SunUp and Sunset genomes revealed impact of particle bombardment mediated transformation and domestication history in papaya.

Patricia Quesada-Rojas, Hansong Yan, Mahpara Fatima, Dessireé Zerpa-Catanho, Xiaodan Zhang, Zhicong Lin, Mei Yang, Nancy J Chen, Eric Mora-Newcomer, Xiaobing Zhao, Antonio Bogantes, Víctor M Jiménez, Haibao Tang, Jisen Zhang, Ming-Li Wang, Robert E Paull, Qingyi Yu, Ray Ming, Shengchen Zhang, Robert VanBuren, Juan Liu, Jingping Fang, Xingtan Zhang, Zhenyang Liao, Ching Man Wai, Xiuming Xu, Shuai Chen, Jingjing Yue, Xiaokai Ma, Yaying Ma, Hongying Yu, Jing Lin, Ping Zhou, Yongji Huang, Ban Deng, Fang Deng

Journal: Nature genetics 2022;54(5):715-724

PMID: 35551309

Full Text on Nature Publishing Group View on PubMed

Abstract

Transgenic papaya is widely publicized for controlling papaya ringspot virus. However, the impact of particle bombardment on the genome remains unknown. The transgenic SunUp and its progenitor Sunset genomes were assembled into 351.5 and 350.3 Mb in nine chromosomes, respectively. We identified a 1.64 Mb insertion containing three transgenic insertions in SunUp chromosome 5, consisting of 52 nuclear-plastid, 21 nuclear-mitochondrial and 1 nuclear genomic fragments. A 591.9 kb fragment in chromosome 5 was translocated into the 1.64 Mb insertion. We assembled a gapless 9.8 Mb hermaphrodite-specific region of the Y chromosome and its 6.0 Mb X counterpart. Resequencing 86 genomes revealed three distinct groups, validating their geographic origin and breeding history. We identified 147 selective sweeps and defined the essential role of zeta-carotene desaturase in carotenoid accumulation during domestication. Our findings elucidated the impact of particle bombardment and improved our understanding of sex chromosomes and domestication to expedite papaya improvement.

Address: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.; Department of Horticulture, Michigan State University, East Lansing, MI, USA.; Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.; College of Life Science, Fujian Normal University, Fuzhou, China.; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China.; Fruit Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China.; Institute of Oceanography, Minjiang University, Fuzhou, China.; Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA.; Estación Experimental Agrícola Fabio Baudrit Moreno, Universidad de Costa Rica, Alajuela, Costa Rica.; Estación Experimental Los Diamantes, Instituto de Innovación y Transferencia de Tecnología Agropecuaria, Guápiles, Costa Rica.; CIGRAS, Universidad de Costa Rica, San Pedro, Costa Rica.; Hawaii Agriculture Research Center, Kunia, HI, USA.; Texas A&M AgriLife Research, Texas A&M University System, Dallas, TX, USA.; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. [email protected].

DOI: 10.1038/s41588-022-01068-1

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MeSH Terms: Carica, Chromosomes, Plant, Domestication, Plant Breeding, Sex Chromosomes