Tea (Camellia sinensis), originating in China over 3,000 years ago, has transitioned from a medicinal herb to a widely consumed beverage. Despite considerable research focusing on tea plants in southwestern China, little attention has been paid to those on Hainan Island. The notable resemblance between Hainan tea and Camellia sinensis var. assamica, alongside the unique geographical and climatic conditions of the island, has presented significant challenges for investigations concerning Hainan tea. New research bridges this gap by collecting 500 tea tree samples from Hainan and employing whole-genome resequencing to examine differences between Hainan tea and cultivated varieties of Camellia sinensis.
Guo et al. confirmed the distinct taxonomic position of Hainan tea within Camellia sinensis, providing valuable insights for resource conservation and molecular breeding. Image credit: Lin2015.
Tea stands as China’s earliest documented tree crop, boasting a domestication history spanning over 3,000 years.
Initially employed as a medicinal herb with roots dating back nearly 5,000 years, it later evolved into a beverage widely embraced for consumption.
On a global scale, cultivated tea plants are classified into two primary groups: Camellia sinensis var. sinensis and Camellia sinensis var. assamica.
Hainan Island, positioned in the northern part of the South China Sea, has a rich history of tea plant cultivation and extensive planting areas.
There were reports of the abundant tea plant resources on Hainan Island at the end of the Qing Dynasty.
For instance, the American missionary and botanist Benjamin Couch Henry uncovered a significant number of wild tea trees during his extensive exploration of the Li ethnic group area in Hainan, confirming the abundance of ancient tea tree resources on the island.
As the Yunnan-Guizhou Plateau is widely recognized as a potential geographical origin of tea, most studies on tea plant population genomics encompass samples from southwestern China, particularly Camellia sinensis var. assamica varieties, leaving research on tea plants in Hainan Island relatively sparse.
“Our study clarifies the taxonomic position of Hainan tea and underscores the importance for conservation and molecular breeding efforts,” said Yunnan Agricultural University researcher Dazhong Guo and colleagues.
In the study, the authors sequenced genomes of 500 tea tree samples — including from ancient tea trees — collected from four major tea-producing regions of Hainan: Ledong, Qiongzhong, Baisha, and Wuzhishan.
They obtained a total of 6.9 terabytes of raw sequencing data, which were filtered and aligned with the reference genome (Yunkang 10) to yield a final average alignment rate of 98.98%.
After variant calling, 32,334,340 single nucleotide polymorphisms (SNPs) were identified, with the majority located in intergenic regions, and a smaller portion in exonic regions.
Phylogenetic analysis using SNP data revealed that Hainan tea samples form a distinct cluster separate from the global Camellia sinensis var. sinensis and Camellia sinensis var. assamica groups, with notable geographic clustering within the Limu Mountain region but no clear pattern in other areas.
Population structure analysis further confirmed that Hainan tea exhibits a unique genetic composition compared to global varieties.
Principal component analysis (PCA) supported these findings, showing that Hainan tea is genetically distinct from Camellia sinensis var. sinensis and Camellia sinensis var. assamica, though it shares some genetic similarities with global Camellia sinensis var. assamica.
Additionally, gene flow analysis suggested limited historical migration between Hainan tea and other tea varieties, reinforcing its distinct genetic lineage.
Kinship analysis indicated that close genetic relationships observed in certain Hainan tea samples were influenced by human activities in managed tea gardens.
Genetic diversity analysis revealed higher diversity levels in Hainan and Limu Mountain populations compared to Camellia sinensis var. sinensis and Camellia sinensis var. assamica, with minimal genetic differentiation between Hainan tea and Limu Mountain tea.
These results highlight the unique evolutionary trajectory of Hainan tea, providing valuable insights into its genetic background and offering implications for conservation and breeding strategies.
Hainan tea’s genetic uniqueness and high diversity highlight its potential as a valuable resource for future breeding programs.
“Our study offers a deeper understanding of the evolution of Camellia sinensis and sets the stage for further research into the genetic foundation of Hainan’s remarkable plant life,” the researchers said.
Their paper was published in the journal Agrobiodiversity.
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Dazhong Guo et al. 2024. Genome resequencing reveals an independently originated Camellia sinensis variety – Hainan tea. Agrobiodiversity 1 (1): 3-12; doi: 10.48130/abd-0024-0003