Comparative RNA-Sequencing and DNA Methylation Analyses of Apple (Malus domestica Borkh.) Buds with Diverse Flowering Capabilities Reveal Novel Insights into the Regulatory Mechanisms of Flower Bud Formation

Abstract

In plants, DNA methylation (i.e. chromatin modification) is important for various biological processes, including growth, development and flowering. Because ‘Fuji’ apple trees are alternate bearing and have a long ripening period and poor-quality flower buds, we used bud types with diverse flowering capabilities to investigate the epigenetic regulatory mechanisms influencing flower bud formation. We examined the DNA methylation changes and the transcriptional responses in the selected apple bud types. We observed that in the apple genome, approximately 79.5%, 67.4% and 23.7% of the CG, CHG and CHH sequences are methylated, respectively. For each sequence context, differentially methylated regions exhibited distinct methylation patterns among the analyzed apple bud types. Global methylation and transcriptional analyses revealed that nonexpressed genes or genes expressed at low levels were highly methylated in the gene-body regions, suggesting that gene-body methylation is negatively correlated with gene expression. Moreover, genes with methylated promoters were more highly expressed than genes with unmethylated promoters, implying promoter methylation and gene expression are positively correlated. Additionally, flowering-related genes (e.g. SOC1, AP1 and SPLs) and some transcription factor genes (e.g. GATA, bHLH, bZIP and WOX) were highly expressed in spur buds (highest flowering rate), but were associated with low methylation levels in the gene-body regions. Our findings indicate a potential correlation between DNA methylation and gene expression in apple buds with diverse flowering capabilities, suggesting an epigenetic regulatory mechanism influences apple flower bud formation.

DNA Methylation and RNA-Sequencing Analysis Show Epigenetic Function During Grain Filling in Foxtail Millet (Setaria italica L.)

“…Previous studies have shown that DNA was methylated differently at different genetic regions, which also could affect gene expression (Ibarra et al, 2012;Liu et al, 2015). More methylated DNAs were found upstream of a gene in certain plants (Xing et al, 2019(Xing et al, , 2020. However, in the present study, the CG methylation of gene-body was significantly higher than that in other regions, which was consistent with earlier reports in strawberry, orange, and peach (Cheng et al, 2018;Huang et al, 2019;Zhu et al, 2020).…”

“…However, mCHH accounted for the highest proportion of total mC in the study, followed by the CG and CHG context. These findings are consistent with studies in apple trees, M. hupehensis, and cotton (Xu et al, 2018;Xing et al, 2019Xing et al, , 2020Zhang et al, 2020). It is worth noting that CHH methylation remained elevated during grain filling (38-46%) and CG and CHG methylation showed the opposite trend (33-29 and 29-25%, respectively).…”

“…Global methylation and transcriptional analyses found that gene-body methylation could repress gene expression. DNA methylation in promoters may increase gene expression during flower bud formation in apples (Xing et al, 2019). In contrast, methylation analysis found that genes with unmethylated promoters presented a higher expression level and gene-body methylation may increase gene expression level under water deficit stress in apples (Xu et al, 2018).…”

“…Deoxyribonucleic acid methylation mediates plant development and phase transition. In apple, DNA methylation influenced apple flower bud formation (Xing et al, 2019). During the juvenile-to-adult phase transition, there was a significant correlation between DNA methylation and gene expression in Malus hupehensis (Xing et al, 2020).…”

Decoding Plant–Environment Interactions That Influence Crop Agronomic Traits

“…2020 ), flower bud formation in apple ( Malus domestica Borkh.) ( Xing et al. 2019 ) and physiological responses in Arabidopsis ( Arabidopsis thaliana ) roots under zinc deficiency ( Chen et al.…”