000), the China Agriculture Research System (CARS-13), and Henan Agriculture Research System (S2012-5). We thank the Indian Council of Agricultural Research, National Agricultural Science Funds, Government of India and the CGIAR Research Program on Grain Legumes and Dryland Cereals for grants to R.K.V. and M.K.P. ICRISAT is a member of the CGIAR. S.S. was supported by the Ramalingwaswami Re-entry Grant (BT/RLF/Re-entry/41/2013) from the Ministry of Science and Technology, India. We thank D. Kudrna at the University of Arizona for high-molecular-weight DNA extractions, S. Simpson of USDA ARS GBRU for valuable support with PacBio sequencing and the USDA National Plant Germplasm System for Arachis seeds.
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