Genetic Analysis Uncovers Six Distinct Lineages of Global Tea Germplasm

Using 150 single-nucleotide polymorphism (SNP) markers across 252 tea accessions from India and China, researchers identified six major genetic groups, including the small-leafed sinensis and five broadleaf assamica populations from India, Indochina, and Yunnan. The findings suggest that assamica teas were independently domesticated from indigenous wild plants rather than from a single ancestral origin.

Tea (Camellia sinensis) is one of the oldest domesticated crops, originating in China around 2737 BC and now consumed more than any other beverage worldwide. Despite its cultural and economic importance, the genetic structure and evolutionary history of tea-particularly of the assamica type-remain debated. Previous molecular studies could not clearly distinguish between broadleaf assamica, small-leaf sinensis, and the intermediate lasiocalyx (Cambod) types. As the two largest producers, China and India harbor vast germplasm resources, yet much of their genetic potential remains underexplored.

A study (DOI: 10.48130/BPR-2023-0020) published in Beverage Plant Research on 04 September 2025 by Wanping Fang's & Dapeng Zhang's team, Nanjing Agricultural University & Beltsville Agricultural Research Center, not only clarifies long-standing taxonomic debates but also provides new genetic insights crucial for breeding climate-resilient and high-quality tea cultivars.

The population structure of global tea germplasm was first investigated using Bayesian clustering (STRUCTURE) and different estimators of the most likely number of genetic groups (K), including Puechmaille's method and the Evanno method. These approaches were applied to 252 tea accessions genotyped with 150 SNP markers, followed by Principal Coordinate Analysis (PCoA), Neighbor-Joining (NJ) phylogeny, summary diversity statistics, and Analysis of Molecular Variance (AMOVA). The clustering analysis suggested that tea accessions were best represented either by three broad groups (K = 3) or by six finer groups (K = 6). At K = 3, all accessions separated into one Camellia sinensis var. sinensis group and two C. sinensis var. assamica groups: (i) India/Cambod/Southwest Yunnan (Jingmai, Mangshi) and (ii) Southeast Yunnan (Jinping, Malipo). At K = 6, the analysis resolved six distinct lineages that aligned with known morphology and origin: (1) var. sinensis; (2) Indian assamica (including material from forests, tribal villages, and historic tea gardens in Northeast India); (3) Cambod ("lasiocalyx") assamica, also including widely used Tocklai Vegetative clones; (4) Southwest Yunnan assamica (Jingmai and Mangshi); (5) Jinping assamica; and (6) Malipo assamica. Hybrid breeding lines from the Tocklai Tea Research Institute were shown to be genetic admixtures mainly of Indian assamica (54.9%), var. sinensis (28.1%), and Cambod assamica (14.0%), with negligible input from Chinese assamica of Yunnan. Using a Q > 0.70 membership cutoff, 248 accessions were assigned to these six lineages, which PCoA cleanly separated; the first three PCoA axes captured 61.3% of total variation. NJ tree topology agreed with STRUCTURE and PCoA, grouping wild Southeast Yunnan populations (Jinping, Malipo) together and clustering Southwest Yunnan with Indian assamica and Cambod. Genetic diversity metrics showed var. sinensis had the highest gene diversity and heterozygosity, whereas Indian assamica and Mangshi populations were lowest. AMOVA and pairwise Fst confirmed strong and significant genetic differentiation among groups (44% of variance among populations; all Fst p < 0.001), with the greatest divergence between Indian assamica and var. sinensis and the least between Jingmai and Mangshi.

This study provides a genetic roadmap for global tea conservation and breeding. By defining clear population boundaries and uncovering underused germplasm, the research paves the way for developing inter-population hybrids that combine yield, flavor, and stress resilience. The identified genetic divergence also offers new opportunities to exploit hybrid vigor and improve adaptability to climate challenges. For conservation, the findings emphasize the importance of preserving wild tea populations across Yunnan and Assam, where much of the original diversity still survives.