Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population

In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant Cardamine leucantha. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed) and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals). We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers). We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP) loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms, particularly for sessile clonal species.对于植物这类固着生物（sessile organisms）而言，种群的空间遗传结构往往呈现出持久稳定的分布格局。学界已在多个类群中开展此类结构的分析，以解析决定生物种群遗传组成的核心过程。对于多数主要通过克隆扩散进行繁殖的固着生物而言，即使未发生遗传变异，克隆个体间的表观遗传状态仍可存在差异。然而，相较于植物种群遗传特性的研究，针对其自然种群表观遗传特性的探究相对匮乏。本研究针对克隆植物白花碎米荠（Cardamine leucantha）的自然种群，同步评估了遗传变异与表观遗传变异的空间结构。我们采用分层贝叶斯模型（hierarchical Bayesian model），以评估基株（genet，即由单粒种子克隆衍生的个体群）归属以及植被覆盖度对分株（ramets，即具备生理独立性的克隆植株）间表观遗传变异的影响。我们在面积为20 m × 20 m的研究样地内采集了332个分株，该样地内共存在137个基株（通过8个简单序列重复（Simple Sequence Repeat, SSR）标记进行鉴定）。我们在24个甲基化敏感扩增片段长度多态性（methylation-sensitive amplified fragment length polymorphism, MS-AFLP）位点处检测到了DNA甲基化相关的表观遗传变异。在所有24个MS-AFLP位点的亚表观位点（subepiloci）分布中，均检测到显著的基株效应。植被覆盖度对多数MS-AFLP位点的变异未产生统计学上的显著影响。因此，表观遗传变异的空间聚集格局，在很大程度上可归因于隶属于同一基株的分株的聚集现象。通过分层贝叶斯分析，我们在基因型与环境因子分布不均的复杂背景下，成功在自然植物种群中鉴定出多个基株特异性的表观遗传状态变化。该研究结果表明，针对多样类群生物自然种群的空间表观遗传结构开展进一步研究十分必要，尤其是针对固着性克隆物种。