Abstract: Many desert ephemeral plants germinate in both spring and autumn, forming distinct cohorts with different phenotypes, yet the epigenetic basis of this variation remains unclear. This study aimed to investigate natural variation in global DNA cytosine methylation and its associations with phenotypes in the typical ephemeral plant Erodium oxyrhinchum. Here, we quantified global DNA cytosine methylation in E. oxyrhinchum at different growth periods. We also integrated ecological and physiological traits to construct plant trait networks (PTNs) for each cohort. DNA methylation in AG increased significantly before winter and decreased afterwards. In contrast, the SG cohort showed elevated methylation in early summer, exceeding AG levels. Notably, global methylation variation was associated with most size- and fecundity-related traits. PTN analysis revealed that plant height and DNA methylation were highly connected in the SG network, while leaf number and soluble sugar were highly connected in the AG network. Moreover, the SG network was more densely connected than the AG network, suggesting tighter trait coordination in SG. These results indicate that the two cohorts differ in methylation patterns and trait association structures. SG methylation was more closely associated with drought-related traits, whereas AG methylation was more closely associated with low-temperature-related traits. Our findings may offer new perspectives on the potential ecological importance of epigenetic heterogeneity in desert ephemeral plant populations.

Key words: Autumn-germinated cohort, spring-germinated cohort, DNA methylation, ephemeral plants, Erodium oxyrhinchum