ArticleNature genetics2022
Two divergent haplotypes from a highly heterozygous lychee genome suggest independent domestication events for early and late-maturing cultivars.
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Article in Nature genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 110 papers.
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110 citing papers in PubMed.
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50 more citing papers are in PubMed but not listed here.
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44 authors.
Guibing Hu *State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.
Junting Feng *State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.
Xu Xiang *Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China.
Jiabao Wang *Danzhou Scientific Observing and Experimental Station of Agro-Environment, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agriculture Sciences, Haikou, China.
Jarkko Salojärvi *School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.ORCID http://orcid.org/0000-0002-4096-6278
Chengming Liu *State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.
Zhenxian Wu *State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.ORCID http://orcid.org/0000-0002-0759-4003
Jisen ZhangCenter for Genomics and Biotechnology, Haixia Institute of Science and Technology Fujian Agriculture and Forestry University, Fuzhou, China.ORCID http://orcid.org/0000-0003-1041-2757
Xinming LiangBGI-Shenzhen, Shenzhen, Guangdong, China.
Zide JiangGuangdong Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China.
Wei LiuKey Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China.
Liangxi OuKey Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China.
Jiawei LiState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.
Guangyi FanBGI-Shenzhen, Shenzhen, Guangdong, China.
Yingxiao MaiState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.
Chengjie ChenState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.
Xingtan ZhangCenter for Genomics and Biotechnology, Haixia Institute of Science and Technology Fujian Agriculture and Forestry University, Fuzhou, China.
Jiakun ZhengState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.
Yanqing ZhangState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.
Hongxiang PengHorticultural Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.
Lixian YaoCollege of Natural Resources and Environment, South China Agricultural University, Guangzhou, China.
Ching Man WaiDepartment of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
Xinping LuoInstitute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, China.
Jiaxin FuState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.
Haibao TangCenter for Genomics and Biotechnology, Haixia Institute of Science and Technology Fujian Agriculture and Forestry University, Fuzhou, China.ORCID http://orcid.org/0000-0002-3460-8570
Tianying LanDepartment of Biological Sciences, University at Buffalo, Buffalo, NY, USA.
Biao LaiState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.
Jinhua SunDanzhou Scientific Observing and Experimental Station of Agro-Environment, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agriculture Sciences, Haikou, China.
Yongzan WeiKey Laboratory for Tropical Fruit Biology of Ministry of Agriculture and Rural Affair, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agriculture Sciences, Zhanjiang, China.ORCID http://orcid.org/0000-0003-3516-5115
Huanling LiDanzhou Scientific Observing and Experimental Station of Agro-Environment, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Chinese Academy of Tropical Agriculture Sciences, Haikou, China.
Jiezhen ChenKey Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China.
Xuming HuangState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.
Qian YanKey Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou, China.
Xin LiuBGI-Shenzhen, Shenzhen, Guangdong, China.ORCID http://orcid.org/0000-0003-3256-2940
Leah K McHaleDepartment of Horticulture and Crop Sciences and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, USA.ORCID http://orcid.org/0000-0003-1028-2315
William RollingCenter for Applied Plant Sciences, The Ohio State University, Columbus, OH, USA.
Romain GuyotIRD, UMR DIADE, EVODYN, Montpellier, France.
David SankoffDepartment of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada.ORCID http://orcid.org/0000-0001-8415-5189
Chunfang ZhengDepartment of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada.
Victor A AlbertSchool of Biological Sciences, Nanyang Technological University, Singapore, Singapore. vaalbert@buffalo.edu.ORCID http://orcid.org/0000-0002-0262-826X
Ray MingDepartment of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. rayming@illinois.edu.ORCID http://orcid.org/0000-0002-9417-5789
Houbin ChenState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China. hbchen@scau.edu.cn.ORCID http://orcid.org/0000-0001-8097-9033
Rui XiaState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China. rxia@scau.edu.cn.ORCID http://orcid.org/0000-0003-2409-1181
Jianguo LiState Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China. jianli@scau.edu.cn.ORCID http://orcid.org/0000-0002-6271-5584
Funding
No grant is acknowledged in the PubMed record.
Abstract
Lychee is an exotic tropical fruit with a distinct flavor. The genome of cultivar 'Feizixiao' was assembled into 15 pseudochromosomes, totaling ~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 haplotype 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.
Indexed as
DomesticationGenome, PlantChinaCrops, AgriculturalEvolution, MolecularFlowersHaplotypesHeterozygoteLitchiMolecular Sequence AnnotationPolymorphism, Single NucleotideSequence Analysis, DNASpecies Specificity
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