Assessment of the Genetic Diversity and Population Structure of a Wild Tea Germplasm Collection in Thailand Using SSR Markers

Abstract

Tea [Camellia sinensis (L.) O. Kuntze] is the most widely consumed beverage worldwide and also has significant economic crop value. Understanding the genetic diversity and population structure of wild tea plants by analyzing their germplasm is essential for effective collection, management, and utilization. In this study, the genetic diversity and population structure of 283 wild tea accessions were analyzed using 16 SSR markers. A total of 81 alleles were detected, ranging from 3 to 8 alleles per marker, with an average of 5.06 alleles per locus. The average polymorphism information content (PIC) value of 0.545 indicates that the SSR marker set was, on average, highly informative. Moreover, the MSG0533 marker showed the presence of a distinct allele (350 bp) exclusively in tea accessions from the Chiang Mai province. This unique allele could be further developed into a DNA marker for accurate identification of tea sourced from this region. Based on the dendrogram, wild tea accessions were grouped into three major clusters exhibiting substantial genetic divergence. Population structure analysis showed two distinct subpopulations. Subpopulation 1 consists of 70 (24.73%) accessions from the provinces of Lampang, Mae Hong Son, Nan, and Phrae, whereas all 213 (75.27%) accessions in subpopulation 2 originate from the provinces of Chiang Mai and Chiang Rai. Analysis of molecular variance (AMOVA) identified 13% variance among and 56% variance within populations, while 31% was attributed to individuals, indicating a high gene exchange rate between the two subpopulations. These findings provide comprehensive information for future breeding and genetic studies of tea.