Integrative analysis of genome‐wide DNA methylation and gene expression profiles reveals important epigenetic genes related to milk production traits in dairy cattle

Abstract

Epigenetic modification plays a critical role in establishing and maintaining cell differentiation, embryo development, tumorigenesis and many complex diseases. However, little is known about the epigenetic regulatory mechanisms for milk production in dairy cattle. Here, we conducted an epigenome‐wide study, together with gene expression profiles to identify important epigenetic candidate genes related to the milk production traits in dairy cattle. Whole‐genome bisulphite sequencing and RNA sequencing were employed to detect differentially methylated genes (DMG) and differentially expressed genes (DEG) in blood samples in dry period and lactation period between two groups of cows with extremely high and low milk production performance. A total of 10,877 and 6,617 differentially methylated regions were identified between the two groups in the two periods, which corresponded to 3,601 and 2,802 DMGs, respectively. Furthermore, 156 DEGs overlap with DMGs in comparison of the two groups, and 131 DEGs overlap with DMGs in comparison of the two periods. By integrating methylome, transcriptome and GWAS data, some potential candidate genes for milk production traits in dairy cattle were suggested, such as DOCK1, PTK2 and PIK3R1. Our studies may contribute to a better understanding of epigenetic modification on milk production traits of dairy cattle.

DNA methylation of GDF-9 and GHR genes as epigenetic regulator of milk production in Egyptian Zaraibi goat

“…Wanting et al . ( 2020 ), compared the transcriptional profiles and genome-wide DNA methylation patterns of cows with highly diverse milk production performances using genome-wide DNA methylation sequencing and RNA-seq on blood tissue, and revealed that blood tissue alterations in DNA methylation and gene expression for the DOCK1, PTK2, and PIK3R1 genes had variations in milk production among cattle. In addition, the quantity of methionine, lysine, choline, and folate in the diet, among other dietary elements that impact milk supply and composition, has been shown by Ana Lesta et al ( 2023 ) to change the methylation status of certain genes in dairy cows.…”

“… 2014 and Wanting et al . 2020 ). A considerable number of reports have estimated the methylation status of many candidate genes for their correlation with milk production in different livestock (Pauwels et al 2017 ; Chen et al 2018 ; Zhao et al 2019 ).…”

Testing Two Somatic Cell Count Cutoff Values for Bovine Subclinical Mastitis Detection Based on Milk Microbiota and Peripheral Blood Leukocyte Transcriptome Profile

“…Blood, however, is relatively easy to collect and is responsible for various substance and molecule exchanges with the mammary gland. Moreover, the presence of some immune cells within the blood, such as leukocytes, enables blood transcriptome to reflect the overall physiological condition of cows [16,17]. Therefore, our study used peripheral blood leukocyte transcriptome as a proxy for mammary gland transcriptome.…”

Identification and characterization of whole blood gene expression and splicing quantitative trait loci during early to mid-lactation of dairy cattle

“…Whole blood can reflect the physiological conditions of cows as it is responsible for transporting various substances used in milk production [ 12 ]. Some studies have shown that individuals with different milk production performances have different gene expression levels, and potential molecular biomarkers in the blood transcriptome related to milk performance traits have been identified [ 12 , 13 ]. In addition, blood leukocytes are widely used as immune cells in transcriptional surveys of health traits, such as mastitis [ 14 ] and ketosis [ 15 ].…”