Multiple distinctive lineages of Assam tea (Camellia sinensis var. assamica) from India and China revealed by Single Nucleotide Polymorphism markers.

Knowledge of genetic diversity is fundamental for improving conservation and utilization of tea plant genetic resources. One hundred fifty SNP markers were used to assess the genetic diversity in 252 tea accessions covering a wide range of geographical origins including Assam, India, Southwest and Southeast Yunnan and Eastern China. Multivariate and Bayesian clustering analysis revealed six distinctive genetic lineages, corresponding to Chinese tea (C. s. var sinensis) and five Assam type tea viz. var. assamica from India, Indochina, Southwest Yunnan, and Southeast Yunnan. Fst among these different lineages ranges from 0.161 to 0.493 and all are highly significant (p < 0.001). The present study suggests that there are at least five different genetic populations of var. assamica in their primary gene pool, including 1) India var. assamica, 2) Cambod (or Southern form), 3) Southwest Yunnan, 4) Jingping, Yunnan and 5) Malipo, Yunnan. We further suggest that the populations of var. assamica were independently domesticated based on the indigenous wild tea trees, rather than introduced cultigens from a single origin. Geographically, the five var. assamica populations could be grouped into two large clusters. The West cluster includes India Assam, Cambod and Southwest Yunnnan, whereas the East cluster includes Southeast Yunnan. Our result also supports the old postulate that Cambod type var. assamica is a distinctive member of Assam tea C. s. var. assamica. Inferred parentage in hybrid breeding lines from India showed that there was no introgression of China var. assamica germplasm, suggesting the potential of exploring inter-population heterosis using the untapped germplasm.