Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars

Guibing Hu; Junting Feng; Xu Xiang; Jiabao Wang; Jarkko Salojarvi; Chengming Liu; Zhenxian Wu; Jisen Zhang; Xinming Liang; Zide Jiang; Wei Liu; Liangxi Ou; Jiawei Li; Guangyi Fan; Yingxiao Mai; Chengjie Chen; Xingtan Zhang; Jiakun Zheng; Yanqing Zhang; Hongxiang Peng; Lixian Yao; Ching Man Wai; Xinping Luo; Jiaxin Fu; Haibao Tang; Tianying Lan; Biao Lai; Jinhua Sun; Yongzan Wei; Huanling Li; Jiezhen Chen; Xuming Huang; Qian Yan; Xin Liu; Leah K. McHale; William Rolling; Romain Guyot; David Sankoff; Chunfang Zheng; Victor A. Albert; Ray Ming; Houbin Chen; Rui Xia; Jianguo Li

doi:10.1038/s41588-021-00971-3

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Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars

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Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars

Guibing Hu, Junting Feng, Xu Xiang, Jiabao Wang, Jarkko Salojarvi, Chengming Liu, Zhenxian Wu, Jisen Zhang, Xinming Liang, Zide Jiang, …

Nature genetics, Vol.54(1), pp.73-83

01/01/2022

DOI: https://doi.org/10.1038/s41588-021-00971-3

PMID: 34980919

Résumé

Genetics & Heredity

Life Sciences & Biomedicine

Science & Technology

Lychee is an exotic tropical fruit with a distinct flavor. The genome of cultivar 'Feizixiao' was assembled into 15 pseudochromosomes, totaling similar to 470 Mb. High heterozygosity (2.27%) resulted in two complete haplotypic assemblies. A total of 13,517 allelic genes (42.4%) were differentially expressed in diverse tissues. Analyses of 72 resequenced lychee accessions revealed two independent domestication events. The extremely early maturing cultivars preferentially aligned to one haplotype were domesticated from a wild population in Yunnan, whereas the late-maturing cultivars that mapped mostly to the second haplo-type were domesticated independently from a wild population in Hainan. Early maturing cultivars were probably developed in Guangdong via hybridization between extremely early maturing cultivar and late-maturing cultivar individuals. Variable deletions of a 3.7 kb region encompassed by a pair of CONSTANS-like genes probably regulate fruit maturation differences among lychee cultivars. These genomic resources provide insights into the natural history of lychee domestication and will accelerate the improvement of lychee and related crops.

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Titre: Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars
Créateurs - sans rôle: Guibing Hu - South China Agr Univ, Coll Hort,Guangdong Litchi Engn Res Ctr, Minist Agr & Rural Affairs,State Key Lab Conserva, Guangdong Lab Lingnan Modern Agr,Key Lab Biol & G, Guangzhou, Peoples R China
Junting Feng - South China Agr Univ, Coll Hort,Guangdong Litchi Engn Res Ctr, Minist Agr & Rural Affairs,State Key Lab Conserva, Guangdong Lab Lingnan Modern Agr,Key Lab Biol & G, Guangzhou, Peoples R China
Xu Xiang - Guangdong Acad Agr Sci, Guangdong Prov Key Lab Trop & Subtrop Fruit Tree, Minist Agr & Rural Affairs, Inst Fruit Tree Res,Key Lab South Subtrop Fruit B, Guangzhou, Peoples R China
Jiabao Wang - Chinese Acad Trop Agr Sci, Environm & Plant Protect Inst, Minist Agr & Rural Affairs, Danzhou Sci Observing & Expt Stn Agroenvironm, Haikou, Hainan, Peoples R China
Jarkko Salojarvi - Nanyang Technol Univ, Sch Biol Sci, Singapore, Singapore
Chengming Liu - South China Agr Univ, Coll Hort,Guangdong Litchi Engn Res Ctr, Minist Agr & Rural Affairs,State Key Lab Conserva, Guangdong Lab Lingnan Modern Agr,Key Lab Biol & G, Guangzhou, Peoples R China
Zhenxian Wu - South China Agr Univ, Coll Hort,Guangdong Litchi Engn Res Ctr, Minist Agr & Rural Affairs,State Key Lab Conserva, Guangdong Lab Lingnan Modern Agr,Key Lab Biol & G, Guangzhou, Peoples R China
Jisen Zhang - Fujian Agr & Forestry Univ, Ctr Genom & Biotechnol, Haixia Inst Sci & Technol, Fuzhou, Peoples R China
Xinming Liang - BGI Shenzhen, Shenzhen, Guangdong, Peoples R China
Zide Jiang - South China Agr Univ, Coll Plant Protect, Guangdong Key Lab Microbial Signals & Dis Control, Guangzhou, Peoples R China
Wei Liu - Guangdong Acad Agr Sci, Guangdong Prov Key Lab Trop & Subtrop Fruit Tree, Minist Agr & Rural Affairs, Inst Fruit Tree Res,Key Lab South Subtrop Fruit B, Guangzhou, Peoples R China
Liangxi Ou - Guangdong Acad Agr Sci, Guangdong Prov Key Lab Trop & Subtrop Fruit Tree, Minist Agr & Rural Affairs, Inst Fruit Tree Res,Key Lab South Subtrop Fruit B, Guangzhou, Peoples R China
Jiawei Li - South China Agr Univ, Coll Hort,Guangdong Litchi Engn Res Ctr, Minist Agr & Rural Affairs,State Key Lab Conserva, Guangdong Lab Lingnan Modern Agr,Key Lab Biol & G, Guangzhou, Peoples R China
Guangyi Fan - BGI Shenzhen, Shenzhen, Guangdong, Peoples R China
Yingxiao Mai - South China Agr Univ, Coll Hort,Guangdong Litchi Engn Res Ctr, Minist Agr & Rural Affairs,State Key Lab Conserva, Guangdong Lab Lingnan Modern Agr,Key Lab Biol & G, Guangzhou, Peoples R China
Chengjie Chen - South China Agr Univ, Coll Hort,Guangdong Litchi Engn Res Ctr, Minist Agr & Rural Affairs,State Key Lab Conserva, Guangdong Lab Lingnan Modern Agr,Key Lab Biol & G, Guangzhou, Peoples R China
Xingtan Zhang - Fujian Agr & Forestry Univ, Ctr Genom & Biotechnol, Haixia Inst Sci & Technol, Fuzhou, Peoples R China
Jiakun Zheng - South China Agr Univ, Coll Hort,Guangdong Litchi Engn Res Ctr, Minist Agr & Rural Affairs,State Key Lab Conserva, Guangdong Lab Lingnan Modern Agr,Key Lab Biol & G, Guangzhou, Peoples R China
Yanqing Zhang - South China Agr Univ, Coll Hort,Guangdong Litchi Engn Res Ctr, Minist Agr & Rural Affairs,State Key Lab Conserva, Guangdong Lab Lingnan Modern Agr,Key Lab Biol & G, Guangzhou, Peoples R China
Hongxiang Peng - Guangxi Acad Agr Sci, Hort Res Inst, Nanning, Peoples R China
Lixian Yao - South China Agr Univ, Coll Nat Resources & Environm, Guangzhou, Peoples R China
Ching Man Wai - Univ Illinois, Dept Plant Biol, Urbana, IL 61801 USA
Xinping Luo - Yunnan Acad Agr Sci, Inst Trop & Subtrop Cash Crops, Baoshan, Peoples R China
Jiaxin Fu - South China Agr Univ, Coll Hort,Guangdong Litchi Engn Res Ctr, Minist Agr & Rural Affairs,State Key Lab Conserva, Guangdong Lab Lingnan Modern Agr,Key Lab Biol & G, Guangzhou, Peoples R China
Haibao Tang - Fujian Agr & Forestry Univ, Ctr Genom & Biotechnol, Haixia Inst Sci & Technol, Fuzhou, Peoples R China
Tianying Lan - Univ Buffalo, Dept Biol Sci, Buffalo, NY 14260 USA
Biao Lai - South China Agr Univ, Coll Hort,Guangdong Litchi Engn Res Ctr, Minist Agr & Rural Affairs,State Key Lab Conserva, Guangdong Lab Lingnan Modern Agr,Key Lab Biol & G, Guangzhou, Peoples R China
Jinhua Sun - Chinese Acad Trop Agr Sci, Environm & Plant Protect Inst, Minist Agr & Rural Affairs, Danzhou Sci Observing & Expt Stn Agroenvironm, Haikou, Hainan, Peoples R China
Yongzan Wei - Chinese Acad Trop Agr Sci, South Subtrop Crops Res Inst, Key Lab Trop Fruit Biol, Minist Agr & Rural Affair, Zhanjiang, Peoples R China
Huanling Li - Chinese Acad Trop Agr Sci, Environm & Plant Protect Inst, Minist Agr & Rural Affairs, Danzhou Sci Observing & Expt Stn Agroenvironm, Haikou, Hainan, Peoples R China
Jiezhen Chen - Guangdong Acad Agr Sci, Guangdong Prov Key Lab Trop & Subtrop Fruit Tree, Minist Agr & Rural Affairs, Inst Fruit Tree Res,Key Lab South Subtrop Fruit B, Guangzhou, Peoples R China
Xuming Huang - South China Agr Univ, Coll Hort,Guangdong Litchi Engn Res Ctr, Minist Agr & Rural Affairs,State Key Lab Conserva, Guangdong Lab Lingnan Modern Agr,Key Lab Biol & G, Guangzhou, Peoples R China
Qian Yan - Guangdong Acad Agr Sci, Guangdong Prov Key Lab Trop & Subtrop Fruit Tree, Minist Agr & Rural Affairs, Inst Fruit Tree Res,Key Lab South Subtrop Fruit B, Guangzhou, Peoples R China
Xin Liu - BGI Shenzhen, Shenzhen, Guangdong, Peoples R China
Leah K. McHale - Ohio State Univ, Dept Hort & Crop Sci, Columbus, OH 43210 USA
William Rolling - Ohio State Univ, Ctr Appl Plant Sci, Columbus, OH 43210 USA
Romain Guyot - Diversité, adaptation et développement des plantes
David Sankoff - University of Ottawa
Chunfang Zheng - University of Ottawa
Victor A. Albert - Nanyang Technol Univ, Sch Biol Sci, Singapore, Singapore
Ray Ming - University of Illinois Urbana-Champaign
Houbin Chen - South China Agr Univ, Coll Hort,Guangdong Litchi Engn Res Ctr, Minist Agr & Rural Affairs,State Key Lab Conserva, Guangdong Lab Lingnan Modern Agr,Key Lab Biol & G, Guangzhou, Peoples R China
Rui Xia - South China Agr Univ, Coll Hort,Guangdong Litchi Engn Res Ctr, Minist Agr & Rural Affairs,State Key Lab Conserva, Guangdong Lab Lingnan Modern Agr,Key Lab Biol & G, Guangzhou, Peoples R China
Jianguo Li - South China Agr Univ, Coll Hort,Guangdong Litchi Engn Res Ctr, Minist Agr & Rural Affairs,State Key Lab Conserva, Guangdong Lab Lingnan Modern Agr,Key Lab Biol & G, Guangzhou, Peoples R China
Détails de publication: Nature genetics, Vol.54(1), pp.73-83
Éditeur: NATURE PORTFOLIO
Nombre de pages: 29
Note de subvention: 318288 / Academy of Finland (AKA); Research Council of Finland 1442190 / Division Of Environmental Biology; Direct For Biological Sciences; National Science Foundation (NSF); NSF - Directorate for Biological Sciences (BIO) 2030871 / Division Of Environmental Biology; Direct For Biological Sciences; National Science Foundation (NSF); NSF - Directorate for Biological Sciences (BIO) BGQN201979-1 / Bagui Young Scholars Supporting Projects discipline team building projects of Guangdong Academy of Agricultural Sciences in the 13th Five-Year Period Lingnan Fruit Innovation Team 318288 / Academy of Finland; Research Council of Finland LNSG2012-03; LNSG2012-04 / Litchi Breeding Post of Guangdong Modern Agricultural Industry and Technology System '211 Project' Construction Fund for Key Subjects of the College of Horticulture, South China Agricultural University 2019TX05N193 / Special Support Program of Guangdong Province
Identifiants: 99136444309311
Unité académique: Diversité, Adaptation et Développement des plantes - DIADE
Langue: English
Type de ressource: Journal article