Genetic diversity and population structure
A total of 4,155,896 SNPs were identified from GBS data of the 223
genotypes after initial filtering. With these SNPs, we ran both
principal component analysis (PCA) and admixture analysis to determine
the number of populations (K) represented by these individuals. Two
principal components best explained the genetic variation between our
samples, but nearly all individuals clustered together (Table S1).
According to the admixture analysis result, the best K value was one
(Fig. S2). We also plotted the admixture of each tree. We found that the
identified “populations” when K=2 completely overlapped geographically
(Fig. 1 B and Fig. S3). Thus, we concluded that the sampled genotypes
belong to one interbreeding population and used K = 1 for the
association analysis.