The bracteatus pineapple genome and domestication of clonally propagated crops
2019
Chen, Li-Yu | Vanburen, Robert | Paris, Margot | Zhou, Hongye | Zhang, Xingtan | Wai, Ching Man | Yan, Hansong | Chen, Shuai | Alonge, Michael | Ramakrishnan, Srividya | Liao, Zhenyang | Liu, Juan | Lin, Jishan | Yue, Jingjing | Fatima, Mahpara | Lin, Zhicong | Zhang, Jisen | Huang, Lixian | Wang, Hao | Hwa, Teh-Yang | Kao, Shu-Min | Choi, Jae Young | Sharma, Anupma | Song, Jian | Wang, Lulu | Yim, Won C. | Cushman, John C. | Paull, Robert E. | Matsumoto, Tracie | Qin, Yuan | Wu, Qingsong | Wang, Jianping | Yu, Qingyi | Wu, Jun | Zhang, Shaoling | Boches, Peter | Tung, Chih-Wei | Wang, Ming-Li | Sanewski, Garth M. | Purugganan, Michael D. | Schatz, Michael C. | Bennetzen, Jeffrey L. | Lexer, Christian | Ming, Ray | Fujian Agriculture and Forestry University (FAFU) | University of Illinois at Urbana-Champaign [Urbana] (UIUC) ; University of Illinois System | Department of Horticulture ; University of Wisconsin-Madison | Department of Biology ; Northern Arizona University [Flagstaff] | Department of Genetics ; University of Georgia [USA] | Johns Hopkins University (JHU) | National Taiwan University | New York University [New York] (NYU) ; NYU System (NYU) | Texas A&M University System | Department of agronomy ; University of Florida [Gainesville] (UF) | Department of Biochemistry and Molecular Biology ; University of Nevada [Reno] | University of Hawai‘i [Mānoa] (UHM) | USDA-ARS : Agricultural Research Service | South Subtropical Crops Research Institute, CATAS ; Partenaires INRAE | Nanjing Agricultural University (NAU) | Hawaii Agriculture Research Center ; Partenaires INRAE | Queensland Department of Agriculture and Fisheries | Department of Botany and Biodiversity Research ; Universität Wien = University of Vienna | Department of Science and Technology of Fujian Province : 2016NZ0001-1 ; National Natural Science Foundation of China : U1605212, 31628013, 31701874 ; Fuzhou Science and Technology project : 2017-N-33 ; Distinguished Young Scholars Fund in Fujian Agriculture and Forestry University : xjq201609 ; National Science Foundation (NSF) : DBI-1401572, DBI1350041 ; United States Department of Health & Human Services, National Institutes of Health (NIH) - USA : R01-HG006677 ; NSF Plant Genome grants : 0607123, 043707-01, IOS-1546218 ; Zegar Family Foundatio : A16-0051-001 ; Swiss National Science Foundation (SNSF) : CRSII3_147630
International audience
Show more [+] Less [-]English. Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a 'one-step operation'. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars 'Smooth Cayenne' and 'Queen' exhibited ancient and recent admixture, while 'Singapore Spanish' supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops.
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