MSAP markers and global cytosine methylation in plants: a literature survey and comparative analysis for a wild growing species

Methylation of DNA cytosines affects whether transposons are silenced and genes are expressed, and is a major epigenetic mechanism whereby plants respond to environmental change. Analyses of methylation-sensitive amplification polymorphism (MS-AFLP or MSAP) have been often used to assess methyl-cytosine changes in response to stress treatments and, more recently, in ecological studies of wild plant populations. MSAP technique does not require a sequenced reference genome and provides many anonymous loci randomly distributed over the genome for which the methylation status can be ascertained. Scoring of MSAP data, however, is not straightforward, and efforts are still required to standardize this step to make use of the potential to distinguish between methylation at different nucleotide contexts. Furthermore, it is not known how accurately MSAP infers genome-wide cytosine methylation levels in plants. Here, we analyse the relationship between MSAP results and the percentage of global cy...DNA胞嘧啶甲基化（DNA cytosine methylation）可调控转座子（transposons）的沉默与基因的表达，是植物响应环境变化的关键表观遗传机制（epigenetic mechanism）。甲基化敏感扩增多态性（methylation-sensitive amplification polymorphism，MS-AFLP或MSAP）分析技术常被用于评估胁迫处理下的胞嘧啶甲基化变化，近年来也逐步应用于野生植物种群的生态学研究。MSAP技术无需依赖已测序的参考基因组（sequenced reference genome），可在全基因组范围内获取大量随机分布的匿名位点（anonymous loci），并能对这些位点的甲基化状态（methylation status）进行检测。然而，MSAP数据的评分流程较为繁琐，目前仍需开展标准化工作以充分发挥其区分不同核苷酸背景下甲基化差异的潜力。此外，目前尚不明确MSAP技术对植物全基因组胞嘧啶甲基化水平（genome-wide cytosine methylation levels）的推断精度。本研究旨在分析MSAP检测结果与全球胞...