DNA methylation pattern of the goat PITX1 gene and its effects on milk performance

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

BACKGROUND

DNA methylation is an epigenetic mechanism that takes place at gene promoters and a potent epigenetic marker to regulate gene expression.

OBJECTIVE

The study aimed to improve the milk production of Zaraibi goats by addressing the methylation pattern of two milk production-related genes: the growth hormone receptor (GHR) and the growth differentiation factor-9 (GDF-9).

METHODS

54 and 46 samples of low and high milk yield groups, respectively, were collected. Detection of methylation was assessed in two CpG islands in the GDF-9 promoter via methylation-specific primer assay (MSP) and in one CpG island across the GHR promoter using combined bisulfite restriction analysis (COBRA).

RESULTS

A positive correlation between the methylation pattern of GDF-9 and GHR and their expression levels was reported. Breeding season was significantly effective on both peak milk yield (PMY) and total milk yield (TMY), where March reported a higher significant difference in PMY than November. Whereas single birth was highly significant on TMY than multiple births. The 3rd and 4th parities reported the highest significant difference in PMY, while the 4th parity was the most effective one on TMY.

CONCLUSION

These results may help improve the farm animals' milk productive efficiency and develop prospective epigenetic markers to improve milk yield by epigenetic marker-assisted selection (eMAS) in goat breeding programs.

DNA methylation and gene expression changes in mouse mammary tissue during successive lactations: part II - the impact of lactation rank

Mastitis is among the main reasons women cease breastfeeding. In farm animals, mastitis results in significant economic losses and the premature culling of some animals. Nevertheless, the effect of inflammation on the mammary gland is not completely understood. This article discusses the changes to DNA methylation in mouse mammary tissue caused by lipopolysaccharide-induced inflammation after in vivo intramammary challenges and the differences in DNA methylation between 1^st and 2^nd lactations. Lactation rank induces 981 differential methylations of cytosines (DMCs) in mammary tissue. Inflammation in 1^st lactation compared to inflammation in 2^nd lactation results in the identification of 964 DMCs. When comparing inflammation in 1^st vs. 2^nd lactations with previous inflammation history, 2590 DMCs were identified. Moreover, Fluidigm PCR data show changes in the expression of several genes related to mammary function, epigenetic regulation, and the immune response. We show that the epigenetic regulation of two successive physiological lactations is not the same in terms of DNA methylation and that the effect of lactation rank on DNA methylation is stronger than that of the onset of inflammation. The conditions presented here show that few DMCs are shared between comparisons, suggesting a specific epigenetic response depending on lactation rank, the presence of inflammation, and even whether the cells had previously suffered inflammation. In the long term, this information could lead to a better understanding of the epigenetic regulation of lactation in both physiological and pathological conditions.Abbreviations: RRBS, reduced representation bisulphite sequencing; RT-qPCR, real-time quantitative polymerase chain reaction; MEC, mammary epithelial cells; MaSC, mammary stem cell; TSS, transcription start site; TTS, transcription termination site; UTR, untranslated region; SINE, short interspersed nuclear element; LINE, long interspersed nuclear element; CGI, CpG island; DEG, differentially expressed gene; DMC, differentially methylated cytosine; DMR, differentially methylated region; GO term, gene ontology term; MF, molecular function; BP, biological process.

In vitro transdifferentiated signatures of goat preadipocytes into mammary epithelial cells revealed by DNA methylation and transcriptome profiling

During mammary development, the transdifferentiation of mammary preadipocytes is one of the important sources for lactating mammary epithelial cells (MECs). However, there is limited knowledge about the mechanisms of dynamic regulation of transcriptome and genome-wide DNA methylation in the preadipocyte transdifferentiation process. Here, to gain more insight into these mechanisms, preadipocytes were isolated from adipose tissues from around the goat mammary gland (GM-preadipocytes). The GM-preadipocytes were cultured on Matrigel in conditioned media made from goat MECs to induce GM-preadipocyte-to-MEC transdifferentiation. The transdifferentiated GM-preadipocytes showed high abundance of keratin 18, which is a marker protein of MECs, and formed mammary acinar-like structures after 8 days of induction. Then, we performed transcriptome and DNA methylome profiling of the GM-preadipocytes and transdifferentiated GM-preadipocytes, respectively, and the differentially expressed genes and differentially methylated genes that play underlying roles in the process of transdifferentiation were obtained. Subsequently, we identified the candidate transcription factors in regulating the GM-preadipocyte-to-MEC transdifferentiation by transcription factor-binding motif enrichment analysis of differentially expressed genes and differentially methylated genes. Meanwhile, the secretory proteome of GM-preadipocytes cultured in conditioned media was also detected. By integrating the transcriptome, DNA methylome, and proteome, three candidate genes, four proteins, and several epigenetic regulatory axes were further identified, which are involved in regulation of the cell cycle, cell polarity establishment, cell adhesion, cell reprogramming, and adipocyte plasticity. These findings provide novel insights into the molecular mechanism of preadipocyte transdifferentiation and mammary development.

Epigenetics: New Insights into Mammary Gland Biology

The mammary gland undergoes important anatomical and physiological changes from embryogenesis through puberty, pregnancy, lactation and involution. These steps are under the control of a complex network of molecular factors, in which epigenetic mechanisms play a role that is increasingly well described. Recently, studies investigating epigenetic modifications and their impacts on gene expression in the mammary gland have been performed at different physiological stages and in different mammary cell types. This has led to the establishment of a role for epigenetic marks in milk component biosynthesis. This review aims to summarize the available knowledge regarding the involvement of the four main molecular mechanisms in epigenetics: DNA methylation, histone modifications, polycomb protein activity and non-coding RNA functions.

GWAS-Based Identification of New Loci for Milk Yield, Fat, and Protein in Holstein Cattle

Simple Summary

Understanding the genetic architecture underlying milk production traits in cattle is beneficial so that genetic variants can be targeted toward the genetic improvement. In this study, we performed a genome-wide association study for milk production and quality traits in Holstein cattle. In the total of ten significant single-nucleotide polymorphisms (SNPs) associated with milk fat and protein, six are located in previously reported quantitative traits locus (QTL) regions. The study not only identified the effect of DGAT1 gene on milk fat and protein but also found several novel candidate genes. In addition, some pleiotropic SNPs and QTLs were identified that associated with more than two traits, these results could provide some basis for molecular breeding in dairy cattle.

Abstract

High-yield and high-quality of milk are the primary goals of dairy production. Understanding the genetic architecture underlying these milk-related traits is beneficial so that genetic variants can be targeted toward the genetic improvement. In this study, we measured five milk production and quality traits in Holstein cattle population from China. These traits included milk yield, fat, and protein. We used the estimated breeding values as dependent variables to conduct the genome-wide association studies (GWAS). Breeding values were estimated through pedigree relationships by using a linear mixed model. Genotyping was carried out on the individuals with phenotypes by using the Illumina BovineSNP150 BeadChip. The association analyses were conducted by using the fixed and random model Circulating Probability Unification (FarmCPU) method. A total of ten single-nucleotide polymorphisms (SNPs) were detected above the genome-wide significant threshold (p < 4.0 × 10⁻⁷), including six located in previously reported quantitative traits locus (QTL) regions. We found eight candidate genes within distances of 120 kb upstream or downstream to the associated SNPs. The study not only identified the effect of DGAT1 gene on milk fat and protein, but also discovered novel genetic loci and candidate genes related to milk traits. These novel genetic loci would be an important basis for molecular breeding in dairy cattle.

Novel indel variations of the sheep FecB gene and their effects on litter size

Various studies had shown that the FecB gene (also known as BMPRIB, BMPR1B or ALK-6) was the major gene influencing sheep litter size, for which its SNPs' variations were reportedly linked. Yet, surprisingly, there was no published information on the insertion/deletion (indel) variation of this gene. Herein, using a population of Chinese Australian White sheep (n = 932), we identified five novel indels in the different introns of the FecB gene. Among them, the 12-bp indel was distinguished as a splicing region variation that was completely linked to the 17-bp indel. Analysis of variance revealed that only the 10-bp indel was significantly associated with sheep litter size (P = 0.010), for which the deletion/deletion (DD) genotype was the harmful one for fecundity. Nevertheless, the combined genotypes of these five indels were significantly (P = 0.033) correlated with the litter size. These findings would provide fresh insight into developing a sounder basis to accelerate molecular breeding in sheep via DNA markers in a marker-assisted selection strategy.