Integrating genome-wide methylation and transcriptome-wide analyses to reveal the genetic mechanism of milk traits in Kazakh horses.

This research investigates the genetic mechanisms influencing milk production in Kazakh horses by comparing genome-wide DNA methylation profiles of blood from high and low milk-production groups.

Background

• The horse milk holds significant economical value due to its beneficial quantitative traits, however, the DNA methylation regulators involved in horse milk traits haven’t been demystified.
• Genome-wide DNA methylation patterns could play an essential role in equine milk yield regulation.
• The study focuses on Kazakh horses, which are classified into two categories for analysis: a high-production group (HP) with an average daily milk yield of 7.5 kg, and a low-production group (LP) with an average daily milk yield of 3.2 kg.

Method

• The research employed deep whole-genome bisulfite sequencing to examine DNA methylation profiles in the blood from the two groups.
• The first step was to analyze the proportion of methylation at the CpG sites of both groups, and confirm that it was similar in both.

Findings

• The researchers identified 26,677 differential methylated regions (DMRs) of CG, 15 DMRs of CHG and 480 DMRs of CHH. Additionally, they identified 8268 DMR-related genes (DMGs).
• The researchers performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses on the DMGs, revealing that some of these genes had a role in regulating milk production and composition.
• By comparing the whole-genome bisulfite sequencing data with previous RNA-seq data, 94 overlapping genes were found. These overlapping genes were likely to be the main regulators of milk production and composition in Kazakh horses.
• The study found that 9 DMGs were likely to be ultimately involved in milk production in Kazakh horses.

Conclusion

• This study has systematically explored genome-wide DNA methylation profiles in Kazakh horses and identified specific genes and patterns associated with high and low milk production.
• The identification of DMGs and their roles in horse milk production can serve as a significant scientific contribution to understanding the genetic mechanism behind equine milk traits and can further aid in their potential genetic improvement.