Transcriptome-derived SNPs reveal genomic differentiation among Chamaecyparis hodginsii provenances with contrasting wood-property profiles

Chamaecyparis hodginsii is an economically important conifer characterized by high-quality wood and a large genome, but genomic differentiation among its geographic provenances remains poorly characterized. In this study, we reanalyzed previously generated RNA-seq data from 13 representative provenances to develop transcriptome-derived SNP resources and investigate genomic differentiation among provenance groups with contrasting wood-property profiles. Coverage-aware joint genotyping yielded 53,041 quality-filtered transcriptome-derived SNPs, of which 19,469 SNPs were retained after a stricter missingness filter for population-structure and Fst analyses. PCA and SNP-based maximum-likelihood clustering consistently grouped L6, L11, and L12 as Pop1, whereas the remaining ten provenances formed Pop2. Mean and weighted Fst between the two SNP-defined groups were 0.0764 and 0.0918, respectively. XP-CLR analysis identified 81 top-5% candidate windows, which were merged into 10 non-overlapping genomic regions showing elevated differentiation between Pop1 and Pop2. Strict SIFT4G filtering of SNPs within these regions retained 12 predicted deleterious nonsynonymous variants in five preliminary candidate genes. Analysis across all 51,873 splice-junction-filtered SNPs further showed a higher normalized SIFT4G-predicted deleterious alternative-allele burden in Pop2 than in Pop1. This study provides a coverage-aware transcriptome-derived SNP resource and characterizes genomic differentiation among C. hodginsii provenance groups with contrasting wood-property profiles. The differentiated genomic regions and the functional variants and genes located within them represent preliminary candidates for future population-genetic and functional validation, rather than statistically established loci underlying wood-property variation.