Cis-meQTL mapping reveals genetic architecture of DNA methylation in a giga-genome species

Whether variation in plant DNA methylation is mostly under genetic control (and therefore heritable and accessible to selection) or driven by environmental cues remains unsolved, which has consequences for epigenetic breeding and for understanding heritable phenotypic plasticity. We addressed this question by running cis-methylation quantitative trait locus (cis-meQTL) mapping across all three methylation contexts (CpG, CHG, and CHH) in 602 Norway spruce ( Picea abies (L.) H. Karst.) seedlings, pairing exome capture sequencing and targeted enzymatic methylation sequencing across the same genomic regions in a pedigree-structured breeding cohort and natural populations. Two complementary association frameworks yielded 6,954 and 18,480 robust SNP-methylation pairs in the breeding and natural cohorts, respectively (FDR < 1×10⁻ ¹⁰), with approximately 70% of breeding-cohort cis-meQTL positions recovered in natural populations across all three contexts. We found that methylation variation in this giga-genome conifer is substantially genetically encoded, providing a foundation for incorporating epigenomic markers into genomic selection programs.