The bracteatus pineapple genome and domestication of clonally propagated crops

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, Coppens D'Eeckenbrugge Geo, Sanewski Garth M., Purugganan Michael D., Schatz Michael C., Bennetzen Jeffrey L., Lexer Christian, Ming Ray. 2019. The bracteatus pineapple genome and domestication of clonally propagated crops. Nature Genetics, 51 (10) : 1549-1558.

Url - jeu de données - Entrepôt autre : https://www.ebi.ac.uk/ena/data/view/PRJEB33121

Quartile : Outlier, Sujet : GENETICS & HEREDITY

Liste HCERES des revues (en SHS) : oui

Thème(s) HCERES des revues (en SHS) : Psychologie-éthologie-ergonomie

Résumé : 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.

Mots-clés Agrovoc : Ananas comosus, génome, ressource génétique végétale, domestication des plantes, multiplication végétative

Mots-clés géographiques Agrovoc : Amérique du Sud, Amérique latine

Mots-clés complémentaires : Filière, Ananas bracteatus

Mots-clés libres : Ananas, Domestication, Ressources génétiques, Propagation végétative

Classification Agris : F30 - Génétique et amélioration des plantes
F02 - Multiplication végétative des plantes

Champ stratégique Cirad : CTS 1 (2019-) - Biodiversité

Auteurs et affiliations

• Chen Li-Yu, Fujian Agriculture and Forestry University (CHN)
• VanBuren Robert, University of Illinois (USA)
• Paris Margot, Université de Fribourg (CHE)
• Zhou Hongye, University of Georgia (USA)
• Zhang Xingtan, Fujian Agriculture and Forestry University (CHN)
• Wai Ching Man, University of Illinois (USA)
• Yan Hansong, Fujian Agriculture and Forestry University (CHN)
• Chen Shuai, Fujian Agriculture and Forestry University (CHN)
• Alonge Michael, Johns Hopkins University (USA)
• Ramakrishnan Srividya, Johns Hopkins University (USA)
• Liao Zhenyang, Fujian Agriculture and Forestry University (CHN)
• Liu Juan, Fujian Agriculture and Forestry University (CHN)
• Lin Jishan, Fujian Agriculture and Forestry University (CHN)
• Yue Jingjing, Fujian Agriculture and Forestry University (CHN)
• Fatima Mahpara, Fujian Agriculture and Forestry University (CHN)
• Lin Zhicong, Fujian Agriculture and Forestry University (CHN)
• Zhang Jisen, Fujian Agriculture and Forestry University (CHN)
• Huang Lixian, Fujian Agriculture and Forestry University (CHN)
• Wang Hao, University of Georgia (USA)
• Hwa Teh-Yang, National Taiwan University (TWN)
• Kao Shu-Min, National Taiwan University (TWN)
• Choi Jae Young, State University of New York (USA)
• Sharma Anupma, Texas A & M University (USA)
• Song Jian, University of Florida (USA)
• Wang Lulu, Fujian Agriculture and Forestry University (CHN)
• Yim Won C., University of Nevada (USA)
• Cushman John C., University of Nevada (USA)
• Paull Robert E., University of Hawaii (USA)
• Matsumoto Tracie, USDA (USA)
• Qin Yuan, Fujian Agriculture and Forestry University (CHN)
• Wu Qingsong, CATAS (CHN)
• Wang Jianping, Fujian Agriculture and Forestry University (CHN)
• Yu Qingyi, Texas A & M University (USA)
• Wu Jun, Nanjing Agricultural University (CHN)
• Zhang Shaoling, Nanjing Agricultural University (CHN)
• Boches Peter, USDA (USA)
• Tung Chih-Wei, National Taiwan University (TWN)
• Wang Ming-Li, HARC (USA)
• Coppens D'Eeckenbrugge Geo, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-1970-0627
• Sanewski Garth M., Queensland Department of Agriculture and Fisheries (AUS)
• Purugganan Michael D., State University of New York (USA)
• Schatz Michael C., Johns Hopkins University (USA)
• Bennetzen Jeffrey L., University of Georgia (USA) - auteur correspondant
• Lexer Christian, Universität Wien (AUT) - auteur correspondant
• Ming Ray, Fujian Agriculture and Forestry University (CHN) - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/593577/)

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