April 21, 2020  |  

The bracteatus pineapple genome and domestication of clonally propagated crops.

Authors: Chen, Li-Yu and VanBuren, Robert and Paris, Margot and Zhou, Hongye and Zhang, Xingtan and Wai, Ching Man and Yan, Hansong and Chen, Shuai and Alonge, Michael and Ramakrishnan, Srividya and Liao, Zhenyang and Liu, Juan and Lin, Jishan and Yue, Jingjing and Fatima, Mahpara and Lin, Zhicong and Zhang, Jisen and Huang, Lixian and Wang, Hao and Hwa, Teh-Yang and Kao, Shu-Min and Choi, Jae Young and Sharma, Anupma and Song, Jian and Wang, Lulu and Yim, Won C and Cushman, John C and Paull, Robert E and Matsumoto, Tracie and Qin, Yuan and Wu, Qingsong and Wang, Jianping and Yu, Qingyi and Wu, Jun and Zhang, Shaoling and Boches, Peter and Tung, Chih-Wei and Wang, Ming-Li and Coppens d'Eeckenbrugge, Geo and Sanewski, Garth M and Purugganan, Michael D and Schatz, Michael C and Bennetzen, Jeffrey L and Lexer, Christian and Ming, Ray

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.

Journal: Nature genetics
DOI: 10.1038/s41588-019-0506-8
Year: 2019

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