摘要：SummaryHybrid breeding is one of the efficacious methods of crop improvement. Here, we report our work towards understanding the molecular basis of F1 hybrid heterosis fromCapsicum chinenseandC. frutescenscross. Bisulfite sequencing identified a total of 70597 CG, 108797 CHG, and 38418 CHH differentially methylated regions (DMRs) across F1hybrid and parents, and of these, 4891 DMRs showed higher methylation in F1compared to the mid-parental methylation values (MPMV). Transcriptome analysis showed higher expression of 46–55% differentially expressed genes (DE-Gs) in the F1hybrid. The qRT-PCR analysis of 24 DE-Gs with negative promoter methylation revealed 91.66% expression similarity with the transcriptome data. A few metabolites and 65–72% enriched genes in metabolite biosynthetic pathways showed overall increased expression in the F1hybrid compared to parents. These findings, taken together, provided insights into the integrated role of DNA methylation, and genes and metabolites expression in the manifestation of heterosis inCapsicum.Graphical abstractDisplay OmittedHighlights•Global methylation identified significantly different proportions of mCs in hybrid•Of common DMRs, 33.08% showed different methylation in hybrid from the mid-parental value•Negatively correlated DEG pDMR-genes were enriched in metabolic pathways•Significant higher expression of metabolites and DE-Gs were identified in the F1hybridBiological sciences; Natural sciences; Plant biology; Plant Genetics.
