The Potential of Methylation Sensitive Amplification Polymorphism (MSAP) Technique to Study Global DNA Methylation Changes in Plants: Basic Principles and Perspective

Abstract

Originally introduced as a regulation to persuade different gene expressions during an organism’s developmental process to display new characteristics through environmental stimuli, epigenetics has become an exciting field of study. Epigenetics, particularly its contribution to plant plasticity in response to the changing environmental pressure, is gaining more attention nowadays. Benefiting from the low cost of the latest next generation sequencing technologies, recent techniques such as whole genome bisulfite sequencing provide epigenome data at a single-base resolution. However, the application of such technology is skewed to model organisms with known genome reference data. Here, we aim to revisit the methylation sensitive amplification polymorphism (MSAP), an indirect technique to analyze the change in DNA methylation level that is cost-effective and applicable for species with no reference genome available or having a large and complex genome. We found that MSAP is a pragmatic approach for application in a wide range of plant species and fields of study. Key steps in MSAP, such as the sequence of primers, primer pair combinations, and data interpretation, are summarized, providing a one-stop beginner’s guidance for evaluating DNA methylation changes.