The impact of genetic variants related to the fatty acid metabolic process pathway on milk production traits in Jersey cows

The synthesis of fatty acids plays a critical role in shaping milk production characteristics in dairy cattle. Thus, identifying effective haplotypes within the fatty acid metabolism pathway will provide novel and robust insights into the genetics of dairy cattle. This study aimed to comprehensively examine the individual and combined impacts of fundamental genes within the fatty acid metabolic process pathway in Jersey cows. A comprehensive phenotypic dataset was compiled, considering milk production traits, to summarize a cow's productivity across three lactations. Genotyping was conducted through PCR-RFLP and Sanger sequencing, while the association between genotype and phenotype was quantified using linear mixed models. Moderate biodiversity and abundant variation suitable for haplotype analysis were observed across all examined markers. The individual effects of the FABP3, LTF and ANXA9 genes significantly influenced both milk yield and milk fat production. Additionally, this study reveals novel two-way interactions between genes in the fatty acid metabolism pathway that directly affect milk fat properties. Notably, we identified that the GGAAGG haplotype in FABP3×LTF×ANXA9 interaction may be a robust genetic marker concerning both milk fat yield and percentage. Consequently, the genotype combinations highlighted in this study serve as novel and efficient markers for assessing the fat content in cow's milk.

A common regulatory haplotype doubles lactoferrin concentration in milk

BACKGROUND

Bovine lactoferrin (Lf) is an iron absorbing whey protein with antibacterial, antiviral, and antifungal activity. Lactoferrin is economically valuable and has an extremely variable concentration in milk, partly driven by environmental influences such as milking frequency, involution, or mastitis. A significant genetic influence has also been previously observed to regulate lactoferrin content in milk. Here, we conducted genetic mapping of lactoferrin protein concentration in conjunction with RNA-seq, ChIP-seq, and ATAC-seq data to pinpoint candidate causative variants that regulate lactoferrin concentrations in milk.

RESULTS

We identified a highly-significant lactoferrin protein quantitative trait locus (pQTL), as well as a cis lactotransferrin (LTF) expression QTL (cis-eQTL) mapping to the LTF locus. Using ChIP-seq and ATAC-seq datasets representing lactating mammary tissue samples, we also report a number of regions where the openness of chromatin is under genetic influence. Several of these also show highly significant QTL with genetic signatures similar to those highlighted through pQTL and eQTL analysis. By performing correlation analysis between these QTL, we revealed an ATAC-seq peak in the putative promotor region of LTF, that highlights a set of 115 high-frequency variants that are potentially responsible for these effects. One of the 115 variants (rs110000337), which maps within the ATAC-seq peak, was predicted to alter binding sites of transcription factors known to be involved in lactation-related pathways.

CONCLUSIONS

Here, we report a regulatory haplotype of 115 variants with conspicuously large impacts on milk lactoferrin concentration. These findings could enable the selection of animals for high-producing specialist herds.

Using QTL to Identify Genes and Pathways Underlying the Regulation and Production of Milk Components in Cattle

Milk is a complex liquid, and the concentrations of many of its components are under genetic control. Many genes and pathways are known to regulate milk composition, and the purpose of this review is to highlight how the discoveries of quantitative trait loci (QTL) for milk phenotypes can elucidate these pathways. The main body of this review focuses primarily on QTL discovered in cattle (Bos taurus) as a model species for the biology of lactation, and there are occasional references to sheep genetics. The following section describes a range of techniques that can be used to help identify the causative genes underlying QTL when the underlying mechanism involves the regulation of gene expression. As genotype and phenotype databases continue to grow and diversify, new QTL will continue to be discovered, and although proving the causality of underlying genes and variants remains difficult, these new data sets will further enhance our understanding of the biology of lactation.

Milk lactoferrin concentration of primiparous and multiparous sows during lactation

Lactoferrin (LF), a sialylated iron-binding glycoprotein, has numerous vital physiological functions including immunomodulation and protection against a large group of microorganisms, improving neurodevelopment, health, growth performance, and milk production. Lactoferrin occurs in human milk at a higher concentration compared with bovine milk, but little information is available on LF concentrations in porcine milk and the effects of sow parity on milk LF concentration. The objective of this study was to quantify the LF concentration in porcine milk and to compare that concentration between gilts and sows during lactation. We also investigated the effect of genetic background and litter size of the female pig on the LF concentration of porcine milk. The milk from 30 gilts and 35 sows was collected at 3 stages of lactation, namely colostrum, transition, and mature milk. Standard and experimental samples were analyzed by ultra-high performance liquid chromatography using a diode array UV detector. The following findings were reported: (1) porcine milk contained significant levels of LF with the highest concentration in colostrum, which decreased by ∼62% and ∼67% in transitional and mature milk, respectively; (2) mature gilt milk contained a 22% higher concentration of LF compared with sow milk, which was statistically significant; (3) breed line had an overall significant effect on the LF content of porcine milk; however, when the breed was considered, no significant difference was observed; and (4) LF concentration of porcine milk was not significantly influenced by the litter size. The presence of LF in a higher concentration in porcine milk suggests that LF is an important constituent of pig milk that might contribute to the optimum growth and development of piglets.

The evolving role of Fourier-transform mid-infrared spectroscopy in genetic improvement of dairy cattle

Over the last 100 years, significant advances have been made in the characterisation of milk composition for dairy cattle improvement programs. Technological progress has enabled a shift from labour intensive, on-farm collection and processing of samples that assess yield and fat levels in milk, to large-scale processing of samples through centralised laboratories, with the scope extended to include quantification of other traits. Fourier-transform mid-infrared (FT-MIR) spectroscopy has had a significant role in the transformation of milk composition phenotyping, with spectral-based predictions of major milk components already being widely used in milk payment and animal evaluation systems globally. Increasingly, there is interest in analysing the individual FT-MIR wavenumbers, and in utilising the FT-MIR data to predict other novel traits of importance to breeding programs. This includes traits related to the nutritional value of milk, the processability of milk into products such as cheese, and traits relevant to animal health and the environment. The ability to successfully incorporate these traits into breeding programs is dependent on the heritability of the FT-MIR predicted traits, and the genetic correlations between the FT-MIR predicted and actual trait values. Linking FT-MIR predicted traits to the underlying mutations responsible for their variation can be difficult because the phenotypic expression of these traits are a function of a diverse range of molecular and biological mechanisms that can obscure their genetic basis. The individual FT-MIR wavenumbers give insights into the chemical composition of milk and provide an additional layer of granularity that may assist with establishing causal links between the genome and observed phenotypes. Additionally, there are other molecular phenotypes such as those related to the metabolome, chromatin accessibility, and RNA editing that could improve our understanding of the underlying biological systems controlling traits of interest. Here we review topics of importance to phenotyping and genetic applications of FT-MIR spectra datasets, and discuss opportunities for consolidating FT-MIR datasets with other genomic and molecular data sources to improve future dairy cattle breeding programs.

Estimation of genetic parameters for mid-infrared-predicted lactoferrin and milk fat globule size in Holstein cattle

Lactoferrin (LF) and milk fat globule (MFG) are 2 biologically active components of milk with great economical and nutritional value in the dairy industry. The objectives of this study were to estimate (1) the heritability of mid-infrared (MIR)-predicted LF and MFG size (MFGS) and (2) the genetic correlations between predicted LF and MFGS with milk, fat, and protein yields, fat and protein percentages, and somatic cell score in first-parity Canadian Holstein cattle. A total of 109,029 test-day records from 22,432 cows and 1,572 farms for MIR-predicted LF and 109,212 test-day records from 22,424 cows and 1,559 farms for MIR-predicted MFGS were used in the analyses. Four separate 5-trait random regression test-day models were used. The models included days in milk, herd test date, and a polynomial regression on DIM nested in age-season of calving classes as fixed effects, random polynomial regressions on DIM nested in herd-year of calving, animal additive genetic and permanent environment classes, and a residual effect. Regression curves were modeled using orthogonal Legendre polynomials of order 4 for the fixed age-season of calving effect and of order 5 for the random effects. Moderate overall heritability estimates of 0.34 and 0.46 were estimated for the MIR-predicted LF and MIR-predicted MFGS, respectively. These heritability estimates were similar to the ones estimated for the direct measure of MFGS in a previous study. The genetic correlations between predicted MFGS and fat percentage (0.53) and between predicted LF and protein percentage (0.41) were both moderate and positive. Predicted LF and somatic cell score showed a weaker correlation (0.06) compared with other studies. The moderate genetic correlation between MIR-predicted MFGS and fat percentage and between MIR-predicted LF and protein percentage suggests that MIR predictions of MFGS and LF are not simply a function of the amount of fat and protein percentage, respectively, in the milk (i.e., the prediction equations are not simply predicting fat or protein percentages). Thus, these MIR-predicted values may provide additional information for selecting for fine milk components in Holstein cattle.

Phenotypic investigation of fine milk components in bovine milk and their prediction using mid-infrared spectroscopy

This study aimed to examine the phenotypic variation observed in fine milk components, the use of mid-infrared (MIR) spectroscopy to predict these components, and the correlations with other milk production traits. A total of 4116 milk samples were collected from 414 dairy cows from 44 Canadian herds. Overall 3117 samples were analyzed for casein micelle size, 986 and 937 for total and soluble calcium, respectively, and 2054 for lactoferrin. Individual milk MIR spectra were obtained. Linear mixed models with repeated records were used to test the effects of herd nested within breed, breed, days in milk class, parity, and season on milk components. Lactoferrin content in milk increased with stage of lactation and parity number. Prediction equations were developed by partial least squares regression to predict each milk component using MIR spectroscopy, with the greatest coefficient of determination achieved for lactoferrin (0.55). Pearson correlation coefficients for lactoferrin with somatic cell score and protein percentage were 0.49% and 0.40%, respectively. The estimated correlation increased to 0.53% for predicted lactoferrin and protein percentage. The examined fine milk components exhibited variation, but low accuracies for their MIR prediction may limit the utility of this technology for their phenotyping.

Invited review: Breeding and ethical perspectives on genetically modified and genome edited cattle

The hot topic of genetic modification and genome editing is sometimes presented as a rapid solution to various problems in the field of animal breeding and genetics. These technologies hold potential for future use in agriculture but we need to be aware of difficulties in large-scale application and integration in breeding schemes. In this review, we discuss applications of both classical genetic modifications (GM) using vectors and genome editing in dairy cattle breeding. We use an interdisciplinary approach considering both ethical and animal breeding perspectives. Decisions on how to make use of these techniques need to be made based not only on what is possible, but on what is reasonable to do. Principles of animal integrity, naturalness, risk perception, and animal welfare issues are examples of ethically relevant factors to consider. These factors also influence public perception and decisions about regulations by authorities. We need to acknowledge that we lack complete understanding of the genetic background of complex traits. It may be difficult, therefore, to predict the full effect of certain modifications in large-scale breeding programs. We present 2 potential applications: genome editing to dispense with dehorning, and insertion of human genes in bovine genomes to improve udder health as an example of classical GM. Both of these cases could be seen as beneficial for animal welfare but they differ in other aspects. In the former case, a genetic variant already present within the species is introduced, whereas in the latter case, transgenic animals are generated-this difference may influence how society regards the applications. We underline that the use of GM, as well as genome editing, of farm animals such as cattle is not independent of the context, and should be considered as part of an entire process, including, for example, the assisted reproduction technology that needs to be used. We propose that breeding organizations and breeding companies should take an active role in ethical discussions about the use of these techniques and thereby signal to society that these questions are being responsibly addressed.

Advances in lactoferrin research concerning bovine mastitis

Lactoferrin is a multifunctional, iron-binding glycoprotein found in milk and other exocrine secretions. Lactoferrin in milk plays vital roles in the healthy development of newborn mammals, and is also an innate resistance factor involved in the prevention of mammary gland infection by microorganisms. Inflammation of the udder because of bacterial infection is referred to as mastitis. There have been many investigations into the relationships between lactoferrin and mastitis, which fall into several categories. The main categories are fluctuations in the lactoferrin concentration of milk, lactoferrin activity against mastitis pathogens, elucidation of the processes underlying the onset of mastitis, participation of lactoferrin in the immune system, and utilization of lactoferrin in mastitis treatment and prevention. This minireview describes lactoferrin research concerning bovine mastitis. In the 1970s, many researchers reported that the lactoferrin concentration fluctuates in milk from cows with mastitis. From the late 1980s, many studies clarified the infection-defense mechanism in the udder and the contribution of lactoferrin to the immune system. After the year 2000, the processes underlying the onset of mastitis were elucidated in vivo and in vitro, and lactoferrin was applied for the treatment and prevention of mastitis.

Antimicrobial activity of buttermilk and lactoferrin peptide extracts on poultry pathogens

Antibiotics are commonly used in poultry feed as growth promoters. This practice is questioned given the arising importance of antibiotic resistance. Antimicrobial peptides can be used as food additives for a potent alternative to synthetic or semi-synthetic antibiotics. The objective of this study was to develop a peptide production method based on membrane adsorption chromatography in order to produce extracts with antimicrobial activity against avian pathogens (Salmonella entericavar. Enteritidis,Salmonella entericavar. Typhimurium, and twoEscherichia colistrains, O78:H80 and TK3 O1:K1) as well asStaphylococcus aureus. To achieve this, buttermilk powder and purified lactoferrin were digested with pepsin. The peptide extracts (<10 kDa) were fractionated depending on their charges through high-capacity cation-exchange and anion-exchange adsorptive membranes. The yields of cationic peptide extracts were 6·3 and 15·4% from buttermilk and lactoferrin total peptide extracts, respectively. Antimicrobial activity was assessed using the microdilution technique on microplates. Our results indicate that the buttermilk cationic peptide extracts were bactericidal at less than 5 mg/ml against the selected avian strains, with losses of 1·7 log CFU/ml (Salm.Typhimurium) to 3 log CFU/ml (E. coliO78:H80); viability decreased by 1·5 log CFU/ml forStaph. aureus, a Gram-positive bacterium. Anionic and non-adsorbed peptide extracts were inactive at 5 mg/ml. These results demonstrate that membrane adsorption chromatography is an effective way to prepare a cationic peptide extract from buttermilk that is active against avian pathogens.

Genetic variability detected at the lactoferrin locus (LTF) in the Italian Mediterranean river buffalo

Lactoferrin (LTF) is a multi-functional protein belonging to the whey protein fractions of milk. The gene LTF encoding for such protein is considered a potential candidate for body measurement, milk composition and yield. This study reports on the genetic variability at the LTF locus in the Italian Mediterranean river buffalo and its possible association with milk yield. Eleven polymorphic sites were found in the DNA fragment spanning exons 15–16. In particular, intron 15 was extremely polymorphic with nine single nucleotide polymorphisms (SNPs) detected, whereas the remaining two SNPs were exonic mutations (g.88G > A at exon 15 and g.1351G > A at exon 16) and both synonymous. The genotyping of the informative samples evidenced three haplotypes, whose frequencies were 0.6, 0.3 and 0.1, respectively, whereas the analysis of the exonic SNPs showed a perfect condition of linkage disequilibrium (g.88A/g.1351G and g.88G/g.1351A). The association study carried out by using the SNP g.88G > A showed that buffalo LTF gene has no statistically significant influence on daily milk yield. This study adds knowledge to the genetic variability of a species less investigated than the other ruminant species. These findings may serve as a useful tool for large-scale screening of buffalo populations.

Association of polymorphism within LTF gene promoter with lactoferrin concentration in milk of Holstein cows

This study analyzed the association between single nucleotide polymorphism (A/C) in position -28 located in the TATA box of LTF gene and the lactoferrin concentration in bovine milk secreted by healthy and infected udders. Out of 241, 69 cows were selected into the experimental group and were divided into 3 groups according to mean value of somatic cell count (SCC): I < 180,000 cells/mL, II: 180,000-350,000 cells/mL and III > 350,000 cells/mL. In each SCC group, three LTF genotypes: AA, AC and CC were identified by PCR-SSCP method. A total of 604 milk samples were collected monthly and lactoferrin concentration was measured by ELISA. The 1-way ANOVA within SCC groups was performed to estimate association of -28 A/C genotypes with mean lactoferrin concentration per lactation. In the group of healthy cows (< 180,000 cells/mL) LTF concentration in milk cows with the AA genotype (107.58 ± 17.92 μg/mL) was significantly higher than in homozygotes CC (52.09 ± 19.01 μg/mL). Unexpectedly, in cows with elevated SCC (> 350,000 cells/mL) we observed a significant opposite relationship (207.21 ± 28.50 in CC vs 115.0 ± 28.6 μg/mL in AA). We hypothesized that a promoter with allele C, which cannot be recognized as a TATA sequence is becoming more accessible for other transcription factors, which may induce alternative LTF gene expression. We assume that our results demonstrate a very interesting effect of differential gene expression depending on polymorphism in a key regulatory motif (TATA box) and also on the health status of mammary tissues.

Invited review: overview of new traits and phenotyping strategies in dairy cattle with a focus on functional traits

For several decades, breeding goals in dairy cattle focussed on increased milk production. However, many functional traits have negative genetic correlations with milk yield, and reductions in genetic merit for health and fitness have been observed. Herd management has been challenged to compensate for these effects and to balance fertility, udder health and metabolic diseases against increased production to maximize profit without compromising welfare. Functional traits, such as direct information on cow health, have also become more important because of growing concern about animal well-being and consumer demands for healthy and natural products. There are major concerns about the impact of drugs used in veterinary medicine on the spread of antibiotic-resistant strains of bacteria that can negatively impact human health. Sustainability and efficiency are also increasingly important because of the growing competition for high-quality, plant-based sources of energy and protein. Disruptions to global environments because of climate change may encourage yet more emphasis on these traits. To be successful, it is vital that there be a balance between the effort required for data recording and subsequent benefits. The motivation of farmers and other stakeholders involved in documentation and recording is essential to ensure good data quality. To keep labour costs reasonable, existing data sources should be used as much as possible. Examples include the use of milk composition data to provide additional information about the metabolic status or energy balance of the animals. Recent advances in the use of mid-infrared spectroscopy to measure milk have shown considerable promise, and may provide cost-effective alternative phenotypes for difficult or expensive-to-measure traits, such as feed efficiency. There are other valuable data sources in countries that have compulsory documentation of veterinary treatments and drug use. Additional sources of data outside of the farm include, for example, slaughter houses (meat composition and quality) and veterinary labs (specific pathogens, viral loads). At the farm level, many data are available from automated and semi-automated milking and management systems. Electronic devices measuring physiological status or activity parameters can be used to predict events such as oestrus, and also behavioural traits. Challenges concerning the predictive biology of indicator traits or standardization need to be solved. To develop effective selection programmes for new traits, the development of large databases is necessary so that high-reliability breeding values can be estimated. For expensive-to-record traits, extensive phenotyping in combination with genotyping of females is a possibility.