3.5 | Trait-associated loci
Difference in phenotypic values between the inland and coastal sites and dependence of phenotypic values on the Qd ancestry varied among the eight traits (Figures S8, S9). Phenotypic values of each trait were scaled in each site separately. Scaled phenotypic values of the 224 sampled trees in both sites were pooled and applied to mixed linear models with effects of genetic structure and kinship relationship. Based on PCA of SNP genotypes at ddRAD loci, genetic variation betweenQc and Qd mainly determined genetic structure in the first PC (Figure S10), and some northern-edge Qd populations had unique genetic properties in the second, third, and fourth PCs (Figure S10b­–d). Q-Q plots of association mapping of SNP genotypes and admixture mapping of local ancestry showed consistent relationships between expected and observed log-likelihood values at loci with a lower range of –log10 p values, which represented the majority of unassociated loci, indicating successful fitting (Figures S11, S12).
We did not detect any loci significantly associated with the eight traits (FDR > 0.05) but found some loci potentially associated with one taxon-specific trait and three habitat-specific traits (0.051 ≤ FDR ≤ 0.148; Figure 7, Table S2). Association mapping detected three loci in chromosomes 2, 7, and 9 associated with lateral vein interval (Figure 7c), and admixture mapping also supported one locus in chromosome 2 of the three loci (Figure 7d). For loci associated with stellate hair density, association mapping detected one locus in chromosome 1 (Figure 7i), and admixture mapping detected loci in two genomic regions in chromosomes 10 and 11 (Figure 7j). Admixture mapping detected loci associated with LMA in chromosome 11 (Figure 7l), and association mapping detected one locus associated with shoot diameter in chromosome 1 (Figure 7m). Among them, a locus in chromosome 9 potentially associated with lateral vein interval showed a high value of the Patterson’s D statistics (D = 0.51; Figure S7), and a region of loci potentially associated with stellate hair density in chromosome 11 showed high local ancestry from Qd (1.33 Qdalleles; Figure 6b).
From 31 genes around the loci potentially associated with the four traits, we obtained 39 GO terms, in which most frequently observed terms were DNA binding and protein binding (Table S2). Among the 31 genes, we obtained 10 protein names (Table S2), some of which were related to drought stress resistance (Lorenzo et al. 2002; Kushiro et al. 2004), disease resistance (Van Damme et al. 2009; Mokryakova et al. 2014), and senescence (Engqvist et al. 2011).