Genetic diversity, population structure and core collection analysis of Hunan tea plant germplasm through genotyping-by-sequencing

Tea is considered to be a well-known and widely consumed beverage and Hunan province is rich in tea plant germplasm. In order to better conserve and utilize Hunan tea plant resources, 110 tea accessions from seven geographical origins were used to assess genetic diversity of Hunan tea plant germplasm through genotyping by sequencing (GBS) technology. As a result, a total of 311,044 high-quality single nucleotide polymorphism (SNP) markers were obtained. Population structure, phylogenetic relationships and principal component analysis (PCA) divided the entire accessions into three groups. The genetic diversity and population differentiation analysis showed that the mean observed heterozygosity (Ho) ranged from 0.16 to 0.24, while the mean polymorphic information content (PIC) ranged from 0.14 to 0.17, and mean minor allele frequency (MAF) ranged from 0.11 to 0.14. Analysis of molecular variance (AMOVA) indicated that 81.38% of the total variance was derived from within populations, which suggested a rich genetic diversity in Hunan tea germplasms. Furthermore, a core tea germplasm set was developed, which was comprised of 22 tea plant accessions and maintained the whole genetic diversity of the entire collection. This work should be valuable for conservation and utilization of tea germplasm in Hunan.