Integrated Comparative Genomics and Population Genomics Reveal the Genomic and Epigenomic Basis of Barley (Hordeum vulgare) Evolution and Domestication.

Barley (Hordeum vulgare) is one of the earliest domesticated cereal crops and remains important for global feed, food, and malting industries. Although high-quality genomic resources are now available, its large repeat-rich genome has complicated genome-wide characterization of genomic features associated with barley evolution and domestication. Here, we integrated comparative genomics, methylomics, population genomics, and Hi-C analyses to investigate genome evolution and domestication in barley. Comparative analyses across representative grass species revealed that barley exhibits lineage-specific genome expansion associated with the extensive proliferation of long terminal repeat retrotransposons. Genome-wide DNA methylation analyses revealed distinct cytosine methylation landscapes in barley. Population genomic analyses of 291 wild and domesticated barley accessions revealed relatively slow linkage disequilibrium decay and identified 243 candidate domestication-associated genes. These candidate genes were enriched in starch and sucrose metabolism pathways. Comparative Hi-C analyses of three barley accessions further uncovered differences in A/B chromatin compartments and topologically associating domain (TAD) organization despite their largely conserved gene content. In addition, the enrichment of DNA transposons and Copia retrotransposons at TAD boundaries suggests potential associations between specific TE classes and higher-order chromatin organization. Together, these complementary analyses connect genome expansion, epigenetic regulation, domestication-associated selection, and chromatin organization into a unified framework for understanding barley genome evolution and domestication.