DNA Methylation Polymorphism Amongst Genetically Uniform Yet Phenotypically Diverse East African Highland Banana Cultivars

Bananas are a major staple food of the East African highlands, with most of the production derived from a set of cultivars with nearly-identical DNA fingerprints consistent with being clonal variants of an ancient clone set (M Kitavi et al, unpublished data). Yet, these East African Highland banana (EAHB) cultivars exhibit extensive phenotypic variations among and within clone sets. DNA methylation is a potential source of inter-individual phenotypic variation because of its propensity to alter gene expression which could generate phenotypic variation. However, there is little data on methylation polymorphism patterns across accessions of this Musasubgroup and whether this could be contributing to the observed phenotypic variation. We studied the levels and patterns of DNA methylation polymorphisms at CCGG sites across 90 accessions of triploid (3x) EAHB cultivars, using a methylation-sensitive amplified polymorphism (MSAP) technique. The results indicate extensive DNA methylation across the EAHB cultivars, whereby 44% of CCGG sites surveyed were methylated. Almost all (98%) of these methylated CCGG sites displayed some level of DNA methylation polymorphism across the EAHB cultivars.  Cluster analysis did not reveal any distinct DNA methylation patterns related to morphological clone sets. Epigenetic variation as measured by DNA methylation was structured into distinct within (98%) and between (2%) population components and was highly significant (p = 0.002).  DNA methylation diversity levels were similar between the EAHB clone sets, despite the known phenotypic variation. Our results indicate that while DNA methylation polymorphisms are common amongst EAHB cultivars, MSAP does not detect any obvious relationship between DNA methylation variation and phenotypic variation in East African Highland bananas.