Epigenómica poblacional revela impulsores epigenéticos de la evolución replicada y la heredabilidad faltante en la soja

Heritable epimutations can lead to transmittable phenotypic variation. However, the contribution of epigenetic variations to phenotypic diversity in plant evolution and crop domestication remains elusive. Here, we constructed a comprehensive DNA methylation atlas of 1,102 soybean accessions including wild soybeans, landraces and improved cultivars. Integrated analysis of methylome, variome and transcriptome unveiled that de novo epimutations contributed to an increase in epigenetic diversity following the domestication bottleneck and played a role in modulating gene expression during soybean evolution. Epigenome-wide association study and targeted DNA methylation editing validated an epiallele governing expression of GmFT5a, which contributed to replicated evolution of earlier flowering during high-latitude adaptation of both wild and cultivated soybeans. Notably, the integration of both genetic and epigenetic variants substantially increased the proportion of phenotypic variance explained, capturing a larger fraction of the heritability for these agronomic traits. This study emphasizes the considerable potential of epialleles for crop improvement and may pave the way for epigenetics-driven breeding.