Fig. 3: Genome-wide screening of the loci associated with local environmental adaptation. | Nature Communications

Fig. 3: Genome-wide screening of the loci associated with local environmental adaptation.

From: Genomic insights into local adaptation and future climate-induced vulnerability of a keystone forest tree in East Asia

Fig. 3: Genome-wide screening of the loci associated with local environmental adaptation.The alt text for this image may have been generated using AI.

a Manhattan plot for variants associated with the Maximum Temperature of the Warmest Month (BIO5) (red, upper panel) and the Precipitation of the Wettest Month (BIO13) (blue, lower panel). Dashed horizontal lines represent significance thresholds (blue or red represents the FDR correction, adjusted P = 0.05; gray represents the Bonferroni correction, adjusted P = 0.05). Selected candidate genes are labeled in the plot at their respective genomic positions. b, f Upper panels: the gene structure of CRL1 (b) and HSP60-3A (f) (blue triangles: representative candidate adaptive SNPs corresponding to the sites shown in c–e and g–i). Lower panels: local magnification of the Manhattan plots (blue circles: SNPs; yellow triangles: indels; red squares: SVs) around the selected genes (gray shadows). c, g Allele frequencies of candidate adaptive SNPs (c, LG04:25159299; g LG07:4796402) associated with BIO5 (c) and BIO13 (g) across the 24 populations. Colors on the map are based on variations of the relevant climate variables across the distribution range. d, h Decay of EHH for two alternative alleles around LG04:25159299 (d) and LG07:4796402 (h). e, i Dynamic relative expression level of CRL1 (e) and HSP60-3A (i) genes between the two genotypes using qRT-PCR under submergence (e) and heat (i) treatments. Error bars represent standard deviation, n = 3 biologically independent samples. Source data are provided as a Source Data file.

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