Search Results (101)

Goat caseins are highly polymorphic proteins that affect milk functional properties. In this study, an in silico approach was employed to analyze the influence of goat casein allelic variants on the quantity and bioactivity potential of peptides released after enzymatic hydrolysis. The reported protein sequences from the most frequent allelic variants in Capra hircus caseins (α-S1, β, α-S2, and κ-casein) were analyzed in the BIOPEP-UWM database to determine the frequency of occurrence of bioactive fragments from each casein. After specific hydrolysis with pepsin, trypsin, and chymotrypsin A, important differences in the peptide profile and bioactivity potential were observed within and between the casein allelic variants. The β-casein A and C alleles, α-S1-casein allele E, and α-S2-casein allele F presented the highest bioactivity potential, and some allele-specific peptides were also released, highlighting the impact of genotype on the predicted bioactivity. The inhibition of angiotensin-converting enzyme (ACE-I) and dipeptidyl peptidase IV (DPP-IV) activities was the most frequent bioactivity of the released peptides, suggesting possible antihypertensive and antidiabetic effects. Once confirmed by experimental studies, the use of goat casein genotyping could direct efforts to enhance the functional quality of goat milk. Full article

Nuclear receptor coactivator 6 is a gene that produces a protein that regulates transcriptional activity. It is also involved in many processes like cell survival, metabolism, homeostasis, and embryonic development. This study focused on studying the genetic influence of single-nucleotide polymorphisms (SNPs) within the NCOA6 gene on lactation performance characteristics. The objective of this study was to determine the genetic impact of SNPs of the NCOA6 gene on milk production traits. After the random selection of twenty cows, PCR amplification and sequencing were performed from their blood samples to find the SNPs present in the bovine NCOA6 gene. As a result, two SNPs, g.71544C > T and g.87310A > G, were found. Then, the genotyping of the cows (n = 985) was conducted using a Sequenom MassARRAY based on previously identified SNP information. The least-square method was applied to study the links between lactation traits, somatic cell score (SSC), and 305-day milk output. The results indicated that the SNP g.87310A > G was strongly associated with g.71544C > T in linkage disequilibrium. The single-nucleotide polymorphism g.87310A > G showed a very strong association with daily milk yield and 305-day milk production. Individuals with the AA genotype exhibited a notable increase in daily milk production by 1.64 kg, and their 305-day milk yield was approximately 500 kg higher. This variation demonstrated a significant genetic effect on milk output. In brief, the pleiotropic influence of the cattle NCOA6 gene on lactation traits was revealed in this study. However, additional research will provide a basis for further exploring the underlying correlation and theoretical framework of the molecular genetics of milk composition and the production attributes of Holstein cows. Full article

Mastitis is an important disease limiting milk production in dairy cows. Somatic cell score is commonly used as one of the main ways to gauge the level of mastitis in dairy cows, with higher somatic cell scores usually indicating possible mastitis. However, the main molecular markers affecting somatic cell scores remain unknown. The aim of this study was to investigate the association between single nucleotide polymorphisms in the SLC11A1 gene and somatic cell score in Chinese Holstein cows. In this study, 210 Chinese Holstein cows were genotyped and potential SNPs were detected by DNA sequencing, PCR-SSCP and PCR-RFLP analysis. Our results revealed two SNPs were identified in the CDS region of SLC11A1: c.723C>T and c.1144C>G. For the c.723C>T polymorphic site, two genotypes (AA, AB) were found and the genotype frequencies were 0.790 and 0.210, respectively. The results of the association analysis showed that the mean somatic cell score of the AA genotypes were significantly lower than those of the AB genotypes, suggesting that the A allele is a potential marker for improving mastitis resistance in Chinese Holstein cows. For the c.1144C>G polymorphic site, three genotypes (CC, CD, and DD) were found and the genotype frequencies were 0.629, 0.352 and 0.019, respectively. The association analysis revealed that the mean somatic cell score of CC genotypes was lower than that of CD and DD genotypes, however, no significant differences were observed among the various genotype groups when subjected to pair-wise comparisons. The bioinformatic analysis showed that these mutations affected the secondary and tertiary structure of SLC11A1 mRNA, suggesting that they may affect gene expression or protein translation and function. Finally, we predicted the SLC11A1 protein interaction network and found that SPI1, NOD2, TLR2 and S100A12 interacted with SLC11A1 and were reported as candidate genes associated with mastitis resistance. The results indicated that the SNP (c.723C>T) could be potential molecular marker for improving mastitis resistance traits in Chinese Holstein cows. We recommend further validation of this SNP in larger populations and its potential integration into breeding programs to enhance mastitis resistance in dairy cows. Full article

Understanding the genetic basis of economically important traits is essential for enhancing the productivity, fertility, and health of dairy cattle. This study aimed to identify the pleiotropic genes associated with the 305-day milk yield (MY305), days open (DO), and milk fat-to-protein ratio (FPR) in Thai-Holstein crossbred dairy cattle using a genome-wide association study (GWAS) approach. The dataset included 18,843 records of MY305 and milk FPR, as well as 48,274 records of DO, collected from first-lactation Thai-Holstein crossbred dairy cattle. A total of 868 genotyped animals and 43,284 informative SNPs out of 50,905 were used for the analysis. The single-nucleotide polymorphism (SNP) effects were evaluated using a weighted single-step GWAS (wssGWAS), which estimated these effects based on genomic breeding values (GEBVs) through a multi-trait animal model with single-step genomic BLUP (ssGBLUP). Genomic regions explaining at least 5% of the total genetic variance were selected for candidate gene analysis. Single-step genomic REML (ssGREML) with a multi-trait animal model was used to estimate components of (co)variance. The heritability estimates from additive genetic variance were 0.262 for MY305, 0.029 for DO, and 0.102 for milk FPR, indicating a moderate genetic influence on milk yield and a lower genetic impact on fertility and milk FPR. The genetic correlations were 0.559 (MY305 and DO), −0.306 (MY305 and milk FPR), and −0.501 (DO and milk FPR), indicating potential compromises in genetic selection. wssGBLUP showed a higher accuracy than ssGBLUP, although the improvement was modest. A total of 24, 46, and 33 candidate genes were identified for MY305, DO, and milk FPR, respectively. Pleiotropic effects, identified by SNPs showing significant influence with more than trait, were observed in 14 genes shared among all three traits, 17 genes common between MY305 and DO, 14 genes common between MY305 and milk FPR, and 26 genes common between DO and milk FPR. Overall, wssGBLUP is a promising approach for improving the genomic prediction of economic traits in multi-trait analyses, outperforming ssGBLUP. This presents a viable alternative for genetic evaluation in dairy cattle breeding programs in Thailand. However, further studies are needed to validate these candidate genes and refine marker selection for production, fertility, and health traits in dairy cattle. Full article

Fatty acid synthase (FAS) is a fundamental metabolic enzyme that catalyzes the synthesis of endogenous fatty acids; TACR3, also known as tachykinin receptor 3 or NK3R, is an important G-protein-coupled receptor that is primarily responsible for responding to neuropeptides such as neurokinin B (NKB) and plays a crucial role in embryonic development, organ formation, and cell differentiation. This study aimed to explore the association between the single-nucleotide polymorphisms (SNPs) of the FAS and TACR3 genes and the milk quality of Gannan yak and to determine them as potential molecular marker loci for the milk quality of yaks. The genotyping of 162 Gannan yaks was performed using liquid-phase chip technology. Association analyses were conducted between the obtained SNP loci genotypes and milk composition traits, including milk protein, casein, non-fat solids, and acidity. Comparative sequence analysis of two genes (FAS and TACR3) across multiple species revealed that the yak FAS gene exhibited the highest homology with Bos taurus and Bos indicus, while the yak TACR3 gene showed the greatest sequence similarity to Bos taurus. Hardy–Weinberg equilibrium tests were performed on four SNP loci, and the equilibrium indices of the four loci were 0.799, 0.368, 0.689, and 0.948 (p > 0.05), indicating that all of these loci are in Hardy–Weinberg equilibrium state. g.13,276T>C (FAS) was significantly correlated with lactose content traits (p < 0.05); g.74,382C>G (FAS) was significantly correlated with casein, protein, total solids, non-fat solids, and acidity traits (p < 0.05); g.40,529A>G (TACR3) was significantly correlated with protein, non-fat solids, citric acid, and acidity traits (p < 0.05). The influence of g.40,555C>T (TACR3) on these traits did not reach a significant level (p > 0.05). This study suggests that two genes can serve as potential candidate genes affecting the quality of Gannan yak milk, providing reference genes for improving the quality of Gannan yak milk. Full article

Lactation traits are critical economic attributes in domestic animals. This study investigates genetic markers and functional genes associated with lactation traits in Xinjiang donkeys. We analyzed 112 Xinjiang donkeys using 10× whole genome re-sequencing to obtain genome-wide single nucleotide polymorphisms (SNPs). Genome-wide association analyses were conducted using PLINK 2.0 and GEMMA 0.98.5 software, employing mixed linear models to assess several lactation traits: average monthly milk yield (AY), fat percentage (FP), protein percentage (PP), and lactose percentage (LP). A total of 236 SNPs were significantly associated with one or more milk production traits (p < 0.000001). While the two-software identified distinct SNP associations, they consistently detected the same 11, 95, 5, and 103 SNPs for AY, FP, PP, and LP, respectively. Several of these SNPs are located within potential candidate genes, including glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1 (GPIHBP1), FLII actin remodeling protein (FLII), mitochondrial topoisomerase 1 (TOP1MT), thirty-eight-negative kinase 1 (TNK1), polo like kinase 1 (PLK1), notch homolog 1 (NOTCH1), developmentally regulated GTP-binding protein 2 (DRG2), mitochondrial elongation factor 2 (MIEF2), glutamine-fructose-6-phosphate transaminase 2 (GFPT2), and dual-specificity tyrosine phosphorylation-regulated kinase 2 (DYRK2). Additionally, we validated the polymorphism of 16 SNPs (10 genes) using Kompetitive Allele Specific PCR, revealing that TOP1MT_g.9133371T > C, GPIHBP1_g.38365122C > T, DRG2_g.4912631C > A, FLII_g.5046888C > T, and PLK1_g.23585377T > C were significantly correlated with average daily milk yield and total milk yield in the studied donkeys. This study represents the first genome-wide association analysis of markers and milk components in Xinjiang donkeys, offering valuable insights into the genetic mechanisms underlying milk production traits. Further research with larger sample sizes is essential to confirm these findings and identify potential causal genetic variants. Full article

In view of the threat to local breeds resulting from intensive animal production, many studies are conducted in search of arguments confirming their importance in food production. In the case of milk production, not only is its quantity important, but its quality is as well, including its chemical composition. Particular focus has recently been placed on the casein proteins beta-casein (CSN2) and kappa-casein (CSN3), due to their potential impact on human health or on the suitability of milk for cheese production. The present study analysed the polymorphism of these proteins in 1777 cows belonging to two local cattle breeds, Polish Red and Polish White-Backed, using Illumina Infinium XT SNP technology on a EuroGenomics MD chip. The results indicate that the Polish White-Backed breed is predisposed to produce ‘A2 milk’, as the frequency of the CSN2 A2 allele in the population was 61.2%. The Polish Red breed was characterised by a higher frequency of the CNS3 B allele (35%), which according to extensive scientific literature is associated with better coagulation properties, and increased whey expulsion. The highest yield of milk and its constituents, confirmed at p ≤ 0.01, was obtained for Polish White-Backed cows with the A2A2 genotype in CSN2 and cows with the AA genotype in CSN3. In the Polish Red breed, no statistically significant differences were obtained between means for milk production traits. Full article

This study critically examines the limitations of the official Italian methodology used for detecting bovine adulteration milk in Protected Designation of Origin (PDO) Mozzarella di Bufala Campana (MdBC). This method focuses on the whey fraction of cheese samples, which comprises about 1% of total MdBC proteins, and is based on a high-performance liquid chromatography (HPLC) quantification of the bovine β-lactoglobulin A (β-Lg A) as a marker. Here, we have demonstrated that this official methodology suffers from measurement inconsistencies due to its reliance on raw bovine whey standards, which fail to account for β-Lg genetic polymorphisms in real MdBC samples and protein thermal modifications during cheesemaking. To overcome these limitations, we propose a dual proteomics-based approach using matrix-assisted laser desorption ionization (MALDI-TOF) mass spectrometry (MS) and nano-HPLC-electrospray (ESI)−tandem mass spectrometry (MS/MS) analysis of MdBC extracted whey. MALDI-TOF-MS focused on identifying proteotypic peptides specific to bovine and buffalo β-Lg and α-lactalbumin (α-La), enabling high specificity for distinguishing the two animal species at adulteration levels as low as 1%. Complementing this, nano-HPLC-ESI-MS/MS provided a comprehensive profile by identifying over 100 bovine-specific peptide markers from β-Lg, α-La, albumin, lactoferrin, and osteopontin. Both methods ensured precise detection and quantification of bovine milk adulteration in complex matrices like pasta filata cheeses, achieving high sensitivity even at minimal adulteration levels. Accordingly, the proposed dual proteomics-based approach overcomes challenges associated with whey protein polymorphism, heat treatment, and processing variability, and complements casein-based methodologies already validated under European standards. This integrated framework of analyses focused on whey and casein fraction enhances the reliability of adulteration detection and safeguards the authenticity of PDO buffalo mozzarella, upholding its unique quality and integrity. Full article

Reportedly, the number of κ-casein (κ-CN) B alleles increases the proportion of κ-CN to total protein and the κ-CN content. This phenomenon is caused by single-nucleotide polymorphisms (SNPs) in the promoter region of CSN3, which encodes the B variant. Therefore, a series of 5′-deleted promoter plasmids were constructed to define the core promoter of CSN3. The promoter activity was analyzed by comparing the luciferase activity among the recombinant vectors with truncated promoters. No mutation occurred in the core promoter region (5′-ctatcgtcagatctttcctttctgtcatcttcctattggtg-3′) of CSN3 in 40 cows. A 2092 bp promoter region of CSN3 was re-sequenced for detection, and nine variants were found, of which only three variants had mutation frequencies > 40%, which were −1002T>−, −1654T>A, and −2039T>G. The CSN3 promoter polymorphisms did not correlate with the CSN3 A and B alleles according to the Pearson’s chi-square test (p > 0.05). Moreover, the luciferase activity analysis of the CSN3 promoter showed no difference among pGL3 recombinants with different polymorphic CSN3 promoters (p > 0.05). In the genetic selection of dairy cows, mutations in the CSN3 core promoter should be focused upon. These findings provide a reference for the regulatory mechanism of bovine milk proteins and offer guidance for the genetic selection and breeding of cows. Full article

Our previous study identified the apolipoprotein M (APOM) and cytochrome P450 family 7 subfamily A polypeptide 1 (CYP7A1) genes as candidates for milk traits in dairy cattle, which were significantly up-regulated in liver tissue of Holstein cows between the dry and lactation periods. The two genes play critical roles in the peroxisome proliferator-activated receptor (PPAR) pathway. In this study, we further confirmed whether the APOM and CYP7A1 genes had significant genetic impacts on milk production traits in a Chinese Holstein population. By dual-direction sequencing of the polymerase chain reaction (PCR) products of the complete coding sequences and 2000 bp of the 5′ and 3′ flanking regions on pooled DNA sample, seven and three single nucleotide polymorphisms (SNPs) were identified in APOM and CYP7A1, respectively. With SAS 9.2, phenotype-genotype association analysis revealed such SNPs were significantly associated with at least one of the milk production traits, including 305-day milk yield, milk fat yield, milk fat percentage, milk protein yield, and milk protein percentage in the first and second lactations (p = <0.01~0.04). With Haploview 4.2, we further found that six SNPs in APOM and thee SNPs in CYP7A1 formed one haplotype, respectively. The haplotypes were significantly associated with at least one of milk production traits as well (p = <0.01~0.02). Of note, we found the SNPs in the 5′ regulatory region, rs209293266 and rs110721287 in APOM and rs42765359 in CYP7A1, significantly impacted the gene transcriptional activity after mutation (p < 0.01) through changing the transcription factor binding sites by using luciferase assay experiments. Additionally, with RNAfold Web Server, rs110098953 and rs378530166 changed the mRNA secondary structures of APOM and CYP7A1 genes, respectively. In summary, our research is the first to demonstrate that APOM and CYP7A1 genes have significantly genetic effects on milk yield and composition traits, and the identified SNPs may serve as available genetic markers for genomic selection program in dairy cattle. Full article

This study aimed to find SNPs that have an effect on the estimated breeding values (EBVs) of milk (MY), fat (FY), and protein yield (PY) of Holstein Friesian cows in Hungary. Holstein Friesian cows (n = 2963) were genotyped on a Eurogenomics (EuroG_MDv4) chip. The EBVs for MY, FY, and PY were obtained from the Association of Hungarian Holstein Breeders (AHHB). The loci associated with the EBVs were identified via three approaches: the calculation of genetic distance of the SNPs (F_{st_marker}), linear regression, and haplotype association tests. Nine SNPs were significantly associated with MY, FY, and PY located on BTA 2, 5, 28, and X. Among the nine SNPs identified, BTB-00219372 on BTA 5 had a positive β coefficient for MY and a negative β coefficient for FY and PY. In addition, BovineHD3000027615 on BTA X had a positive β coefficient for both MY and PY, as well as a negative β coefficient for FY. The identified SNPs were located near several genes that remain unstudied in cattle, which are potential targets for closer scrutiny in relation to milk properties. The markers associated with two or three EBVs could be used in selection with high efficiency to accelerate genetic development and help AHHB experts achieve their breeding. Most marker effects point in the same direction on EBVs; however, we found that BTB-00219372 and BovineHD3000027615 could be used with caution to increase one EBV while decreasing the other EBV or EBVs. Full article

κ-casein (CSN3) polymorphisms are closely related to productive performance and dairy processing performance. In this study, CSN3 3’UTR polymorphisms in Chinese Holstein cows (n = 50) and the effects of these polymorphisms on the gene expression of four caseins, the protein expression of κ-casein, the binding of microRNAs (miRNAs), and cow production performance were investigated. There were two main haplotypes for the CSN3 3’UTR in Chinese Holstein cows: Haplotype 1 (0 mutations, n = 16) and Haplotype 10 (a combination of 7 mutations, n = 17). The gene and protein expression levels of CSN3 in Haplotype 1 were significantly greater than those in Haplotype 10 (p < 0.05). The ability of bta-miR-708 to bind to the CSN3 3’UTR with Haplotype 10 was significantly greater than that with Haplotype 1 (p < 0.05), potentially explaining why the gene and protein expression of CSN3 with Haplotype 10 were lower than those with Haplotype 1. Dairy herd improvement (DHI) data, including 305-d milk production, fat-corrected milk, fat (%), protein (%), and fat/protein ratio, were not significantly different between the two haplotypes (p > 0.05). Results suggest that the two major CSN3 3’UTR polymorphisms in Chinese Holstein cows cause significant changes in CSN3 gene expression, CSN3 protein expression, and bta-miR-708 binding ability but no significant alterations in macroscopic DHI data. Therefore, CSN3 3’UTR polymorphisms should be investigated further. Full article

The IQ motif containing GTPase activating protein 2 (IQGAP2) gene functions as a tumor suppressor, reducing the malignant properties of breast cancer cells. The circulating cartilage acidic protein 1 (CRTAC1) gene, present in the whey protein fraction of dairy cows throughout lactation, is significantly correlated with fatty acids in milk. In this study, we investigated the correlation between single nucleotide polymorphisms (SNPs) in the IQGAP2 and CRTAC1 genes and milk quality traits in Gannan yaks, aiming to identify potential molecular marker loci for enhancing milk quality. Using the Illumina Yak cGPS 7K liquid chip, we genotyped 162 yaks and identified five SNPs in the IQGAP2 (g.232,769C>G, g.232,922G>C) and CRTAC1 (g.4,203T>C, g.5,348T>G, g.122,451T>C) genes. Genetic polymorphism analysis revealed that these five SNPs were moderately polymorphic and in Hardy–Weinberg equilibrium. An association analysis results showed that, at the g.232,769C>G locus of the IQGAP2 gene, the heterozygous CG genotype had significantly higher lactose content than the CC and GG homozygous genotypes (p < 0.05). Similarly, at the g.232,922G>C locus, the heterozygous GC and mutant CC genotypes significantly increased the contents of milk fat, lactose, and total solids (TS) (p < 0.05). In the CRTAC1 gene (g.4,203T>C, g.5,348T>G, g.122,451T>C), the mutant CC genotype significantly increased milk fat content, while the heterozygous TG genotype significantly increased lactose content (p < 0.05). In summary, mutations at the loci of g.232,769C>G, g.232,922G>C, g.4,203T>C, g.5,348T>G, and g.122,451T>C significantly elevated the lactose, milk fat, and TS content in Gannan yak milk, providing potential molecular marker candidates for improving Gannan yak milk quality. Full article

Bovine milk proteins account for 10% of the global protein supply, which justifies the importance of thoroughly understanding their digestive processes. Extensive research on digestion is being conducted both in vivo and in vitro. However, interpretations and comparisons across different studies require a thorough understanding of the methodologies used. Both the rate and extent of milk protein digestion can be affected by several intrinsic and extrinsic factors with potential implications for overall digestibility and physiological responses. Among intrinsic factors, the impact of genetic variants in native milk proteins has emerged as a growing research area. To these, further complexity is added by the processing conditions frequently applied to milk prior to consumption. The main aim of this work is to provide an overview of the current knowledge on the impact of variations in milk protein profiles (particularly whey: casein ratio and protein polymorphisms), the treatments applied during processing (pasteurisation, homogenisation) and consumption (temperature changes) on protein digestion. To support the interpretation of the current literature, this manuscript also presents a historical perspective into research in this field and summarizes the protocols that are most frequently used, presently, on in vitro digestion studies. Full article

The Murciano-Granadina goat (MUG) is a renowned dairy breed, known for its adaptability and resilience, as well as for its exceptional milk traits characterized by high protein and fat content, along with low somatic cell counts. These traits are governed by complex biological processes, crucial in shaping phenotypic diversity. Thus, it is imperative to explore the factors regulating milk production and lactation for this breed. In this study, we investigated the genetic architecture of seven milk traits in MUGs, employing a two-step computational analysis to examine genotype–phenotype associations. Initially, a random forest algorithm identified the relative importance of each single-nucleotide polymorphism (SNP) in determining the traits of interest. The second step applied an information theory-based approach to exploring the complex genetic architecture of quantitative milk traits, focusing on epistatic interactions that may have been overlooked in the first step. These approaches allowed us to identify an almost distinct set of candidate genes for each trait. In contrast, by analyzing the promoter regions of these genes, we revealed common regulatory networks among the milk traits under study. These findings are crucial for understanding the molecular mechanisms underlying gene regulation, and they highlight the pivotal role of transcription factors (TFs) and their preferential interactions in the development of these traits. Notably, TFs such as DBP, HAND1E47, HOXA4, PPARA, and THAP1 were consistently identified for all traits, highlighting their important roles in immunity within the mammary gland and milk production during lactation. Full article