Elucidating the evolution of litchi: insights into the population genomics of ancient trees on origin, dispersal, and adaptive genetic basis
Abstract
Litchi (Litchi chinensis Sonn.) is a high-value subtropical fruit tree native to eastern Yunnan, China. Its cultivation was recorded in the second century BC. Ancient litchi trees are widespread across southern China, some over 1000 years old, yet their genetic potential remains largely uninvestigated. Here, we analyzed resequencing data from 93 in situ ancient litchi trees with integrated public datasets and simulated paleoclimate species distribution models (SDMs) using over 20 000 ancient litchi distribution records. This approach led to several significant findings. First, population analyses identified two wild lineages (Yunnan, Hainan) and five admixed clusters. SDMs indicate last glacial maximum contraction with a Hainan refugium, followed by postglacial expansion across South China while Yunnan lagged. Principal component analysis and runs of homozygosity further revealed fine-scale population structure. Second, several historical dispersal events of litchi were uncovered. Most ancient Sichuan trees were derived from the Yunnan wild lineage, with fragmented montane habitats supporting human-mediated introduction. Ancient Fujian and Guangdong trees are chiefly admixed cultivars, with genetic distances indicating clonal spread across regions. Third, we identified signals where variation in flowering time and disease resistance coincides with highly heterozygous genomic blocks and haplotype-biased transcription. This pattern is observed in flowering differences between cultivars ‘Feizixiao’ and ‘Nuomici’ and in disease responses between the ancient resistant cultivar ‘Heiye’ and the susceptible cultivar ‘Guiwei’. Our research provides a genomic resource for ancient litchi trees, offering new insights into litchi dispersal, cultivation, and priorities for breeding.
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BibTeX
@article{wang2026elucidating,
title = {{Elucidating the evolution of litchi: insights into the population genomics of ancient trees on origin, dispersal, and adaptive genetic basis}},
author = {Han Wang and Xiaoqian Yu and Lianlian Rao and Mianqiao Pan and Zuanxian Su and Houbin Chen},
journal = {Horticulture research},
year = {2026},
month = jul,
doi = {10.1093/hr/uhag226},
url = {https://europepmc.org/article/PMC/PMC13722864},
note = {CC BY},
}
RIS
TY - JOUR
TI - Elucidating the evolution of litchi: insights into the population genomics of ancient trees on origin, dispersal, and adaptive genetic basis
AU - Han Wang
AU - Xiaoqian Yu
AU - Lianlian Rao
AU - Mianqiao Pan
AU - Zuanxian Su
AU - Houbin Chen
PY - 2026
DA - 2026/07/13
JO - Horticulture research
DO - 10.1093/hr/uhag226
UR - https://europepmc.org/article/PMC/PMC13722864
AB - Litchi (Litchi chinensis Sonn.) is a high-value subtropical fruit tree native to eastern Yunnan, China. Its cultivation was recorded in the second century BC. Ancient litchi trees are widespread across southern China, some over 1000 years old, yet their genetic potential remains largely uninvestigated. Here, we analyzed resequencing data from 93 in situ ancient litchi trees with integrated public datasets and simulated paleoclimate species distribution models (SDMs) using over 20 000 ancient litchi distribution records. This approach led to several significant findings. First, population analyses identified two wild lineages (Yunnan, Hainan) and five admixed clusters. SDMs indicate last glacial maximum contraction with a Hainan refugium, followed by postglacial expansion across South China while Yunnan lagged. Principal component analysis and runs of homozygosity further revealed fine-scale population structure. Second, several historical dispersal events of litchi were uncovered. Most ancient Sichuan trees were derived from the Yunnan wild lineage, with fragmented montane habitats supporting human-mediated introduction. Ancient Fujian and Guangdong trees are chiefly admixed cultivars, with genetic distances indicating clonal spread across regions. Third, we identified signals where variation in flowering time and disease resistance coincides with highly heterozygous genomic blocks and haplotype-biased transcription. This pattern is observed in flowering differences between cultivars ‘Feizixiao’ and ‘Nuomici’ and in disease responses between the ancient resistant cultivar ‘Heiye’ and the susceptible cultivar ‘Guiwei’. Our research provides a genomic resource for ancient litchi trees, offering new insights into litchi dispersal, cultivation, and priorities for breeding.
SN - 2662-6810
SN - 2052-7276
ER -