Population-level gene copy number variations reveal distinct genetic properties of different Malus species.

Background: Copy number variations (CNVs) are crucial in plant evolution, adaptation, and domestication. In this study, we explored how CNVs contribute to genetic diversity, evolution, and adaptation during apple domestication. We examined the genome-wide CNV profiles and segmental duplications (SDs) in 116 Malus accessions, including domesticated apple (Malus domestica) and its primary progenitor species (M. sieversii and M. sylvestris).

Results: On average, two accessions of the same species showed differences in at least 7,000 genes with varying copy number (CN) profiles. In contrast, accessions from different species had at least 20,000 genes with differing CN profiles. Notably, 700 genes exhibited distinct CN profiles between M. domestica and M. sieversii, with an enrichment in defense response genes. Genes related to fruit ripening, flavor, and anthocyanin biosynthesis had higher copy numbers in M. domestica. Additionally, 360 genes showed differential CN profiles between M. domestica and M. sylvestris, with enrichment in polygalacturonase activity, which may influence differences in fruit flavor. The study also identified 3,000 genes with significant CN differentiation (V > 0.28) between M. domestica rootstock and scion cultivars enriched in lignin metabolic pathways, underscoring their role in stress resistance and mechanical support. Segmental duplications were particularly enriched in genes related to sorbitol metabolism, fruit development, and fruit quality traits, highlighting their evolutionary importance in defining apple morphology and physiology.

Conclusions: These findings offer valuable insights into the evolutionary mechanisms driving apple domestication and adaptation and provide a comprehensive resource for future research and apple breeding.