Guizhou is one of the centers of origin for the tea plant (Camellia sinensis (L.) Kuntze). The location contains highly diverse ancient tea plant germplasms in its Sandu Aquarium Autonomous County. After a prolonged course of continuous evolution, these ancient plants have gained a wealth of genetic diversity. Their resources could be harnessed for the selection and breeding of fine varieties of tea plant, as well as for the effective utilization and protection of germplasm resources. In this study, the specific locus-amplified fragment (SLAF) sequencing method was used to analyze the population structure and conduct a genome-wide association study (GWAS) for the three traits of 125 ancient tea plants in the Sandu County of Guizhou province, China. A total of 807,743 SLAF tags and 9,428,309 population single-nucleotide polymorphism (SNP) tags were obtained. The results of the phylogenetic tree analysis, cluster analysis, and principal component analysis showed that 125 germplasms were clustered into four groups, and the heterozygosity rates for groups I, II, III, and IV, were 0.211, 0.504, 0.144, and 0.192, respectively. Additionally, GWAS analysis suggested that seven candidate genes were related to altitude at the origin of the plants, eight were related to tree shape, and three were associated with leaf color. In this study, we clarified genetic relationships between four ancient tea plant-producing areas in Sandu County and obtained candidate genes related to their development associated with altitude, tree shape, and leaf color. The study provides useful information for tea plant-breeding development and molecular identification.

The ancient tea plant germplasm is an important resource for breeding new tea plant varieties and has great economic value. However, due to man-made and natural disturbances, it has become endangered. In order to have a better management of the conserved tea plant germplasm, it is a requirement to understand the genetic and phenotypic diversity. The aim of this study was to evaluate the genetic and phenotypic diversity of 145 ancient tea plant germplasm resources from five populations in Sandu County of Guizhou province in China. To explore the population genetics of tea plant, we successfully identified 15 simple sequence repeat (SSR) markers, which were highly polymorphic. Additionally, we applied traditional phenotypic methods to evaluate the tea plant diversity. The results suggested that the genetic and phenotypic diversity were relatively high. A total of 96 alleles were identified, and the mean polymorphic information content (PIC) value was found to be 0.66. The analysis of molecular variance (AMOVA) showed that genetic variation within the populations was greater than among the populations. Overall, our results are the valuable baseline data in developing more efficient management and breeding plans for one of the most popular non-alcoholic beverage crops, the tea plant species.