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The genome sequence of segmental allotetraploid peanut Arachis hypogaea

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Title The genome sequence of segmental allotetraploid peanut Arachis hypogaea
 
Creator Bertioli, David J.
Jenkins, Jerry
Clevenger, Josh
Dudchenko, Olga
Gao, Dongying
Seijo, Guillermo
Leal-Bertioli, Soraya C. M.
Ren, Longhui
Farmer, Andrew D.
Pandey, Manish K.
Samoluk, Sergio S.
Abernathy, Brian
Agarwal, Gaurav
Ballén-Taborda, Carolina
Cameron, Connor
Campbell , Jacqueline
Chavarro, Carolina
Chitikineni, Annapurna
Chu, Ye
Dash, Sudhansu
Baidouri, Moaine El
Guo, Baozhu
Huang, Wei
Kim, Kyung Do
Korani, Walid
Lanciano, Sophie
Lui, Christopher G.
Mirouze, Marie
Moretzsohn, Márcio C.
Pham, Melanie
Shin, Jin Hee
Shirasawa, Kenta
Sinharoy, Senjuti
Sreedasyam, Avinash
Weeks, Nathan T.
Zhang, Xinyou
Zheng, Zheng
Sun, Ziqi
Froenicke, Lutz
Aiden, Erez L.
Michelmore, Richard
Varshney, Rajeev K.
Holbrook, C. Corley
Cannon, Ethalinda K. S.
Scheffler, Brian E.
Grimwood, Jane
Ozias-Akins, Peggy
Cannon, Steven B.
Jackson, Scott A.
Schmutz , Jeremy
 
Subject Genomics
Plant genetics
Arachis hypogaea
peanut
segmental allotetraploid
genome sequence
 
Description Accepted date: 28 March 2019
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.
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.
 
Date 2019-05-06T06:54:47Z
2019-05-06T06:54:47Z
2019
 
Type Article
 
Identifier Nature Genetics, 51(5): 877-884
1546-1718
http://223.31.159.10:8080/jspui/handle/123456789/947
https://www.nature.com/articles/s41588-019-0405-z
https://doi.org/10.1038/s41588-019-0405-z
 
Language en_US
 
Format application/pdf
 
Publisher Springer Nature Publishing AG