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Nature genetics
01, 2022;54 (1): 73-83.

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 Salojärvi, 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
Author Information
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. Jarkko Salojärvi: School of Biological Sciences, Nanyang Technological University, Singapore, Singapore. ORCID
  6. 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.
  7. 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
  8. Jisen Zhang: Center for Genomics and Biotechnology, Haixia Institute of Science and Technology Fujian Agriculture and Forestry University, Fuzhou, China. ORCID
  9. Xinming Liang: BGI-Shenzhen, Shenzhen, Guangdong, China.
  10. Zide Jiang: Guangdong Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, China.
  11. Wei Liu: 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.
  12. Liangxi Ou: 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.
  13. Jiawei Li: 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.
  14. Guangyi Fan: BGI-Shenzhen, Shenzhen, Guangdong, China.
  15. Yingxiao Mai: 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.
  16. Chengjie Chen: 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.
  17. Xingtan Zhang: Center for Genomics and Biotechnology, Haixia Institute of Science and Technology Fujian Agriculture and Forestry University, Fuzhou, China.
  18. Jiakun Zheng: 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.
  19. Yanqing Zhang: 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.
  20. Hongxiang Peng: Horticultural Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China.
  21. Lixian Yao: College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China.
  22. Ching Man Wai: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  23. Xinping Luo: Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, China.
  24. Jiaxin Fu: 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.
  25. Haibao Tang: Center for Genomics and Biotechnology, Haixia Institute of Science and Technology Fujian Agriculture and Forestry University, Fuzhou, China. ORCID
  26. Tianying Lan: Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA.
  27. Biao Lai: 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.
  28. Jinhua Sun: 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.
  29. Yongzan Wei: Key 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
  30. Huanling Li: 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.
  31. Jiezhen Chen: 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.
  32. Xuming Huang: 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.
  33. Qian Yan: 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.
  34. Xin Liu: BGI-Shenzhen, Shenzhen, Guangdong, China. ORCID
  35. Leah K McHale: Department of Horticulture and Crop Sciences and Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, USA. ORCID
  36. William Rolling: Center for Applied Plant Sciences, The Ohio State University, Columbus, OH, USA.
  37. Romain Guyot: IRD, UMR DIADE, EVODYN, Montpellier, France.
  38. David Sankoff: Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada. ORCID
  39. Chunfang Zheng: Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada.
  40. Victor A Albert: School of Biological Sciences, Nanyang Technological University, Singapore, Singapore. vaalbert@buffalo.edu. ORCID
  41. Ray Ming: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. rayming@illinois.edu. ORCID
  42. Houbin Chen: 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. hbchen@scau.edu.cn. ORCID
  43. Rui Xia: 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. rxia@scau.edu.cn. ORCID
  44. Jianguo Li: 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. jianli@scau.edu.cn. ORCID
PMID: 34980919 DOI: 10.1038/s41588-021-00971-3

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.

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MeSH Term

China
Crops, Agricultural
Domestication
Evolution, Molecular
Flowers
Genome, Plant
Haplotypes
Heterozygote
Litchi
Molecular Sequence Annotation
Polymorphism, Single Nucleotide
Sequence Analysis, DNA
Species Specificity
Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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