Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heterotic Capsicum F1 hybrid

Novel methylation specific bisulfite primer pairs for epigenetic studies of Capsicum spp.

“…Subsequent investigations have provided compelling evidence to support the notion that methylation of cytosine nucleotides within promoters holds greater significance when compared to methylation patterns observed in exons and introns. This finding suggests that methylation processes are significant in the control of gene expressions (Karaca et al, 2016a;Xiao et al, 2020;Cai et al, 2022;Jaiswal et al, 2022). The current work demonstrates that there are variations in DNA cytosine methylation levels among genes, gene locations, promoters, and gene body components such as introns and exons.…”

Toward understanding and utilizing crop heterosis in the age of biotechnology

“…Differential analysis of transcripts and proteins in various kinds of organs in hybrids compared to parents revealed relationships between gene expression regulation and heterotic phenotypes. 8 , 31 , 36 , 37 , 42 Epigenetic comparison between hybrids and parents also indicated chromosome modification changes correlated with gene expression changes. 28 , 29 , 30 , 31 , 33 , 36 Notably, molecular-level complementation was found to be a common reason for hybrid gene expression performance 38 , 39 , 46 , 47 , 48 and a key driver of the heterotic phenotype ( Figure 1 C).…”

“… 8 , 31 , 36 , 37 , 42 Epigenetic comparison between hybrids and parents also indicated chromosome modification changes correlated with gene expression changes. 28 , 29 , 30 , 31 , 33 , 36 Notably, molecular-level complementation was found to be a common reason for hybrid gene expression performance 38 , 39 , 46 , 47 , 48 and a key driver of the heterotic phenotype ( Figure 1 C). 8 Gene regulatory network analysis in Arabidopsis showed that the regulatory network changes in hybrid compared to parents and the network hub gene expression complementation between different biological pathways occurred in hybrid during different developmental periods and in different organs contribute to biomass heterosis.…”

“…How heterosis is generated has been explored at multiple levels of biology, including the community, population, organism, organ, tissue, and single cell ( Figure 1 A). Multiomics profiles such as those of the genome, 10 , 12 , 13 , 24 , 25 , 26 , 27 epigenome, 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 transcriptome, 8 , 28 , 29 , 31 , 33 , 38 , 39 , 40 , 41 proteome, 42 , 43 and metabolome 37 , 42 of hybrid combinations in different kinds of species have revealed some important biological pathways or key genes associated with heterosis. According to these results, the underpinnings of heterosis appear to vary for different combinations and traits.…”

Analysis of DNA Methylation Differences during the JIII Formation of Bursaphelenchus xylophilus

“…Changes in DNA methylation often lead to changes in gene expression, making the joint analysis of DNA methylation and transcriptome crucial in the thorough investigation of biological growth and environmental adaptation [29,30]. Bisulfite sequencing is currently one of the most accurate and effective methods for obtaining single-base resolution biological DNA methylation profiles, enabling the description of genome-wide DNA methylation profiles [31].…”