Genome-Wide Resequencing Reveals Genetic Relationships between Main Gardenia jasminoides Ellis Cultivars

Nineteen samples of Gardenia jasminoides Ellis from China were used for genome resequencing. The clean Q30 base rates ranged from 91.19% to 92.94%. When mapping with the reference genome, a total of 7,568,199 inDel sites and 61,535,595 SNP sites were detected, with variations of heterozygosity ratios ranging from 44.86% to 92.69% and from 41.53% to 90.38%, respectively. Genome location and function annotation of SNP and inDel in different samples were carried out. SNP and inDel were mainly located in the intergenic region, with the ratios of 67.2360% and 62.6415%, respectively. Based on the phylogenetic tree constructed by the maximum likelihood method, the 19 samples could be divided into four categories. Among them, Y_10 and Y_38 were put into one category, while Y_2 was put into a separate category. These two were first differentiated from other cultivars and species. Similar conclusions can be drawn from the results of genetic structure and principal component analysis. This study provided sequence foundation for the identifying of the molecular marker and genotype of G. jasminoides. It also provided theoretical foundation for subsequent resource conservation and utilization, the genetic localization of important agronomical traits, and high-quality variety formulation and breeding.