Molecular markers and phenotypic identification reveal the genetic diversity and structure of four local tea plant populations in China

Abstract The local tea plant population resources are rich in genetic variation, which is the natural treasure house of tea genes and the main source of breeding excellent tea cultivars. However, the genetic information of most local tea plant populations is still unknown. In this study, the genetic diversity and population structure of four main local tea plant populations in Jiangxi Province of China were explored by combining phenotypic characters identification and simple sequence repeats (SSR), and the loci associated with phenotypic characters were screened. The results of genetic diversity analysis of phenotype and SSR were consistent. It was found that the genetic diversity of population species was higher than that of wild species. The order of genetic diversity index of the four tea plant populations was Wuyuan > Fuliang > Suichuan > Ningdu. The single-plants of each population were heterozygotes, and Wuyuan had the highest heterozygosity. The clustering results of phenotypes and SSR on tea plant populations were not completely consistent. SSR could more effectively distinguish tea plant populations. Four tea populations could be clustered into three groups. Further analysis found that the geographical location of tea population distribution would affect its gene exchange. In addition, 9 SSR loci were screened and were significantly associated with 9 phenotypic characters (P < 0.01), and the interpretation rate of phenotypic variation ranged from 6.94–33.90%. These phenotypic characters related to the yield and mechanical harvest of tea varieties.