Changes in DNA methylation patterns affect ripening time in Satsuma mandarin fruit

Differences in DNA methylation patterns might lead to differences in fruit maturation time in the citrus Satsuma, but the underlying mechanism is unclear. Here, we explored the differences in methylation patterns during fruit ripening in Satsuma among 20 early- and late-maturing Satsuma varieties and compared DNA methylation patterns in two Satsuma cultivars (Ooita wase and Aoshima unshiu) at different developmental stages using methylation-sensitive fragment length polymorphism (MSAP) analysis. We cloned and sequenced DNA from different bands to identify differentially methylated genes involved in fruit ripening. The internal methylation of CCGG sequences occurred more frequently in the early-maturing Satsuma cultivars (8.47%) than the late-maturing cultivars (6.74%), whereas the external methylation of CCGG sequences occurred less frequently in the early-maturing cultivars (24.98%) compared to the late-maturing types (27.27%). Genes encoding the G protein alpha subunit and zinc-binding protein of the histidine triad (HIT) family and two unknown genes homologous to expressed sequence tag (EST) sequences (CX052976.1 and CX071135.1) were found to be modified by methylation during the fruit ripening process. These findings suggest that DNA methylation might play important roles in regulating fruit ripening in Satsuma. Our results lay the foundation for analysing the molecular mechanism underlying fruit ripening in this important citrus crop.