Profiling Genome-Wide DNA Methylation in Almond x Peach Interspecific Hybrids to Explore Putative Markers for Early Detection of Non-Infectious Bud-Failure

Elizabeth Anderson
Staff Researcher
Jonathan Fresnedo Ramirez
Horticulture and Crop Science

Non-infectious bud-failure (BF) is an age-related disorder that negatively affects almond production by reducing the number of viable vegetative buds and, therefore, indirectly affecting yield. The lack of a biomarker for early BF detection puts popular and important almond cultivars at risk. In our research group, DNA methylation has been proposed and studied as a biomarker due to its heritability in almond germplasm, its association with aging, and evidence of an association with BF-status. To elucidate patterns of DNA methylation in almond with and without BF, we examined interspecific almond x peach hybrids with divergent BF exhibition. Despite their close genetic relationship, evident from their ability to interbreed, almonds exhibit BF while peaches do not. Therefore, interspecific hybrids may reveal novel information on epigenetic features associated with BF since there should only be one copy of the DNA methylation signatures (i.e. epialleles) contributing to BF development. We extracted DNA from six hybrids discordant for BF, prepared enzymatic methyl-seq libraries to generate DNA methylation profiles, and calculated whole-genome, weighted-percent methylation in each sequence context (CG, CHH, and CHG). We then identified regions of differential methylation (DMRs) in the hybrids based on alignment to both the peach and almond genome sequences. Although no divergent genome-wide DNA methylation was observed between BF and no-BF hybrids, thousands of significant DMRs were identified. This finding contrasts with previous studies performed exclusively with almond germplasm discordant for BF exhibition, where few DMRs (hundreds) were identified. In addition to identifying DMRs, weighted-percent methylation was found to be higher in BF hybrids when compared to no-BF hybrids in the CG and CHG contexts but lower in the CHH context. Additionally, BF hybrids showed higher overall methylation with respect to alignment to almond genome than no-BF hybrids but lower overall methylation with respect to alignment with the peach genome. These patterns and the identified DMRs lay the groundwork for DNA methylation-based biomarkers to screen germplasm for BF-potential and will further our understanding of aging and its impacts in perennial plants.