Comparative Study of Genetic Structure and Genetic Diversity between Wild and Cultivated Populations of Taxus cuspidata, Northeast China

Taxus cuspidata is a rare plant with important medicinal and ornamental value. Aiming at the obvious differences between wild and cultivated populations of T. cuspidata from Northeast China, a total of 61 samples, that is, 33 wild yews and 28 cultivated yews were used to analyze the differences and correlations of the kinship, genetic diversity, and genetic structure between them by specific length amplified fragment sequencing (SLAF-seq). Finally, 470725 polymorphic SLAF tags and 58622 valid SNP markers were obtained. Phylogenetic analysis showed that 61 samples were classified into 2 clusters: wild populations and cultivated populations, and some wild yews were categorized into the cultivated populations; the genetic diversity analysis showed that the Nei diversity index of wild populations (0.4068) was smaller than that of cultivated populations (0.4414), and the polymorphic information content (PIC) of wild populations (0.2861) was smaller than that of cultivated populations (0.3309). The genetic differentiation analysis showed that the total populations of gene diversity (H_t) of cultivated and wild populations were respectively 0.8159 and 0.5685, the coefficient of gene differentiation (G_st) of cultivated and wild populations was respectively 0.3021 and 0.1068, and the gene flow (N_m) (2.4967) of wild populations was larger than cultivated populations (0.8199). The molecular variance (AMOVA) revealed that inter-population variation accounted for 29.57% of the total genetic variation, while intra-population variation accounted for 70.42% of the total genetic variation (p < 0.001), this suggested that the genetic variation in the T. cuspidata is mainly attributed to within-population factors. In conclusion, the genetic distance between geographical ecological groups of wild populations was generally smaller than that of cultivated populations, and the degree of genetic diversity and genetic differentiation was smaller than that of cultivated populations. As evident, the utilization of SLAF-seq technology enables efficient and accurate development of SNP markers suitable for genetic analysis of T. cuspidata species. These developed SNP markers can provide a molecular foundation for T. cuspidata breeding, construction of genetic maps, variety identification, and association analysis of agronomic traits.