Methylation-sensitive Amplified Polymorphism as a Tool to Analyze Wild Potato Hybrids

Abstract

Methylation-Sensitive Amplification Polymorphism (MSAP) is a versatile marker for analyzing DNA methylation patterns in non-model species. The implementation of this technique does not require a reference genome and makes it possible to determine the methylation status of hundreds of anonymous loci distributed throughout the genome. In addition, the inheritance of specific methylation patterns can be studied. Here, we present a protocol for analyzing DNA methylation patterns through MSAP markers in potato interspecific hybrids and their parental genotypes.

Exploring japonica rice epigenetic diversity in the main production regions of Heilongjiang Province

“…The methylation-sensitive amplified polymorphism (MSAP) technique, as a molecular technology that is a modification of amplified fragment length polymorphism (AFLP) techniques 21 , has been widely employed to analyse genomic DNA methylation levels and patterns in many species due to its dependability, high sensitivity, and convenience. It is possible to determine the methylation status of hundreds of anonymous loci distributed throughout the genome without requiring a reference genome 22 . MSAP is dependent on two different DNA methylation sensitive restriction isoschizomers, Hpa II and Msp I , which recognize the same tetranucleotide restriction site (5’-CCGG-3’), but Hpa II is sensitive to full methylation and cleaves the hemimethylated external cytosine, while Msp I is sensitive to only external cytosine methylation of the restriction site 23 .…”

Pathogen-induced alterations in methylome during Lr48-mediated APR in wheat (Triticum aestivum L.) 

“…A variety of methods that are available for analysis of DNA methylation include the following: (i) methylsensitive ampli ed polymorphism (MSAP), which involves the use AFLP following digestion of genomic DNA with two pairs of enzymes, which include a pair of isoschizomers 16,22 ; (ii) methylation sensitive restriction enzymes-seq (MRE-seq), which involves sequencing of genomic DNA following treatment with the same restriction enzymes that are used in MSAP 23 . (iii) methylated DNA immunoprecipitation sequencing (MeDIP-seq), which involves sequencing of chromatin-immunoprecipitated methylated DNA 16,24,25 , and (iv) whole genome bisulphite-sequencing (WGBS/BS) including reduced representation bisul te sequencing (RRBS) 26,27 .…”