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The bracteatus pineapple genome and domestication of clonally propagated crops.

  • Chen LY FAFU and UIUC-SIB Joint 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.
  • VanBuren R Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Paris M Department of Biology, University of Fribourg, Fribourg, Switzerland.
  • Zhou H Department of Genetics, University of Georgia, Athens, GA, USA.
  • Zhang X FAFU and UIUC-SIB Joint 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.
  • Wai CM Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Yan H FAFU and UIUC-SIB Joint 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.
  • Chen S FAFU and UIUC-SIB Joint 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.
  • Alonge M Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
  • Ramakrishnan S Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
  • Liao Z FAFU and UIUC-SIB Joint 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.
  • Liu J FAFU and UIUC-SIB Joint 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.
  • Lin J FAFU and UIUC-SIB Joint 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.
  • Yue J FAFU and UIUC-SIB Joint 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.
  • Fatima M FAFU and UIUC-SIB Joint 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.
  • Lin Z FAFU and UIUC-SIB Joint 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.
  • Zhang J FAFU and UIUC-SIB Joint 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.
  • Huang L FAFU and UIUC-SIB Joint 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.
  • Wang H Department of Genetics, University of Georgia, Athens, GA, USA.
  • Hwa TY Department of Agronomy, National Taiwan University, Taipei, ROC.
  • Kao SM Department of Agronomy, National Taiwan University, Taipei, ROC.
  • Choi JY Department of Biology, Center for Genomics and Systems Biology, New York University, NY, New York, USA.
  • Sharma A Texas A&M AgriLife Research, Texas A&M University System, Dallas, TX, USA.
  • Song J Department of Agronomy, University of Florida, Gainesville, FL, USA.
  • Wang L FAFU and UIUC-SIB Joint 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.
  • Yim WC Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV, USA.
  • Cushman JC Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV, USA.
  • Paull RE Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA.
  • Matsumoto T USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI, USA.
  • Qin Y FAFU and UIUC-SIB Joint 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.
  • Wu Q South Subtropical Crops Research Institute, CATAS, Zhanjiang, China.
  • Wang J FAFU and UIUC-SIB Joint 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.
  • Yu Q FAFU and UIUC-SIB Joint 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.
  • Wu J Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.
  • Zhang S Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.
  • Boches P USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI, USA.
  • Tung CW Department of Agronomy, National Taiwan University, Taipei, ROC.
  • Wang ML Hawaii Agriculture Research Center, Kunia, HI, USA.
  • Coppens d'Eeckenbrugge G Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR AGAP, Montpellier, France.
  • Sanewski GM Queensland Department of Agriculture and Fisheries, Nambour, Queensland, Australia.
  • Purugganan MD Department of Biology, Center for Genomics and Systems Biology, New York University, NY, New York, USA.
  • Schatz MC Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
  • Bennetzen JL Department of Genetics, University of Georgia, Athens, GA, USA. maize@uga.edu.
  • Lexer C Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria. christian.lexer@univie.ac.at.
  • Ming R FAFU and UIUC-SIB Joint 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. rayming@illinois.edu.
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  • 2019-10-02
Published in:
  • Nature genetics. - 2019
Ananas
Bromelains
Crops, Agricultural
Domestication
Gene Expression Regulation, Plant
Genome, Plant
Phenotype
Plant Proteins
Plants, Genetically Modified
Population Dynamics
Quantitative Trait, Heritable
Sugars
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.
Language
  • English
Open access status
hybrid
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Persistent URL
https://folia.unifr.ch/global/documents/242280
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