Association of new SNPs at DGAT1 gene with milk quality in Egyptian Zaraibi goat breed

This study aimed to detect putative genomic loci in candidate genes associated with milk composition in Egyptian Zaraibi goats. A total number of 50 samples were tested to detect polymorphism in exons 15 and 16 of the diacylglycerol acyltransferase 1 (DGAT1) gene. The PCR products were sequenced and aligned. Sequence analysis showed three new genotypes in the studied samples: T1C1 (T12C SNP), T2C2 (T84C), and AG (G219A), then three groups were created: the first group was BB with C1T1 and AG genotypes, the second was DD which contains C2T2 and AG genotypes, and the third was AG with only AG genotype. GLM showed that the DD group with C84T and G219A SNPs had significantly the highest fat percent. Meanwhile, the BB group with C84T and G219A SNPs recorded significantly the highest total solids levels. On the other hand, the AG group which has G219A SNP showed a non-significant effect on milk components. Those new SNPs were submitted to GenBank and approved to be published. Moreover, translation of those sequences showed that the G219A SNP causes a substitution of Glycine to Serine in exon 16 at position 106. This SNP (G106S) was predicted to be tolerated by SIFT with a score of 0.48.

CSN1S1 and LALBA Polymorphisms and Other Factors Influencing Yield, Composition, Somatic Cell Score, and Technological Properties of Cow's Milk

We evaluated the influence of CSN1S1 and LALBA polymorphisms on cow's milk yield and quality. The analysis was done on Czech Simmental and Holstein cows. Non-genetic factors were included as well. CSN1S1 did not influence the milk performance in the first lactation. In the second lactation, cows with the BB genotype had significantly higher milk, protein, and fat yields than BC. The differences between LALBA genotypes were non-significant in the first lactation, while in the second lactation, the fat percentage was significantly higher in BB than in AB. The farm significantly influenced milk, protein, and fat yields in both the first and second lactations and fat percentage in the first lactation. The effect of CSN1S1 and LALBA genotypes on the milk technological quality was non-significant. Breed did not influence any of the evaluated technological traits and SCS. The ethanol test was not influenced by farm, season, lactation phase, protein percentage, breed, or non-fat solids percentage. Farm, season, and protein percentage significantly influenced milk fermentation ability, renneting, and SCS. The lactose content is a good indicator of udder health.

Effect of Protein Genotypes on Physicochemical Properties and Protein Functionality of Bovine Milk: A Review

Milk protein comprises caseins (CNs) and whey proteins, each of which has different genetic variants. Several studies have reported the frequencies of these genetic variants and the effects of variants on milk physicochemical properties and functionality. For example, the C variant and the BC haplotype of αS1-casein (αS1-CN), β-casein (β-CN) B and A1 variants, and κ-casein (κ-CN) B variant, are favourable for rennet coagulation, as well as the B variant of β-lactoglobulin (β-lg). κ-CN is reported to be the only protein influencing acid gel formation, with the AA variant contributing to a firmer acid curd. For heat stability, κ-CN B variant improves the heat resistance of milk at natural pH, and the order of heat stability between phenotypes is BB > AB > AA. The A2 variant of β-CN is more efficient in emulsion formation, but the emulsion stability is lower than the A1 and B variants. Foaming properties of milk with β-lg variant B are better than A, but the differences between β-CN A1 and A2 variants are controversial. Genetic variants of milk proteins also influence milk yield, composition, quality and processability; thus, study of such relationships offers guidance for the selection of targeted genetic variants.

Association of DGAT1 With Cattle, Buffalo, Goat, and Sheep Milk and Meat Production Traits

Milk fatty acids are essential for many dairy product productions, while intramuscular fat (IMF) is associated with the quality of meat. The triacylglycerols (TAGs) are the major components of IMF and milk fat. Therefore, understanding the polymorphisms and genes linked to fat synthesis is important for animal production. Identifying quantitative trait loci (QTLs) and genes associated with milk and meat production traits has been the objective of various mapping studies in the last decade. Consistently, the QTLs on chromosomes 14, 15, and 9 have been found to be associated with milk and meat production traits in cattle, goat, and buffalo and sheep, respectively. Diacylglycerol O-acyltransferase 1 (DGAT1) gene has been reported on chromosomes 14, 15, and 9 in cattle, goat, and buffalo and sheep, respectively. Being a key role in fat metabolism and TAG synthesis, the DGAT1 has obtained considerable attention especially in animal milk production. In addition to milk production, DGAT1 has also been a subject of interest in animal meat production. Several polymorphisms have been documented in DGAT1 in various animal species including cattle, buffalo, goat, and sheep for their association with milk production traits. In addition, the DGAT1 has also been studied for their role in meat production traits in cattle, sheep, and goat. However, very limited studies have been conducted in cattle for association of DGAT1 with meat production traits in cattle. Moreover, not a single study reported the association of DGAT1 with meat production traits in buffalo; thus, further studies are warranted to fulfill this huge gap. Keeping in view the important role of DGAT1 in animal production, the current review article was designed to highlight the major development and new insights on DGAT1 effect on milk and meat production traits in cattle, buffalo, sheep, and goat. Moreover, we have also highlighted the possible future contributions of DGAT1 for the studied species.

Influence of the Casein Composite Genotype on Milk Quality and Coagulation Properties in the Endangered Agerolese Cattle Breed

The aim of this study was the characterization of CSN1S1, CSN2 and CSN3 genetic variability in Agerolese cattle, and the investigation of the effect of casein composite genotypes (CSN1S1, CSN2 and CSN3) on quality and coagulation traits of the corresponding milk. To these purposes, blood and milk from 84 cows were sampled and analysed. Allele frequencies at CSN2 and CSN3 revealed no Hardy-Weinberg equilibrium in the population with a prevalence of allele A² for CSN2 and allele B for CSN3. BBA¹A²AB and BBA²A²AB composite genotypes were the most common in the population. BBA¹A²AB showed a higher total solids and fat content (12.70 ± 0.16 and 3.93 ± 0.10, respectively), while BBA²A²BB showed the best coagulation properties (RCT 12.62 ± 0.81; k₂₀ 5.84 ± 0.37; a₃₀ 23.72 ± 1.10). Interestingly, the A² allele of CSN2 was very widespread in the population; thus, it will be intriguing to verify if A²A² Agerolese cattle milk and the derived cheese may have better nutraceutical characteristics.

DNA Sequence Variants and Protein Haplotypes of Casein Genes in German Black Pied Cattle (DSN)

Casein proteins were repeatedly examined for protein polymorphisms and frequencies in diverse cattle breeds. The occurrence of casein variants in Holstein Friesian, the leading dairy breed worldwide, is well known. The frequencies of different casein variants in Holstein are likely affected by selection for high milk yield. Compared to Holstein, only little is known about casein variants and their frequencies in German Black Pied cattle (“Deutsches Schwarzbuntes Niederungsrind,” DSN). The DSN population was a main genetic contributor to the current high-yielding Holstein population. The goal of this study was to investigate casein (protein) variants and casein haplotypes in DSN based on the DNA sequence level and to compare these with data from Holstein and other breeds. In the investigated DSN population, we found no variation in the alpha-casein genes CSN1S1 and CSN1S2 and detected only the CSN1S1*B and CSN1S2*A protein variants. For CSN2 and CSN3 genes, non-synonymous single nucleotide polymorphisms leading to three different β and κ protein variants were found, respectively. For β-casein protein variants A¹, A², and I were detected, with CSN2*A¹ (82.7%) showing the highest frequency. For κ-casein protein variants A, B, and E were detected in DSN, with the highest frequency of CSN3*A (83.3%). Accordingly, the casein protein haplotype CSN1S1*B-CSN2*A¹-CSN1S2*A-CSN3*A (order of genes on BTA6) is the most frequent haplotype in DSN cattle.

Phenotypic analysis of milk coagulation properties and mineral content of Pinzgauer cattle breed

Abstract. This study aimed to characterize milk coagulation properties (rennet coagulation time, curd-firming time and curd firmness 30 min after rennet addition to milk) and major mineral contents (Ca, Mg, P, K and Na) in Pinzgauer dual-purpose cattle breed. The edited dataset consisted of 7763 milk observations from 851 cows reared in 60 herds in the Alpine area of Bolzano province (Italy). Data were analysed through a linear mixed model which included stage of lactation, parity and their interaction as fixed effects, and cow and herd test date as random effects. Rennet coagulation time, curd-firming time and curd firmness 30 min after rennet addition to milk averaged 22.66 min, 5.53 min and 16.79 mm, respectively. The most abundant minerals were P (1495 mg kg−1) and Ca (1344 mg kg−1), and the least abundant Mg (141 mg kg−1). Compared to their older contemporaries, early-lactating younger animals yielded milk that was more favourable for cheese production (i.e. with shorter coagulation time and stronger curd firmness). Mineral contents were lower in milk of primiparous than multiparous cows, except for Na. Moreover, Ca, Mg, P and Na contents decreased from parturition to peak of lactation and increased thereafter, except for K, which exhibited an opposite trend. Our results showed that Pinzgauer breed produced milk with better coagulation properties and mineral content, from a technological point of view, in first than later parities and in early than late lactation. The characterization of milk coagulation properties and mineral content in autochthonous breeds is important to increase their value and marketability of their products.

Kompetitive Allele Specific PCR (KASP™) genotyping of 48 polymorphisms at different caprine loci in French Alpine and Saanen goat breeds and their association with milk composition

Using a novel and fast genotyping method called Kompetitive Allele Specific PCR (KASP™), we carried out a pilot study on 48 single nucleotide polymorphisms (SNPs) belonging to 40 genes in French Alpine (n = 24) and Saanen (n = 25) goats reared in Romania. Furthermore, the associations of the 13 polymorphic genetic variants with milk production and composition were investigated. Thirty-five SNPs did not show polymorphism in the studied populations. Polymorphic SNPs were detected in the following genes: CAST, CLEC4E, DES, GHRHR, HSP90AA1, IL15RA, IL1RN, IL8, MITF, PPRC1, SOCS3, TNF and TNFSF13. The studied Alpine population was in Hardy-Weinberg disequilibrium at the g.62894878A>G locus (rs671391101) (P < 0.05). The results showed that four SNPs rs671391101 (GHRHR), rs640582069 (IL1RN) rs635583012 (SOCS3) and rs635969404 (IL15RA) out of the 13 polymorphic markers were significantly associated with milk production, protein, fat and lactose content in the Alpine breed. However, no significant effect was recorded in the Saanen population regarding milk yield or milk chemical composition. The current results provide new insights for the development of SNP marker-assisted selection technology in the goat industry and confirm the potential of using SNPs for the GHRHR, IL1RN, SOCS3, and IL15RA genes as candidate genes for selection, highlighting the direct implications of such genes for farm production outputs. The results from this study are relevant for future goat genomic studies and the inclusion of the associated traits into up-to-date selection schemes.

Milk protein polymorphisms and casein haplotypes in Butana cattle

Butana is a Bos indicus dairy cattle breed that is well adapted to the local environment of Sudan. The breed has been gradually declining in number due to breed substitution. Therefore, conservation and improvement strategies are required to maintain this breed. The aim of the present study was to assess genetic variation that is characteristic for Butana cattle in the milk protein genes CSN1S1, CSN2, CSN1S2, CSN3, LALBA, and LGB. In a first step, genomic DNA of five unrelated individuals was comparatively sequenced across all exon and flanking sequences. Ninety-three single nucleotide polymorphisms (SNPs) were identified in Butana cattle compared with the Bos taurus reference sequence at Ensembl. We confirmed the recently identified protein variants CSN2*J, CSN2*L, and LALBA*E. Fifty-two SNPs in non-coding regions are novel. Among the novel SNPs, five are located in promoter regions, three of them are in putative transcription factor binding sites (TFBSs) of the CSN1S2 promoter. Fifteen SNPs potentially affect miRNA target sites. In a second step, 50 unrelated Butana cattle were genotyped. This allowed deriving haplotypes for the casein gene cluster on BTA6. The most frequent haplotype was CSN1S1*C-CSN2*A ² -CSN1S2*A-CSN3*A (C-A ² -A-A, frequency 0.1546). Considering the newly identified CSN1S2 promoter variants, the most frequent haplotype was C-A ² -TTC-A-A (0.1046), with TTC as the promoter variant. The information on protein and promoter variants can be used for the development of conservation and breeding strategies for this local breed.

Biological underpinnings of breastfeeding challenges: the role of genetics, diet, and environment on lactation physiology

Lactation is a dynamic process that has evolved to produce a complex biological fluid that provides nutritive and nonnutritive factors to the nursing offspring. It has long been assumed that once lactation is successfully initiated, the primary factor regulating milk production is infant demand. Thus, most interventions have focused on improving breastfeeding education and early lactation support. However, in addition to infant demand, increasing evidence from studies conducted in experimental animal models, production animals, and breastfeeding women suggests that a diverse array of maternal factors may also affect milk production and composition. In this review, we provide an overview of our current understanding of the role of maternal genetics and modifiable factors, such as diet and environmental exposures, on reproductive endocrinology, lactation physiology, and the ability to successfully produce milk. To identify factors that may affect lactation in women, we highlight some information gleaned from studies in experimental animal models and production animals. Finally, we highlight the gaps in current knowledge and provide commentary on future research opportunities aimed at improving lactation outcomes in breastfeeding women to improve the health of mothers and their infants.

Bos indicus introgression into (peri-)alpine cattle breeds - evidence from the analysis of bovine whey protein variants

The major bovine whey proteins, α-lactalbumin (α-LA) and β-lactoglobulin (β-LG), exhibit breed-specific genetic variation. The aim of this study was to identify possible new protein variants and determine the distribution of variants across a variety of 18 taurine and indicine cattle breeds applying a DNA-based sequencing approach. To this end, the open reading frames of the respective genes (LALBA and LGB) were sequenced in 476 animals. Within the LALBA gene, a previously unknown synonymous and a previously undesignated non-synonymous nucleotide exchange were identified. Furthermore, two known α-LA variants (A and B) and four known β-LG variants (A, B, C and W) were determined. The occurrence of typical indicine variants in some taurine cattle breeds, such as Suisse Eringer, German Hinterwälder and Hungarian Grey Steppe, further supports the hypothesis of ancient Bos indicus introgression into (peri-)alpine cattle breeds.

Revisiting AFLP fingerprinting for an unbiased assessment of genetic structure and differentiation of taurine and zebu cattle

Background

Descendants from the extinct aurochs (Bos primigenius), taurine (Bos taurus) and zebu cattle (Bos indicus) were domesticated 10,000 years ago in Southwestern and Southern Asia, respectively, and colonized the world undergoing complex events of admixture and selection. Molecular data, in particular genome-wide single nucleotide polymorphism (SNP) markers, can complement historic and archaeological records to elucidate these past events. However, SNP ascertainment in cattle has been optimized for taurine breeds, imposing limitations to the study of diversity in zebu cattle. As amplified fragment length polymorphism (AFLP) markers are discovered and genotyped as the samples are assayed, this type of marker is free of ascertainment bias. In order to obtain unbiased assessments of genetic differentiation and structure in taurine and zebu cattle, we analyzed a dataset of 135 AFLP markers in 1,593 samples from 13 zebu and 58 taurine breeds, representing nine continental areas.

Results

We found a geographical pattern of expected heterozygosity in European taurine breeds decreasing with the distance from the domestication centre, arguing against a large-scale introgression from European or African aurochs. Zebu cattle were found to be at least as diverse as taurine cattle. Western African zebu cattle were found to have diverged more from Indian zebu than South American zebu. Model-based clustering and ancestry informative markers analyses suggested that this is due to taurine introgression. Although a large part of South American zebu cattle also descend from taurine cows, we did not detect significant levels of taurine ancestry in these breeds, probably because of systematic backcrossing with zebu bulls. Furthermore, limited zebu introgression was found in Podolian taurine breeds in Italy.

Conclusions

The assessment of cattle diversity reported here contributes an unbiased global view to genetic differentiation and structure of taurine and zebu cattle populations, which is essential for an effective conservation of the bovine genetic resources.

DNA-based identification of novel bovine casein gene variants

In cattle, at least 39 variants of the 4 casein proteins (α(S1)-, β-, α(S2)- and κ-casein) have been described to date. Many of these variants are known to affect milk-production traits, cheese-processing properties, and the nutritive value of milk. They also provide valuable information for phylogenetic studies. So far, the majority of studies exploring the genetic variability of bovine caseins considered European taurine cattle breeds and were carried out at the protein level by electrophoretic techniques. This only allows the identification of variants that, due to amino acid exchanges, differ in their electric charge, molecular weight, or isoelectric point. In this study, the open reading frames of the casein genes CSN1S1, CSN2, CSN1S2, and CSN3 of 356 animals belonging to 14 taurine and 3 indicine cattle breeds were sequenced. With this approach, we identified 23 alleles, including 5 new DNA sequence variants, with a predicted effect on the protein sequence. The new variants were only found in indicine breeds and in one local Iranian breed, which has been phenotypically classified as a taurine breed. A multidimensional scaling approach based on available SNP chip data, however, revealed an admixture of taurine and indicine populations in this breed as well as in the local Iranian breed Golpayegani. Specific indicine casein alleles were also identified in a few European taurine breeds, indicating the introgression of indicine breeds into these populations. This study shows the existence of substantial undiscovered genetic variability of bovine casein loci, especially in indicine cattle breeds. The identification of new variants is a valuable tool for phylogenetic studies and investigations into the evolution of the milk protein genes.

Dual origins of dairy cattle farming--evidence from a comprehensive survey of European Y-chromosomal variation

BACKGROUND

Diversity patterns of livestock species are informative to the history of agriculture and indicate uniqueness of breeds as relevant for conservation. So far, most studies on cattle have focused on mitochondrial and autosomal DNA variation. Previous studies of Y-chromosomal variation, with limited breed panels, identified two Bos taurus (taurine) haplogroups (Y1 and Y2; both composed of several haplotypes) and one Bos indicus (indicine/zebu) haplogroup (Y3), as well as a strong phylogeographic structuring of paternal lineages.

METHODOLOGY AND PRINCIPAL FINDINGS

Haplogroup data were collected for 2087 animals from 138 breeds. For 111 breeds, these were resolved further by genotyping microsatellites INRA189 (10 alleles) and BM861 (2 alleles). European cattle carry exclusively taurine haplotypes, with the zebu Y-chromosomes having appreciable frequencies in Southwest Asian populations. Y1 is predominant in northern and north-western Europe, but is also observed in several Iberian breeds, as well as in Southwest Asia. A single Y1 haplotype is predominant in north-central Europe and a single Y2 haplotype in central Europe. In contrast, we found both Y1 and Y2 haplotypes in Britain, the Nordic region and Russia, with the highest Y-chromosomal diversity seen in the Iberian Peninsula.

CONCLUSIONS

We propose that the homogeneous Y1 and Y2 regions reflect founder effects associated with the development and expansion of two groups of dairy cattle, the pied or red breeds from the North Sea and Baltic coasts and the spotted, yellow or brown breeds from Switzerland, respectively. The present Y1-Y2 contrast in central Europe coincides with historic, linguistic, religious and cultural boundaries.