Epigenetic selection in almond breeding

Abstract

Plant breeding targets the selection of desirable and heritable traits as a strategy for cultivar improvement. Sufficient heritability is required both for the efficient selection of desired genes within a diverse genetic and environmental background and, in seed-propagated crops, to ensure that all grower seed inherit the desired genetic composition. Clonal propagation avoids the requirement for seed progeny inheritance allowing for the direct selection of both genetic and non-genetic (epigenetic) interactions as long as the desired traits remain true-to-type following vegetative propagation. Utilizing Noninfectious-Bud-Failure (NBF) as a relatively well studied example of epigenetic inheritance in almond, methods for epigenetic selection both within and among genotypes have been successfully developed and employed, but remain tedious and time consuming. Molecular marker analysis utilizing methylation-sensitive amplified fragment length polymorphism (MS-AFLP) has documented extensive changes in epigenetic methylation patterns within both individual trees and individual clones. Both MS-AFLP and NBF patterns demonstrate change with both plant as well as clone age, which, while consistent with epigenetic control, confounded the detection of MS-AFLP markers diagnostic for NBF status. The preliminary study of genome-wide methylation profiles in almond identified exceptionally high level of epigenetic polymorphisms when compared to published results from seed-propagated crops. MS-AFLP status changed with both tree-age as well as clone-age, though patterns were detected which facilitate breeding selection. Results document both desirable as well as undesirable epigenetic variability existing within and among almond genotype/cultivars. Until more rapid diagnostics become available, long-term statistical assessment remains the only proven epigenetic selection method. A promising approach is to examine traits where the genetic control has already been identified but where inconsistent inheritance patterns supports the influence of epigenetic factors, as in the recent findings that methylation of the Sf locus in almond is associated with expression of self-compatibility through S-RNase loss of function.