3.3 Genetic structure of A. buergeriana varbuergeriana populations
A total of 16,033,406 raw reads (69,109 ± 731 reads per sample) were obtained by MIG-seq, and after quality control, 15,510,825 reads (66,587 ± 713 reads per sample) were used for further analyses. After de novo SNP detection and filtering, the MIG-seq dataset of 232 samples from 16 populations contained 190 SNPs, distributed among the mountain regions as follows: Utsukushigahara region (63 individuals, 175 SNPs), Norikura+Ontake region (126 individuals, 167 SNPs), Iizuna region (43 individuals, 175 SNPs). Norikura and Ontake regions were combined based on the initial STRUCTURE results. The values of the population genetics parameters varied among populations (H e, 0.0904–0.1450;H o, 0.0593–0.2154; π, 0.0616–0.2248;F IS, –0.0608 to 0.2041; supplementary material, Table S4).
In the PCA results for 190 SNPs of 232 individuals from 16 populations of A. buergeriana var. buergeriana , principal components 1 and 2 (PC1 and PC2, respectively) explained 28.78% of the variance. The geographical structure of the populations is clearly reflected in a plot of PC2 against PC1 (Figure 3), but within populations of A. buergeriana var. buergeriana , red and yellow- and red-flowered individuals did not clearly show genetic isolation. On the basis of the PCA results, the populations could be separated into three regional groups: Utusuhigahara, Norikura+Ontake, and Iizuna populations. The STRUCTURE analysis of all populations showed that, based on ΔK , the appropriate number of genetic clusters was K = 2 (most likely), or K = 3 (next most likely) (supplementary material, Figure S3). The STRUCTURE analysis results also clearly reflected the geographical structure in each region (Figure 4; supplementary material, Figures S3, S4). The appropriate number of genetic clusters in the Utsukushigahara (63 individuals, 175 SNPs), Ontake+Norikura (126 individuals, 167 SNPs), and Iizuna (43 individuals, 175 SNPs) mountain regions were K = 3, 3, and 2, respectively, based on ΔK(supplementary material, Figure S3). Structure among populations within the same mountain region was also detected (Figure 4b–d). In particular, the populations in Norikura+Ontake region could be separated into Norikura and Ontake groups. These two groups were not separated in the initial STRUCTURE analysis. Yellow- and red-flowered individuals in a population were not genetically distinguished in the STRUCTURE analysis results.