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.