Whole-Genome Enzymatic methyl-seq of Prunus Dulcis: Epicormic and Axillary RAVT Samples

Basal epicormic buds have been used to mitigate the symptoms of non-infectious bud failure (NBF) for decades. In Nonpareil and Carmel, two critical varieties, propagation from epicormic sources reduced the presence in NBF or eliminated NBF. Epicormics branches are branches that sprout from dormant buds that elongated in a previous period of growth. Epicormic buds have undergone fewer cell divisions than buds from the upper canopy, and are believed to be epigenetically "younger" than axillary canopy branches on the same tree. However, the underlying mechanism of why epicormic branches exhibit reduced bud failure is poorly understood. Previous research has suggested a connection between variation in DNA methylation and NBF but has failed to pinpoint a precise genetic mechanism due to the high amount of noise present in DNA methylation data. In this study, we samples leaf tissue from branches derived from axillary canopy shoots and basal epicormic shoots to identify differences in methylation between the two shoot types. We samples the two shoot types from four different locations at the University of California Agriculture and Natural Resources Almond Regional Variety trials, then sampled two different varieties of those trials. The goal of the project was to sample across tissue types, locations and varieties in a statistically robust way to reduce noise from other factors outside of tissue type that may contribute to variance in DNA methylation.