Figure 2.

Population structure of early-pedigree and late-cultivar samples. A, PCA plot among all varieties of early-pedigree (red) and late-cultivar (blue). B, Unrooted NJ tree across all samples, the unit of tree scale is P distance. C, Genome-wide averaged distance of LD decayed to r² = 0.2 for the groups of early-pedigree (red), late-cultivar (blue), and all varieties (black). Comparison of levels of D, heterozygosity, E, nucleotide diversity, and F, Hardy–Weinberg equilibrium between the early-pedigree and the late-cultivar. The elements of boxplot are the center line, median; box limits, upper and lower quartiles; whiskers, 1.5 × interquartile range; points, outliers. In heterozygosity, the four outliers in the early group are “Feicui Rose”, “Wuhezaohong”, “Hongbiaowuhe”, and “Chunguang” from low to high; similarly, the five outliers in the late group are “Neijingxiang”, “Tamnara”, “Tano Red”, “Miguang”, and “Catawba”. All outliers belong to Vitis vinifera × Vitis labrusca.