Novel SNPs of butyrophilin (BTN1A1) and milk fat globule epidermal growth factor (EGF) 8 (MFG-E8) are associated with milk traits in dairy goat

Regulation of Milk Fat Synthesis: Key Genes and Microbial Functions

Milk is rich in a variety of essential nutrients, including fats, proteins, and trace elements that are important for human health. In particular, milk fat has an alleviating effect on diseases such as heart disease and diabetes. Fatty acids, the basic units of milk fat, play an important role in many biological reactions in the body, including the involvement of glycerophospholipids and sphingolipids in the formation of cell membranes. However, milk fat synthesis is a complex biological process involving multiple organs and tissues, and how to improve milk fat of dairy cows has been a hot research issue in the industry. There exists a close relationship between milk fat synthesis, genes, and microbial functions, as a result of the organic integration between the different tissues of the cow's organism and the external environment. This review paper aims (1) to highlight the synthesis and regulation of milk fat by the first and second genomes (gastrointestinal microbial genome) and (2) to discuss the effects of ruminal microorganisms and host metabolites on milk fat synthesis. Through exploring the interactions between the first and second genomes, and discovering the relationship between microbial and host metabolite in the milk fat synthesis pathway, it may become a new direction for future research on the mechanism of milk fat synthesis in dairy cows.

Analysis of miRNAs in milk of four livestock species

BACKGROUND

Milk is essential for mammalian nutrition because it provides vital nutrients for growth and development. Milk composition, which is influenced by genetic and environmental factors, supports lactation, a complex process crucial for milk production and quality. Recent research has focused on noncoding RNAs, particularly microRNAs (miRNAs), which are present in body fluids and regulate gene expression post-transcriptionally. This study comprehensively characterizes miRNAs in milk of four livestock species, namely Bubalus bubalis, Capra hircus, Equus asinus, and Ovis aries and identifies potential target genes.

RESULTS

High-throughput sequencing of milk RNA resulted in distinct read counts across species: B. bubalis (8,790,441 reads), C. hircus (12,976,275 reads), E. asinus (9,385,067 reads), and O. aries (7,295,297 reads). E. asinus had the highest RNA mapping rate (94.6%) and O. aries the lowest (84.8%). A substantially greater proportion of miRNAs over other small RNAs was observed for the donkey milk sample (7.74%) compared to buffalo (0.87%), goat (1.57%), and sheep (1.12%). Shared miRNAs, which included miR-200a, miR-200b, miR-200c, and miR-23a among others, showed varying expression levels across species, confirmed by qPCR analysis. Functional annotation of predicted miRNA target genes highlighted diverse roles, with an enrichment in functions linked to metabolism and immunity. Pathway analysis identified immune response pathways as significant, with several miRNAs targeting specific genes across species, suggesting their regulatory function in milk.

CONCLUSIONS

Both conserved and species-specific miRNAs were detected in milk of the investigated species. The identified target genes of these miRNAs have important roles in neonatal development, adaptation, growth, and immune response. Furthermore, they influence milk and meat production traits in livestock.

Milk levels of transforming growth factor beta 1 identify mothers with low milk supply

Human milk is optimal for infant nutrition. However, many mothers cease breastfeeding because of low milk supply (LMS). It is difficult to identify mothers at risk for LMS because its biologic underpinnings are not fully understood. Previously, we demonstrated that milk micro-ribonucleic acids (miRNAs) may be related to LMS. Transforming growth factor beta (TGFβ) also plays an important role in mammary involution and may contribute to LMS. We performed a longitudinal cohort study of 139 breastfeeding mothers to test the hypothesis that milk levels of TGFβ would identify mothers with LMS. We explored whether TGFβ impacts the expression of LMS-related miRNAs in cultured human mammary epithelial cells (HMECs). LMS was defined by maternal report of inadequate milk production, and confirmed by age of formula introduction and infant weight trajectory. Levels of TGF-β1 and TGF-β2 were measured one month after delivery. There was a significant relationship between levels of TGF-β1 and LMS (X2 = 8.92, p = 0.003) on logistic regression analysis, while controlling for lactation stage (X2 = 1.28, p = 0.25), maternal pre-pregnancy body mass index (X2 = 0.038, p = 0.84), and previous breastfeeding experience (X2 = 7.43, p = 0.006). The model accounted for 16.8% of variance in the data (p = 0.005) and correctly predicted LMS for 84.6% of mothers (22/26; AUC = 0.72). Interactions between TGF-β1 and miR-22-3p displayed significant effect on LMS status (Z = 2.67, p = 0.008). Further, incubation of HMECs with TGF-β1 significantly reduced mammary cell number (t = -4.23, p = 0.003) and increased levels of miR-22-3p (t = 3.861, p = 0.008). Interactions between TGF-β1 and miR-22-3p may impact mammary function and milk levels of TGF-β1 could have clinical utility for identifying mothers with LMS. Such information could be used to provide early, targeted lactation support.

Overexpression of ATGL impairs lipid droplet accumulation by accelerating lipolysis in goat mammary epithelial cells

Adipose triglyceride lipase (ATGL) is the key enzyme for the degradation of triacylglycerols (TAGs). It functions in concert with other enzymes to mobilize TAG and supply fatty acids (FAs) for energy production. Dysregulated lipolysis leads to excess concentrations of circulating FAs, which may lead to destructive and lipotoxic effects to the organism. To understand the role of ATGL in mammary lipid metabolism, ATGL was overexpressed in goat mammary epithelial cells (GMECs) by using a recombinant adenovirus system. ATGL overexpression decreased lipid droplet (LD) accumulation and cellular TG content (p < 0.05) along with a decrease in the expression of the key enzyme that catalyzes the final step of TG synthesis (DGAT). Significant increases were observed in the expression of genes related to lipolysis (hormone-sensitive lipase [HSL]) and FA desaturation (SCD) by ATGL overexpression. Genes responsible for FA oxidation (PPARα), LD formation and secretion (ADRP and BTN1A1), and long-chain FA uptake (CD36) were all decreased by ATGL overexpression (p < 0.05). The primary products of TAG lipolysis, free FAs (FFAs), were notably increased in the ATGL-overexpressing cells. Taken together, our results demonstrated that ATGL activation impairs lipid formation partially through accelerating lipolysis in GMECs.

Milk fat globule membrane proteins are involved in controlling the size of milk fat globules during conjugated linoleic acid-induced milk fat depression

Milk fat globule membrane (MFGM) proteins surround the triacylglycerol core comprising milk fat globules (MFG). We previously detected a decrease in the size of fat globules during conjugated linoleic acid (CLA)-induced milk fat depression (MFD), and other studies have reported that some MFGM proteins play a central role in regulating mammary cellular lipid droplet size. However, little is known about the relationship between MFD, MFG size, and MFGM proteins in bovine milk. The aim of this study was to investigate the profile of MFGM proteins during MFD induced by CLA. Sixteen mid-lactating Holstein cows (145 ± 24 d in milk) with similar body condition and parity were divided into control and CLA groups over a 10-d period. Cows were fed a basal diet (control, n = 8) or control plus 15 g/kg of dry matter (DM) CLA (n = 8) to induce MFD. Cow performance, milk composition, and MFG size were measured daily. On d 10, MFGM proteins were extracted and identified by quantitative proteomic analysis, and western blotting was used to verify a subset of the identified MFGM proteins. Compared with controls, supplemental CLA did not affect milk production, DM intake, or milk protein and lactose contents. However, CLA reduced milk fat content (3.73 g/100 mL vs. 2.47 g/100 mL) and the size parameters volume-related diameter D_[4,3] (3.72 μm vs. 3.35 μm) and surface area-related diameter D_[3,2] (3.13 μm vs. 2.80 μm), but increased specific surface area of MFG (1,905 m²/kg vs. 2,188 m²/kg). In total, 177 differentially expressed proteins were detected in milk from cows with CLA-induced MFD, 60 of which were upregulated and 117 downregulated. Correlation analysis showed that MFG size was negatively correlated with various proteins, including XDH and FABP3, and positively correlated with MFG-E8, RAB19, and APOA1. The results provide evidence for an important role of MFGM proteins in regulating MFG diameter, and they facilitate a mechanistic understanding of diet-induced MFD.

Maternal Variants in the MFGE8 Gene are Associated with Perceived Breast Milk Supply

Background: The World Health Organization recommends exclusive breastfeeding for ≥6 months, but many mothers are unable to meet this goal. A major reason why mothers undergo early, unplanned breastfeeding cessation is perceived inadequate of milk supply (PIMS). We hypothesized that defining genetic polymorphisms associated with PIMS could aid early identification of at-risk mothers, providing an opportunity for targeted lactation support. Materials and Methods: This prospective observational cohort study followed 221 breastfeeding mothers for 12 months, collecting medical, demographic, and breastfeeding characteristics. Eighteen mammary secretory genes were assessed for single-nucleotide polymorphisms in 88 women (45 with PIMS and 43 with perceived adequate milk supply [PAMS]), matched by age/race/parity. Hierarchical regressions were used to assess the ability of genotype to aid PIMS prediction. Results: Mothers with PIMS exclusively breastfed for a shorter period (7 ± 12 weeks; p = 0.001) and reported lower milk production (17.6 ± 13.3 oz/day; p = 0.001), and their infants displayed reduced weight-for-length Z-score gains (0.74 ± 1.4; p = 0.038) relative to mothers with PAMS (22 ± 19 weeks; 27.03 ± 12.2 oz/day; 1.4 ± 1.5). Maternal genotype for the rs2271714 variant within milk fat globule EGF and factor V/VIII domain containing gene (MFGE8) was associated with PIMS status (p = 0.009, adjusted p = 0.09, likelihood ratio = 9.33) and duration of exclusive breastfeeding (p = 0.009, adjusted p = 0.09, χ² = 9.39). Addition of MFGE8 genotype to a model employing maternal characteristics (age, parity, previous breast-feeding duration, body mass index, education, and depression status) significantly increased predictive accuracy for PIMS status (p = 0.001; χ² = 13.5; area under the curve = 0.813 versus 0.725). Conclusions: Genotyping one lactogenic gene aided identification of mothers at risk for PIMS. If validated in a larger cohort, such an approach could be used to identify mothers who may benefit from increased lactation support.

A Candidate Gene Association Study for Economically Important Traits in Czech Dairy Goat Breeds

Milk production is influenced by many factors, including genetic and environmental factors and their interactions. Animal health, especially udder health, is usually evaluated by the number of somatic cells. The present study described the effect of polymorphisms in the ACACA, BTN1A1, LPL, and SCD genes on the daily milk yield, fat, and protein percentages and somatic cell count. In this study, 590 White Shorthaired (WSH) and Brown Shorthaired (BSH) goats were included. SNP genotyping was performed by PCR-RFLP and multiplex PCR followed by SNaPshot minisequencing analysis. The linear mixed model with repeated measurement was used to identify the genetic associations between the studied genes/SNPs and chosen traits. All selected genes were polymorphic in the tested goat populations and showed significant associations with milk traits. Only BTN1A1 (SNP g.599 A > G) showed a significant association with the somatic cell score. After Bonferroni correction, a significant effect of LPL g.300G > A on daily milk yield and fat percentage, LPL g.185G > T on protein percentage, and LPL G50C, SCD EX3_15G > A, and SCD EX3_68A > G on fat percentage was found. The importance of environmental factors, such as the herd-year effect, month of milking, and lactation order on all milk performance indicators was confirmed.

Genome-wide association study of birth weight and pre-weaning body weight of crossbred pigs

In piggery, birth weight and body weight remains most vital economic trait as they directly influence on the production performance of the farm. Implementing the genomic selection would pay way for rapid genetic gain along with increased accuracy than conventional breeding. Prior to genomic selection, genome wide association study (GWAS) has to be conducted in order to find informative SNPs associated with the traits of interest in a given population. Under this study 96 crossbred pigs were genotyped using double digest genotype by sequencing (GBS) technique using Hiseq platform. Raw FASTQ data were processed using dDOCENT Pipeline on Reference based method and variants were called using Free Bayes (version 1.1.0-3). Using Plink (v1.09b), variants having MAF>0.01, HWE<0.001 and genotyping rate >80% were filtered out and 20,467 SNPs were retained after quality control, for ascertaining GWAS in 96 pigs. Before conducting association studies, the data were adjusted for significant nongenetic factors affecting the traits of interest. GWAS was performed using Plink software (v1.9b) identified 9, 11, 12, 23, 28, 24, 30, 33 and 42 SNPs significantly (adjusted P<0.001) associated with birth weight, body weight at weekly interval from 1st week to 8th week, respectively. A large proportion of significant (adjusted P<0.001) SNPs were located on SSC10, SSC6, SSC13, SSC8 and SSC1. One genome wide significant SNP and four genome wide suggestive SNPs were identified. Two common SNPs affecting all body weight at different weeks were located on SSC5:40197442 and SSC13:140562 base pair position. This study helps to identify the genome wide scattered significant SNPs associated with traits of interest which could be used for genomic selection, but further validation studies of these loci in larger population are recommended.

The Application of Genomic Technologies to Investigate the Inheritance of Economically Important Traits in Goats

Goat genomics has evolved at a low pace because of a lack of molecular tools and sufficient investment. Whilst thousands and hundreds of quantitative trait loci (QTL) have been identified in cattle and sheep, respectively, about nine genome scans have been performed in goats dealing with traits as conformation, growth, fiber quality, resistance to nematodes, and milk yield and composition. In contrast, a great effort has been devoted to the characterization of candidate genes and their association with milk, meat, and reproduction phenotypes. In this regard, causal mutations have been identified in the αS1-casein gene that has a strong effect on milk composition and the PIS locus that is linked to intersexuality and polledness. In recent times, the development of massive parallel sequencing technologies has allowed to build a reference genome for goats as well as to monitor the expression of mRNAs and microRNAs in a broad array of tissues and experimental conditions. Besides, the recent design of a 52K SNP chip is expected to have a broad impact in the analysis of the genetic architecture of traits of economic interest as well as in the study of the population structure of goats at a worldwide scale.

Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

Polar bears (PBs) are superbly adapted to the extreme Arctic environment and have become emblematic of the threat to biodiversity from global climate change. Their divergence from the lower-latitude brown bear provides a textbook example of rapid evolution of distinct phenotypes. However, limited mitochondrial and nuclear DNA evidence conflicts in the timing of PB origin as well as placement of the species within versus sister to the brown bear lineage. We gathered extensive genomic sequence data from contemporary polar, brown, and American black bear samples, in addition to a 130,000- to 110,000-y old PB, to examine this problem from a genome-wide perspective. Nuclear DNA markers reflect a species tree consistent with expectation, showing polar and brown bears to be sister species. However, for the enigmatic brown bears native to Alaska's Alexander Archipelago, we estimate that not only their mitochondrial genome, but also 5-10% of their nuclear genome, is most closely related to PBs, indicating ancient admixture between the two species. Explicit admixture analyses are consistent with ancient splits among PBs, brown bears and black bears that were later followed by occasional admixture. We also provide paleodemographic estimates that suggest bear evolution has tracked key climate events, and that PB in particular experienced a prolonged and dramatic decline in its effective population size during the last ca. 500,000 years. We demonstrate that brown bears and PBs have had sufficiently independent evolutionary histories over the last 4-5 million years to leave imprints in the PB nuclear genome that likely are associated with ecological adaptation to the Arctic environment.

Exploring polymorphisms of the bovine RARRES2 gene and their associations with growth traits

Retinoic acid receptor responder 2 gene (RARRES2) encodes a novel adipokine protein that plays a crucial role in regulating several biological processes, including immune responses, adipocyte differentiation, type 2 diabetes and metabolic syndrome. In this paper, polymorphisms of the bovine RARRES2 gene were detected in 1300 individuals from six breeds by DNA pooling, CRS-PCR-RFLP and DNA sequencing methods. The results showed that NC_007302:g.117035859A>G, 117035706G>A and 117034290A>G were in the coding region, which resulted in three synonymous mutations and only 117033779C>G was in the 3' UTR. Additionally, associations of the four novel SNPs with growth traits were analyzed in Nanyang cattle up to 2 years of age. In P1-PvuII locus, individuals with genotype BC had greater body height and hucklebone width than those with genotype AA, AC and AB at the age of 24 months. In P3-BamHI locus, individuals with genotype AG had higher hucklebone width than those with genotype GG at the age of 24 months. However, no statistically significant differences were observed in P5-SmaI locus. These results indicated that RARRES2 gene might be a potential candidate gene for marker-assisted selection (MAS).