Skip to main content
ARS Home » Pacific West Area » Hilo, Hawaii » Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center » Tropical Plant Genetic Resources and Disease Research » Research » Publications at this Location » Publication #368526
Research Project: Management, Characterization, and Evaluation of Pacific Tropical and Subtropical Fruit and Nut Genetic Resources and Associated Information

Location: Tropical Plant Genetic Resources and Disease Research

Title: The bracteatus pineapple genome and domestication of clonally propagated crops

Author
item LI-YU, CHEN - University Of Illinois
item VANBUREN, ROBERT - University Of Illinois
item PARIS, MARGOT - University Of Fribourg
item ZHOU, HONGYE - University Of Georgia
item ZHANG, XINGTAN - University Of Illinois
item WAI, CHING MAN - University Of Illinois
item YAN, HANSONG - University Of Illinois
item CHEN, SHUAI - University Of Illinois
item ALONGE, MICHAEL - Johns Hopkins University
item RAMAKRISHNAN, SRIVIDYA - Johns Hopkins University
item LIAO, ZHENYANG - University Of Illinois
item LIU, JUAN - University Of Illinois
item LIN, JISHAN - University Of Illinois
item YUE, JINGJING - University Of Illinois
item FATIMA, MAHPARA - University Of Illinois
item LIN, ZHICONG - University Of Illinois
item ZHANG, JISEN - University Of Illinois
item HUANG, LIXIAN - University Of Illinois
item WANG, HAO - University Of Georgia
item HWA, TEH-YANG - National Taiwan University
item KAO, SHU-MIN - National Taiwan University
item CHOI, JAE - New York University
item SHARMA, ANUPMA - Texas A&M University
item SONG, JIAN - University Of Florida
item WANG, LULU - University Of Illinois
item YIM, WON - University Of Nevada
item CUSHMAN, JOHN - University Of Nevada
item PAULL, ROBERT - University Of Hawaii
item Matsumoto Brower, Tracie
item QIN, YUAN - University Of Illinois
item WU, QINGSONG - Chinese Academy Of Agricultural Sciences
item WANG, JIANPING - University Of Illinois
item YU, QINGYI - University Of Illinois
item WU, JUN - Nanjing Agricultural University
item ZHANG, SHAOLING - Nanjing Agricultural University
item BOCHES, PETER - Retired ARS Employee
item TUNG, CHIH-WEI - National Taiwan University
item WANG, MING-LI - Hawaii Agricultural Research Center
item COPPENSD'EECKENBRUGE, GEO - University Of Montpellier
item SANEWSKI, GARTH - Queensland University - Australia
item PURUGGANAN, MICHAEL - New York University
item SCHATZ, MICHAEL - Texas A&M Agrilife
item BENNETZEN, JEFFREY - University Of Georgia
item LEXER, CHRISTIAN - University Of Vienna
item MING, RAY - University Of Illinois

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/28/2019
Publication Date: N/A
Citation: N/A

Interpretive Summary: Domestically grown plants can be produced either sexually through seed propagation or asexually through cuttings, grafting, air layering, divisions, or tissue culture. Sexually reproducing species undergo hundreds to thousands of generations of recombination during domestication which can be tracked in the plants genome. In contrast, domestication of clonally propagated crops depends on both vegetative and sexual reproduction. It can even be a one-step operation, where selection is completed once a clone is selected. Using pineapple as a model we sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. We compared the genome of Ananas comosus var. bracteatus CB5 with other pineapple cultivars for genomic traits responsible for fiber production, color formation, sugar accumulation and fruit maturation. Pineapple cultivars ‘Smooth Cayenne’ and ‘Queen’ exhibited ancient and recent admixtures, while ‘Singapore Spanish’ represents a one-step operation in the domestication. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops.

Technical Abstract: 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 24 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.