Comparison between the RUMIGEN EpiChip data with reduced representation bisulfite sequencing data
DNA methylation contributes to the elaboration of phenotypes and is hypothesized to account for interindividual variations in farm animals. Currently, methodologies available to investigate DNA methylation in cattle rely on high throughput sequencing, which cannot be applied to large cohorts. To enable large scale DNA methylation analysis, we developed the RUMIGEN EpiChip, the first DNA methylation array specifically designed for cattle. Manufactured by Illumina, the EpiChip contains 43,317 CpG markers allowing analysis of phenotypes of agronomical interest as well as the study of regulatory processes. The assay design drew on data from numerous studies achieved by the scientific community, and includes CpGs where methylation varies with health status, physiological stage, fertility, and environmental challenges, as well as CpGs located in functional genomic elements (promoters, CTCF binding sites, expression quantitative trait loci). The technical performances of the EpiChip were tested on several semen and blood DNA samples and in two laboratories, showing excellent repeatability, accuracy and interoperability. Methylation values were also concordant with those obtained by reduced representation bisulfite sequencing. The RUMIGEN EpiChip is a cost-effective and versatile resource that opens new opportunities for the study of regulatory mechanisms underlying phenotypic variation and for large-scale association analyses in cattle.