The bracteatus pineapple genome and domestication of clonally propagated crops

Li-Yu Chen^#¹, Robert VanBuren^#^{2

3}, Margot Paris^#⁴, Hongye Zhou^#⁵, Xingtan Zhang¹, Ching Man Wai², Hansong Yan¹, Shuai Chen¹, Michael Alonge⁶, Srividya Ramakrishnan⁶, Zhenyang Liao¹, Juan Liu¹, Jishan Lin¹, Jingjing Yue¹, Mahpara Fatima¹, Zhicong Lin¹, Jisen Zhang¹, Lixian Huang¹, Hao Wang⁵, Teh-Yang Hwa⁷, Shu-Min Kao⁷, Jae Young Choi⁸, Anupma Sharma⁹, Jian Song¹⁰, Lulu Wang¹, Won C Yim¹¹, John C Cushman¹¹, Robert E Paull¹², Tracie Matsumoto¹³, Yuan Qin¹, Qingsong Wu¹⁴, Jianping Wang^{1

10}, Qingyi Yu^{1

9}, Jun Wu¹⁵, Shaoling Zhang¹⁵, Peter Boches¹³, Chih-Wei Tung⁷, Ming-Li Wang¹⁶, Geo Coppens d'Eeckenbrugge^{17

18}, Garth M Sanewski¹⁹, Michael D Purugganan⁸, Michael C Schatz⁶, Jeffrey L Bennetzen²⁰, Christian Lexer²¹, Ray Ming^{22

23}

Affiliations

¹ 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.
² Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
³ Department of Horticulture, Michigan State University, East Lansing, MI, USA.
⁴ Department of Biology, University of Fribourg, Fribourg, Switzerland.
⁵ Department of Genetics, University of Georgia, Athens, GA, USA.
⁶ Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
⁷ Department of Agronomy, National Taiwan University, Taipei, ROC.
⁸ Department of Biology, Center for Genomics and Systems Biology, New York University, NY, New York, USA.
⁹ Texas A&M AgriLife Research, Texas A&M University System, Dallas, TX, USA.
¹⁰ Department of Agronomy, University of Florida, Gainesville, FL, USA.
¹¹ Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV, USA.
¹² Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA.
¹³ USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI, USA.
¹⁴ South Subtropical Crops Research Institute, CATAS, Zhanjiang, China.
¹⁵ Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.
¹⁶ Hawaii Agriculture Research Center, Kunia, HI, USA.
¹⁷ Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR AGAP, Montpellier, France.
¹⁸ AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
¹⁹ Queensland Department of Agriculture and Fisheries, Nambour, Queensland, Australia.
²⁰ Department of Genetics, University of Georgia, Athens, GA, USA. maize@uga.edu.
²¹ Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria. christian.lexer@univie.ac.at.
²² 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.
²³ Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. rayming@illinois.edu.

^# Contributed equally.

PMID: 31570895
DOI: 10.1038/s41588-019-0506-8

The bracteatus pineapple genome and domestication of clonally propagated crops

Li-Yu Chen et al. Nat Genet. 2019 Oct.

. 2019 Oct;51(10):1549-1558.

doi: 10.1038/s41588-019-0506-8. Epub 2019 Sep 30.

Authors

Affiliations

¹ 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.
² Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
³ Department of Horticulture, Michigan State University, East Lansing, MI, USA.
⁴ Department of Biology, University of Fribourg, Fribourg, Switzerland.
⁵ Department of Genetics, University of Georgia, Athens, GA, USA.
⁶ Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
⁷ Department of Agronomy, National Taiwan University, Taipei, ROC.
⁸ Department of Biology, Center for Genomics and Systems Biology, New York University, NY, New York, USA.
⁹ Texas A&M AgriLife Research, Texas A&M University System, Dallas, TX, USA.
¹⁰ Department of Agronomy, University of Florida, Gainesville, FL, USA.
¹¹ Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV, USA.
¹² Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA.
¹³ USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI, USA.
¹⁴ South Subtropical Crops Research Institute, CATAS, Zhanjiang, China.
¹⁵ Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.
¹⁶ Hawaii Agriculture Research Center, Kunia, HI, USA.
¹⁷ Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR AGAP, Montpellier, France.
¹⁸ AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
¹⁹ Queensland Department of Agriculture and Fisheries, Nambour, Queensland, Australia.
²⁰ Department of Genetics, University of Georgia, Athens, GA, USA. maize@uga.edu.
²¹ Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria. christian.lexer@univie.ac.at.
²² 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.
²³ Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. rayming@illinois.edu.

^# Contributed equally.

PMID: 31570895
DOI: 10.1038/s41588-019-0506-8

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 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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References

1. Zohary, D. Unconscious selection and the evolution of domesticated plants. Econ. Bot. 58, 5–10 (2004). - DOI
1. Bertoni, M. S. Contributions à l'étude Botanique des Plantes Cultivées (Ex Sylvis. Puerto Bertoni, Alto Parana. PY, 1919).
1. Byers, D. S. Prehistory of the Tehuacan Valley (Univ. of Texas Press, 1967).
1. Coppens d’Eeckenbrugge, G. & Duval, M.-F. The domestication of pineapple: context and hypotheses. Pineapple News 16, 15–27 (2009).
1. Coppens d’Eeckenbrugge, G., Uriza Avila, D. E., Rebolledo Martínez, A. & Rebolledo Martínez, L. The Cascajal Block: another testimony of the antiquity of pineapple in Mexico? Pineapple News, 18, 47–48 (2011).

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The bracteatus pineapple genome and domestication of clonally propagated crops

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The bracteatus pineapple genome and domestication of clonally propagated crops

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Affiliations

Abstract

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