Articles
Epicormic and axillary branches show distinct epigenetic differences in almond (Prunus dulcis (Mill.) D.A. Webb)
Article number
1406_27
Pages
179 – 184
Language
English
Abstract
Epicormic buds are trace meristems hidden underneath the bark of woody perennial species.
Basal epicormic buds have been used for decades to mitigate the symptoms of non-infectious bud failure (NBF), a severe and fatal genetic disease in almonds.
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.
Using enzymatic methyl-seq and strong experimental design principles we have identified specific differentially methylated regions (DMRs) between epicormic and upper canopy axillary branches in almond.
We sampled leaf tissue from epicormic and axillary branches from two different varieties and four different locations in California to account for environmental and variety variation.
We measured the total cytosine methylation, then identified differentially methylated regions using DSS in R. While global methylation levels between epicormic and axillary tissues were not significant (p>0.4177), distinct differentially methylated regions were present.
We identified 102 DMRs at the CpG, CHG and CHH context, then aligned the DMRs to the Nonpareil genome, with significant differences at genes relating to cell division and disease resistance.
These DMRs represent epigenetic differences that could potentially help explain and/or predict NBF.
Basal epicormic buds have been used for decades to mitigate the symptoms of non-infectious bud failure (NBF), a severe and fatal genetic disease in almonds.
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.
Using enzymatic methyl-seq and strong experimental design principles we have identified specific differentially methylated regions (DMRs) between epicormic and upper canopy axillary branches in almond.
We sampled leaf tissue from epicormic and axillary branches from two different varieties and four different locations in California to account for environmental and variety variation.
We measured the total cytosine methylation, then identified differentially methylated regions using DSS in R. While global methylation levels between epicormic and axillary tissues were not significant (p>0.4177), distinct differentially methylated regions were present.
We identified 102 DMRs at the CpG, CHG and CHH context, then aligned the DMRs to the Nonpareil genome, with significant differences at genes relating to cell division and disease resistance.
These DMRs represent epigenetic differences that could potentially help explain and/or predict NBF.
Authors
W.R. Hazzard, J. Fresnedo-Ramirez, E.S. Anderson, T.M. Gradziel
Keywords
methylation, bud failure
Groups involved
Online Articles (66)