Single nucleotide polymorphisms reveal the uniqueness of Gushan semi-rock tea in the tea germplasm resources of Fujian, China

As a renowned tea with a historical significance in China, Gushan semi-rock tea originated from the Gushan Mountain in Fujian, China. This study describes the genetic diversity, population structure, and distribution characteristics of 76 tea samples collected from Gushan Mountain and neighboring regions, using single nucleotide polymorphism (SNP) markers. The results show that the average information index (I) is 0.490, the average observed heterozygosity (Ho) is 0.384, the average expected heterozygosity (He) is 0.329, and the average fixation index (F) is − 0.132. The genetic variation mainly comes from intraregional variation, which accounts for 82% of the total variation. Furthermore, there is a closer connection between tea plants in Southern, Northern, and Eastern Fujian. The frequency of genetic exchange between tea plants in the Gushan semi-rock tea and those in Southern, Northern, and Eastern Fujian is relatively low, showing obvious uniqueness. The findings of this study help fill the gap in tea genome research in the Gushan semi-rock tea and provide valuable information on the genetic diversity of tea resources in Gushan area. The results can be utilized in future genomics, phylogeny, and breeding programs aimed at developing new tea cultivars.