Estimation of Heritability and Genetic Correlations for the Major Fatty Acids in Bovine Milk

Resilience indicator traits in 3 dairy cattle breeds in Baden-Württemberg

In recent years, research in animal breeding has increasingly focused on the topic of resilience, which is expected to continue in the future due to the need for high-yielding, healthy, and robust animals. In this context, an established approach is the calculation of resilience indicator traits with time series analyses. Examples are the variance and autocorrelation of daily milk yield in dairy cows. We applied this methodology to the German dairy cow population. Data from the 3 breeds (German Holstein, German Fleckvieh, and German Brown Swiss) were obtained, which included 13,949 lactations from 36 farms from the state Baden-Württemberg in Germany working with automatic milking systems. Using the milk yield data, the daily absolute milk yields, deviations between observed and expected daily milk yields, and relative proportions of daily milk yields in relation to lactation performance were calculated. We used the variance and autocorrelation of these data as phenotypes in our statistical analyses. We estimated a heritability of 0.047 for autocorrelation and heritabilities between 0.026 and 0.183 for variance-based indicator traits. Furthermore, significant breed differences could be observed, with a tendency of better resilience in Brown Swiss. The breed differences can be due to both genetic and environmental factors. A high value of a variance-based indicator trait indicates a low resilience. Performance traits were positively correlated with variance-based indicator traits calculated from absolute daily milk yields, but they were negatively correlated with variance-based indicators calculated from relative daily milk yields. Thus, they can be considered as different traits. Although variance-based indicators based on absolute daily milk yields were affected by the performance level, variance-based indicators based on relative daily milk yields were corrected for the performance level and also showed higher heritabilities. Thus, they seem to be more suitable for practical use. Further studies need to be conducted to calculate the correlations between resilience indicators, functional traits, and health traits.

Developmental programming of production and reproduction in dairy cows: IV. Association of maternal milk fat and protein percentage and milk fat to protein ratio with offspring's birth weight, survival, productive and reproductive performance and AMH concentration from birth to the first lactation period

Although the association of maternal milk production with developmental programming of offspring has been investigated, there is limited information available on the relationship of maternal milk components with productive and reproductive performance of the offspring. Therefore, the present study was conducted to analyze the association of maternal milk fat and protein percentage and milk fat to protein ratio with birth weight, survival, productive and reproductive performance and AMH concentration in the offspring. In study I, data of birth weight, milk yield and reproductive variables of offspring born to lactating dams (n = 14,582) and data associated with average maternal milk fat percentage (MFP), protein percentage (MPP) and fat to protein ratio (MFPR) during 305-day lactation were retrieved. Afterwards, offspring were classified in various categories of MFP, MPP and MFPR. In study II, blood samples (n = 339) were collected from offspring in various categories of MFP, MPP and MFPR for measurement of serum AMH. Maternal milk fat percentage was positively associated with birth weight and average percentage of milk fat (APMF) and protein (APMP) and milk fat to protein ratio (FPR) during the first lactation, but negatively associated with culling rate during nulliparity in the offspring (P < 0.05). Maternal milk protein percentage was positively associated with birth weight, APMF, APMP, FPR and culling rate, but negatively associated with milk yield and fertility in the offspring (P < 0.05). Maternal FPR was positively associated with APMF and FPR, but negatively associated with culling rate, APMP and fertility in the offspring (P < 0.05). However, concentration of AMH in the offspring was not associated with MFP, MPP and MFPR (P > 0.05). In conclusion, the present study revealed that maternal milk fat and protein percentage and their ratio were associated with birth weight, survival, production and reproduction of the offspring. Yet it was a preliminary research and further studies are required to elucidate the mechanisms underlying these associations.

Developmental programming of reproduction in the female animal

Successful reproduction is a cornerstone in food animal industry in order to sustain food production for human. Therefore, various methods focusing on genetics and postnatal environment have been identified and applied to improve fertility in livestock. Yet there is evidence indicating that environmental factors during prenatal and/or neonatal life can also impact the function of reproductive system and fertility in the animals during adulthood, which is called the developmental programming of reproduction. The current review summarizes data associated with the developmental origins of reproduction in the female animals. In this regard, this review focuses on the effect of plane of nutrition, maternal body condition, hypoxia, litter size, maternal age, parity, level of milk production and milk components, lactocrine signaling, stress, thermal stress, exposure to androgens, endocrine disrupting chemicals, mycotoxins and pollutants, affliction with infection and inflammation, and maternal gut microbiota during prenatal and neonatal periods on the neuroendocrine system, puberty, health of reproductive organs and fertility in the female offspring. It is noteworthy that these prenatal and neonatal factors do not always exert their effects on the reproductive performance of the female by compromising the development of organs directly related to reproductive function such as hypothalamus, pituitary, ovary, oviduct and uterus. Since they can impair the development of non-reproductive organs and systems modulating reproductive function as well (e.g., metabolic system and level of milk yield in dairy animals). Furthermore, when these factors affect the epigenetics of the offspring, their adverse effects will not be limited to one generation and can transfer transgenerationally. Hence, pinpointing the factors influencing developmental programming of reproduction and considering them in management of livestock operations could be a potential strategy to help improve fertility in food animals.

Phenotypic variation in milk fatty acid composition and its association with stearoyl-CoA desaturase 1 (SCD1) gene polymorphisms in Gir cows

Individual variation in milk fatty acid (FA) composition has been partially attributed to stearoyl-CoA desaturase 1 (SCD1) gene polymorphisms in taurine breeds, but much less is known for Zebu breeds. This study investigated the phenotypic variation in milk FA composition, and the influence of SCD1 variants on this trait and on milk fat desaturase indices (DI) in Gir cows. The functional impact of SCD1 variants was predicted using bioinformatics tools. Milk and blood samples were collected from 312 cows distributed in 10 herds from five states of Brazil. SCD1 variants were identified through target sequencing, and milk FA composition was determined by gas chromatography. Phenotypic variation in milk FA composition fell within the range reported for taurine breeds, with SCD18 index showing the lowest variation among the DI. Fourteen SCD1 variants were identified, six of which not previously described. Regarding the A293V polymorphism, all cows were homozygous for the C allele (coding for alanine), whereas all genotypes were detected for the second SNP affecting the 293 codon (G > A), with compelling evidence for functional effects. Significant associations (based on raw p-values) were found between this SNP and C12:0, cis-9, trans-11 CLA and short-chain FA, and between another SNP (rs523411937) and C15:0 and odd-chain linear FA. A new SNP on Chr26:21277069 was associated with trans-11 C18:1, cis-9, trans-11 CLA, C18:3 n-3 and n-3 FA. These findings indicate that SCD1 polymorphisms also contributes to the phenotypic variation in milk FA composition of Gir cows, with potential use in their breeding programmes.

Comparison of Growth Performance and Plasma Metabolomics between Two Sire-Breeds of Pigs in China

The Yorkshire pigs, renowned for their remarkable growth rate, low feed conversion ratio (FCR), and high meat production, emerge as a novel preference for paternal breeding. In this study, we found that purebred paternal Yorkshire pigs (PY) surpass the purebred Duroc breed in terms of growth rate. Specifically, purebred PY attain a weight of 100 kg at an earlier age compared to purebred Duroc (Male, 145.07 vs. 162.91; Female, 145.91 vs. 167.57; p-value < 0.01). Furthermore, different hybrid combinations suggest that offspring involving purebred PY exhibit superior growth performance. Compared with purebred Duroc, the offspring of purebred PY have an earlier age in days (173.23 vs. 183.54; p-value < 0.05) at the same slaughter weight. The changes of plasma metabolites of 60-day-old purebred boars in the two sire-breeds showed that 1335 metabolites in plasma were detected. Compared with Duroc, 28 metabolites were down-regulated and 49 metabolites were up-regulated in PY. Principal component analysis (PCA) discerned notable dissimilarities in plasma metabolites between the two sire-breeds of pigs. The levels of glycerol 3-phosphate choline, cytidine, guanine, and arachidonic acid increased significantly (p-value < 0.05), exerting an impact on their growth and development. According to our results, PY could be a new paternal option as a terminal sire in three-way cross system.

Linseed oil supplementation and DGAT1 K232A polymorphism affect the triacylglycerol composition and crystallization of milk fat

We studied the effect of dietary linseed oil (LSO) supplementation and DGAT1 K232A (DGAT1) polymorphism on the triacylglycerol composition and crystallization of bovine milk fat. LSO supplementation increased unsaturated triacylglycerols, notably in the C52-C54 carbon range, while reducing the saturated C29-C49 triacylglycerols. These changes were associated with an increase in the low-melting fraction and the crystal lamellar thickness, as well as a reduction in the medium and high-melting fractions and the formation of the most abundant crystal type at 20 °C (β'-2 polymorph). Furthermore, DGAT1 KK was associated with higher levels of odd-chain saturated triacylglycerols than DGAT1 AA, and it was also associated with an increase in the high-melting fraction and the endset melting temperature. An interaction between diet and DGAT1 for the unsaturated C54 triacylglycerols accentuated the effects of LSO supplementation with DGAT1 AA. These findings show that genetic polymorphism and cows' diet can have considerable effects on milk fat properties.

Association of Single Nucleotide Polymorphism in the DGAT1 Gene with the Fatty Acid Composition of Cows Milked Once and Twice a Day

A single nucleotide polymorphism (SNP) rs109421300 of the diacylglycerol acyltransferase 1 (DGAT1) on bovine chromosome 14 is associated with fat yield, fat percentage, and protein percentage. This study aimed to investigate the effect of SNP rs109421300 on production traits and the fatty acid composition of milk from cows milked once a day (OAD) and twice a day (TAD) under New Zealand grazing conditions. Between September 2020 and March 2021, 232 cows from a OAD herd and 182 cows from a TAD herd were genotyped. The CC genotype of SNP rs109421300 was associated with significantly (p < 0.05) higher fat yield, fat percentage, and protein percentage, and lower milk and protein yields in both milking frequencies. The CC genotype was also associated with significantly (p < 0.05) higher proportions of C16:0 and C18:0, higher predicted solid fat content at 10 °C (SFC₁₀), and lower proportions of C4:0 and C18:1 cis-9 in both milking frequencies. The association of SNP with fatty acids was similar in both milking frequencies, with differences in magnitudes. The SFC₁₀ of cows milked OAD was lower than cows milked TAD for all three SNP genotypes suggesting the suitability of OAD milk for producing easily spreadable butter. These results demonstrate that selecting cows with the CC genotype is beneficial for New Zealand dairy farmers with the current payment system, however, this would likely result in less spreadable butter.

Heat stress on breeding value prediction for milk yield and composition of a Brazilian Holstein cattle population

Due to the high milk production of Holstein cows, many countries have chosen to import semen to improve local dairy herds. This strategy would be more effective if this semen was used in the same environment conditions in which the bulls were selected. If the effect of genotype by environment (G × E) interaction is not considered, the estimated breeding values (EBVs) may vary, potentially reducing the selection response. We evaluate the impact of heat stress on selection for milk yield and composition of Holstein cows using random regression models. To verify the interference of heat stress in milk yield (MY) and composition traits (fat, protein, total saturated, and total unsaturated fatty acids content in milk), temperature-humidity index (THI) on test-day milk records was used. The threshold value to divide the environments using test-day information from Brazilian Holstein cows was 72 units of THI, i.e., < 72 represented no heat stress and > 72 represented heat stress. Legendre polynomials of second-order (Leg 2) model and two lactation points (33 and 122 DIM) were used to estimate heritabilities and EBVs for five important dairy traits. The heritabilities of milk components and fatty acids were low (0.09-0.29), regardless of lactation period and degree of heat stress, with the exception of protein content (0.30-0.35). Fat content was the only milk component that was reduced according to the degree of heat stress and lactation period. The EBVs tended to decrease in heat stress conditions, thus animals with high genetic potential demonstrated evidence of G × E interaction. However, acclimatization of dairy cows to heat stress in the farm production systems may have been responsible for the low differences among genetic parameters and EBVs with and without heat stress found in this study.

Genetic variants associated with two major bovine milk fatty acids offer opportunities to breed for altered milk fat composition

Background

Although bovine milk is regarded as healthy and nutritious, its high content of saturated fatty acids (FA) may be harmful to cardiovascular health. Palmitic acid (C16:0) is the predominant saturated FA in milk with adverse health effects that could be countered by substituting it with higher levels of unsaturated FA, such as oleic acid (C18:1cis-9). In this work, we performed genome-wide association analyses for milk fatty acids predicted from FTIR spectroscopy data using 1811 Norwegian Red cattle genotyped and imputed to a high-density 777k single nucleotide polymorphism (SNP)-array. In a follow-up analysis, we used imputed whole-genome sequence data to detect genetic variants that are involved in FTIR-predicted levels of C16:0 and C18:1cis-9 and explore the transcript profile and protein level of candidate genes.

Results

Genome-wise significant associations were detected for C16:0 on Bos taurus (BTA) autosomes 11, 16 and 27, and for C18:1cis-9 on BTA5, 13 and 19. Closer examination of a significant locus on BTA11 identified the PAEP gene, which encodes the milk protein β-lactoglobulin, as a particularly attractive positional candidate gene. At this locus, we discovered a tightly linked cluster of genetic variants in coding and regulatory sequences that have opposing effects on the levels of C16:0 and C18:1cis-9. The favourable haplotype, linked to reduced levels of C16:0 and increased levels of C18:1cis-9 was also associated with a marked reduction in PAEP expression and β-lactoglobulin protein levels. β-lactoglobulin is the most abundant whey protein in milk and lower levels are associated with important dairy production parameters such as improved cheese yield.

Conclusions

The genetic variants detected in this study may be used in breeding to produce milk with an improved FA health-profile and enhanced cheese-making properties.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-022-00731-9.

Study of the Fatty Acid Profile of Milk in Different Sheep Breeds: Evaluation by Multivariate Factorial Analysis

Simple Summary

The quality of milk is strongly influenced by its lipid profile. The increase in fats with nutraceutical properties at the expense of those negative for human health, has always been a goal to improve the functional properties of milk. To achieve this goal, it is essential to know the metabolism of the mammary gland and the relationship between the various lipid components. Much is known about bovine milk, while the aspect relating to the sheep species has not been developed. The present work aims to investigate the relationships between the various fatty acids in sheep’s milk through a multivariate approach, which can highlight the mammary role of lipid synthesis.

Abstract

A multivariate analysis was used to investigate the fatty acid (FA) profile in three different Italian sheep breeds: Comisana, Massese, and Sarda. A sample of 852 animals was considered: 118 Massese, 303 Comisana, 431 Sarda. Sarda sheep were divided into two groups, based on their breeding origin (298 and 133 reared in Sardinia and Tuscany, respectively). Sarda sheep, bred both in Sardinia and in Tuscany, were considered in different groups, both because in these two regions most of the sheep of this breed are reared, and because they differ in geographical characteristics and in the farming system. The individual milk FA composition of dairy ewes was analyzed with multivariate factor analysis. The extracted factors were representative of the following eight groups of fatty acids or functions: factor 1 (odd branched fatty acids and long-chain fatty acids), factor 2 (sn3_position), factor 3 (alternative biohydrogenation), factor 4 (SCD_1), factor 5 (SCD_2), factor 6 (SCD_3), factor 7 (fat secretion) and factor 8 (omega-3). A factor analysis suggested the presence of different metabolic pathways for de novo short- and medium-chain fatty acids and Δ9-desaturase products. The ANOVA of factor scores highlighted the significant effects of the breed. The results of the present study showed that breed is an important factor in defining the fatty acid profile of milk, combined with the effect of the diet. Breeds reared in the same farming system (Comisana, Massese and Sarda reared in Tuscany) showed significant differences for all the factors extracted. At the same time, we found differences between the Sarda sheep reared in Sardinia and Tuscany, two different regions of Italy.

Using singleton densities to detect recent selection in Bos taurus

Many quantitative traits are subject to polygenic selection, where several genomic regions undergo small, simultaneous changes in allele frequency that collectively alter a phenotype. The widespread availability of genome data, along with novel statistical techniques, has made it easier to detect these changes. We apply one such method, the "Singleton Density Score" (SDS), to the Holstein breed of Bos taurus to detect recent selection (arising up to around 740 years ago). We identify several genes as candidates for targets of recent selection, including some relating to cell regulation, catabolic processes, neural-cell adhesion and immunity. We do not find strong evidence that three traits that are important to humans-milk protein content, milk fat content, and stature-have been subject to directional selection. Simulations demonstrate that because B. taurus recently experienced a population bottleneck, singletons are depleted so the power of SDS methods is reduced. These results inform on which genes underlie recent genetic change in B. taurus, while providing information on how polygenic selection can be best investigated in future studies.

Feeding System Resizes the Effects of DGAT1 Polymorphism on Milk Traits and Fatty Acids Composition in Modicana Cows

Simple Summary

Genetic selection for single-locus polymorphisms could offer suitable opportunities to rapidly improve milk traits in local unselected cattle breeds characterized by low production levels. Since these hardy breeds are generally raised in traditional extensive and semi-intensive systems, which make wide use of grazing resources, the interactive effect between genotype and feeding system is worthy of investigation. In Modicana cattle breed, milk composition and fatty acid profile were influenced by both genetic polymorphisms at the DGAT1 K232A locus and feeding systems. The milk from homozygous AA cows was associated with a more favorable fatty acid composition due to a lower percentage of total saturated fatty acids, saturated to unsaturated ratio, atherogenic index, and a greater presence of oleic acid and total unsaturated fatty acids. Our finding confirmed the important role of pasture feeding on milk composition: the high nutritional and healthy value of milk obtained in extensive systems by pasture-fed cows. The interaction between the two experimental factors also appears to play a role: in our experimental condition, it seems that high pasture feeding can resize the effect of the DGAT1 genotype on milk traits and fatty acid composition in Modicana cows.

Abstract

The interaction between genetic polymorphism and feeding system on milk traits and fatty acid composition was investigated in Modicana cows. Two DGAT1 K232A genotypes (AK and AA) and two feeding regimes, extensive system (EX) with 8 h of grazing without concentrate (EX) and semi-intensive systems (SI) with 2 h of grazing with concentrate, were investigated. DGAT1 genotype did not influence milk yield and composition. The feeding system affected milk composition: protein was significantly higher in SI and lactose in the EX system. A significant genotype × feeding system interaction was observed: the protein and casein levels of AK cows were higher in the SI compared to the EX system. Milk fatty acids profile, total saturated to total unsaturated fatty acids, n-6 to n-3 ratios, and atherogenic index were affected by the feeding system, improving the healthy properties of milk from animals reared in the extensive system. DGAT1 genotype influenced the fatty acid composition: milk from AA cows had a more favorable fatty acid composition due to lower total saturated fatty acids, saturated to unsaturated ratio, atherogenic index, and higher levels of oleic acid and total unsaturated fatty acids. Furthermore, an interaction genotype x feeding system was observed: the AK milk was richer in short-chain FAs (C4:0–C8:0) and C10:0 only in the EX but not in the SI system. Our data suggest that a high amount of green forage in the diet of Modicana cows can resize the effect of the DGAT1 genotype on milk traits and fatty acids composition.

Genetic correlations between fertility traits and milk composition and fatty acids in Holstein-Friesian, Brown Swiss, and Simmental cattle using recursive models

This study aimed to investigate the genetic and putative causal relationships between fertility traits [i.e., days open (DO) and calving rate (CR)] and milk quality, composition, and fatty acid contents (milk composition traits) in Holstein-Friesian, Brown Swiss, and Simmental cattle, using recursive models within a Bayesian framework. Trivariate animal models were run, each including one fertility trait, one milk composition trait, and, in all models, milk yield. The DO and CR data were merged with the test days closest to the insemination date for milk composition traits. After editing, 16,468 to 23,424 records for Holstein-Friesian, 23,424 to 46,660 for Brown Swiss, and 26,105 to 35,574 for Simmental were available for the analyses. Recursive animal models were applied to investigate the possible causal influences of milk composition traits on fertility and the genetic relationships among these traits. The results suggested a potential cause-and-effect relationship between milk composition traits and fertility traits, with the first trait influencing the latter. We also found greater recursive effects of milk composition traits on DO than on CR, the latter with some putative differences among breeds in terms of sensitivity. For instance, the putative causal effects of somatic cell score on CR (on the observed scale, %) varied from -0.96 to -1.39%, depending on the breed. Concerning fatty acids, we found relevant putative effects of C18:0 on CR, with estimates varying from -7.8 to -9.9%. Protein and casein percentages, and short-chain fatty acid showed larger recursive effects on CR, whereas fat, protein, and casein percentages, C16:0, C18:0, and long-chain fatty acid had larger effects on DO. The results obtained suggested that these milk traits could be considered as effective indicators of the effects of animal metabolic and physiological status on fertility.

Genomic prediction for latent variables related to milk fatty acid composition in Holstein, Simmental and Brown Swiss dairy cattle breeds

Genomic selection (GS) reports on milk fatty acid (FA) profiles have been published quite recently and are still few despite this trait represents the most important aspect of milk nutritional and sensory quality. Reasons for this can be found in the high costs of phenotype recording but also in issues related to its nature of complex trait constituted by multiple genetically correlated variables with low heritabilities. One possible strategy to deal with such constraint is represented by the use of dimension reduction methods. We analysed 40 individual FAs from Italian Brown Swiss, Holstein and Simmental milk through multivariate factor analysis (MFA) to study the genetics of milk FA-related latent variables (factors) and assess their potential use in breeding. A total of nine factors were obtained, and their genetic parameters were inferred under a Bayesian framework using two statistical approaches: the classical pedigree best linear unbiased prediction (ABLUP) and the single-step genomic BLUP (ssGBLUP). The resulting factorial solutions were able to represent groups of FAs with common origin and function and can be considered concise pathway-level phenotypes. The heritability (h² ) values showed relevant variations across different factors in each breed (0.03 ≤ h²  ≤ 0.38). The accuracies of breeding values predicted were low to high, ranging from 0.13 to 0.72 and from 0.18 to 0.74 considering the pedigree and the genomic model, respectively. The gain in accuracy in genetic prediction due to the addition of genomic information was ~30% and ~5% in validation and training groups respectively, confirming the contribution of genomic information in yielding more accurate predictions compared to the traditional ABLUP methodology. Our results suggest that MFA in combination with GS can be a valuable tool in dairy cattle breeding and deserves to be further investigated for use in future breeding programs to improve cow's milk FA-related traits.

Genetic Parameters of Bovine Milk Fatty Acid Profile, Yield, Composition, Total and Differential Somatic Cell Count

The growing interest of consumers for milk and dairy products of high nutritional value has pushed researchers to evaluate the feasibility of including fatty acids (FA) in selection programs to modify milk fat profile and improve its nutritional quality. Therefore, the aim of this study was to estimate genetic parameters of FA profile predicted by mid-infrared spectroscopy, milk yield, composition, and total and differential somatic cell count. Edited data included 35,331 test-day records of 25,407 Italian Holstein cows from 652 herds. Variance components and heritability were estimated using single-trait repeatability animal models, whereas bivariate repeatability animal models were used to estimate genetic and phenotypic correlations between traits, including the fixed effects of stage of lactation, parity, and herd-test-date, and the random effects of additive genetic animal, cow permanent environment and the residual. Heritabilities and genetic correlations obtained in the present study reflected both the origins of FA (extracted from the blood or synthesized de novo by the mammary gland) and their grouping according to saturation or chain length. In addition, correlations among FA groups were in line with correlation among individual FA. Moderate negative genetic correlations between FA and milk yield and moderate to strong positive correlations with fat, protein, and casein percentages suggest that actual selection programs are currently affecting all FA groups, not only the desired ones (e.g., polyunsaturated FA). The absence of association with differential somatic cell count and the weak association with somatic cell score indicate that selection on FA profile would not affect selection on resistance to mastitis and vice versa. In conclusion, our findings suggest that genetic selection on FA content is feasible, as FA are variable and moderately heritable. Nevertheless, in the light of correlations with other milk traits estimated in this study, a clear breeding goal should first be established.

Potential candidate gene markers for milk fat in bovines: A review

In dairy animals, the principal goal of selection is to improve quality and quantity of milk. Genetic information inferred from single nucleotide polymorphism (SNP) primarily linked to Quantitative Trait Loci (QTL) can be used to improve selection for milk and milk constituent traits in bovines. Selection for a marker allele known to be associated with a beneficial QTL increases the frequency of that allele and hence, dairy performance can be enhanced. One of the potential benefit of selection based on molecular marker is that the marker genotypes can be determined in a dairy animal just after birth. Thus, marker information can be used to predict an animal's genotype before its actual performance recording for a trait is available, which considerably reduces generation interval and thus improves genetic gain in a herd for milk and its constituent traits. This review article is an attempt to comprehend the idea behind marker based selection for milk fat and genes regulating milk fat with significant effects that can be targeted specifically in selection of superior dairy animals. Once an association is established, itcan be utilized in a marker assisted breeding program for improvement of bovines.

Use of multivariate factor analysis of detailed milk fatty acid profile to perform a genome-wide association study in Italian Simmental and Italian Holstein

Milk fatty acid (FA) profile is a clear example of complex and multiple correlated traits whose genetic basis is difficult to assess. Although genome-wide association (GWA) studies have been successful in the identification of significant genetic variants for complex traits, when correlated phenotypes are analysed separately, the outcomes are difficult to compare and interpret in a metabolic context. Here, we performed a multivariate factor analysis (MFA) on Italian Simmental and Italian Holstein milk fat profiles to extract latent unobserved factors able to explain correlation structure and common metabolic function among different FAs. Individual factor scores obtained by MFA were used to perform a single-SNP based GWA. In both breeds, MFA was able to extract ten latent factors with specific biological meaning, notably: de novo synthesis, desaturation activity and biohydrogenation. The GWA result confirmed the increased power of joint association analysis on multiple correlated traits and allowed us to identify major candidate genes with well-documented function consistent with the metabolic classification of factors obtained, such as DGAT1, FASN and SCD.

Genetic correlations of milk fatty acid contents predicted from milk mid-infrared spectra in New Zealand dairy cattle

The objective of this study was to estimate genetic correlations among milk fatty acid (FA) concentrations in New Zealand dairy cattle. Concentrations of each of the most common FA, expressed as a percentage of the total FA, were determined by gas chromatography on a specific cohort of animals. Using this data set, prediction equations were derived using mid-infrared (MIR) spectroscopy data collected from the same samples. These prediction equations were applied to a large data set of MIR measurements in 34,141 milk samples from 3,445 Holstein-Friesian, 2,935 Jersey, and 3,609 crossbred Holstein-Friesian × Jersey cows, sampled an average of 3.42 times during the 2007-2008 season. Data were analyzed using univariate and bivariate repeatability animal models. Heritability of predicted FA concentration in milk fat ranged from 0.21 to 0.42, indicating that genetic selection could be used to change the FA composition of milk. The de novo synthesized FA (C6:0, C8:0, C10:0, C12:0, and C14:0) showed strong positive genetic correlations with each other, ranging from 0.24 to 0.99. Saturated FA were negatively correlated with unsaturated (-0.93) and polyunsaturated (-0.84) FA. The saturated FA were positively correlated with milk fat yield and fat percentage, whereas the unsaturated FA were negatively associated with fat yield and fat percentage. Our results indicate that bovine milk FA composition can be changed through genetic selection using MIR as a phenotypic proxy.

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.

Genetic parameters for milk fatty acid composition of Holstein in Korea

Objective

Milk fatty acid (FA) is a main nutritional component that markedly effects human health. Intentional modification of the FA profile has the potential to improve milk quality. This study aimed at the factors affecting elevated FA levels and the estimation of the genetic parameters for milk FAs in the Korean Holstein population.

Methods

Total 885,249 repeated test-day milk records including, milk yield, saturated fatty acids (SFA), polyunsaturated fatty acids (PUFA), monounsaturated fatty acids (MUFA), total unsaturated fatty acids (TUFA), fat and protein percentages were analyzed using CombiFoss FT+ system (Foss Analytical A/S, Denmark). Genetic parameters were estimated by the restricted maximum likelihood procedure based on the repeatability model using the Wombat program.

Results

The FA profile varies along with the lactation and the energy balance (EB). With the negative EB in early lactation, mobilization of body fat reserves elevates the desirable FA levels. As a result of that, milk quality is increased by means of nutritionally and usability aspects during the early lactation. Moreover, heritability estimates for SFA, MUFA, PUFA, TUFA were 0.33, 0.42, 0.37, 0.41 respectively. According to the parity wise heritability analysis, first parity cows had relatively lower heritability for SFAs (0.19) than later parities (0.28).

Conclusion

Genetic parameters indicated that FAs were under stronger genetic control. Therefore, we suggest implementing animal breeding programs towards improving the milk FA profile.

Genome-wide association study on Fourier transform infrared milk spectra for two Danish dairy cattle breeds

Background

Infrared spectral analysis of milk is cheap, fast, and accurate. Infrared light interacts with chemical bonds present inside the milk, which means that Fourier transform infrared milk spectra are a reflection of the chemical composition of milk. Heritability of Fourier transform infrared milk spectra has been analysed previously. Further genetic analysis of Fourier transform infrared milk spectra could give us a better insight in the genes underlying milk composition. Breed influences milk composition, yet not much is known about the effect of breed on Fourier transform infrared milk spectra. Improved understanding of the effect of breed on Fourier transform infrared milk spectra could enhance efficient application of Fourier transform infrared milk spectra. The aim of this study is to perform a genome wide association study on a selection of wavenumbers for Danish Holstein and Danish Jersey. This will improve our understanding of the genetics underlying milk composition in these two dairy cattle breeds.

Results

For each breed separately, fifteen wavenumbers were analysed. Overall, more quantitative trait loci were observed for Danish Jersey compared to Danish Holstein. For both breeds, the majority of the wavenumbers was most strongly associated to a genomic region on BTA 14 harbouring DGAT1. Furthermore, for both breeds most quantitative trait loci were observed for wavenumbers that interact with the chemical bond C-O. For Danish Jersey, wavenumbers that interact with C-H were associated to genes that are involved in fatty acid synthesis, such as AGPAT3, AGPAT6, PPARGC1A, SREBF1, and FADS1. For wavenumbers which interact with –OH, associations were observed to genomic regions that have been linked to alpha-lactalbumin.

Conclusions

The current study identified many quantitative trait loci that underlie Fourier transform infrared milk spectra, and thus milk composition. Differences were observed between groups of wavenumbers that interact with different chemical bonds. Both overlapping and different QTL were observed for Danish Holstein and Danish Jersey.

Impact of inbreeding on milk fatty acids of a Brazilian Holstein cattle

Context Reproductive technologies may either contribute to the increase of genetic gains or inbreeding levels in dairy cattle breeding programs and herds. In general, studies have evaluated the impacts of inbreeding on traditional traits, such as production and reproduction. However, studies on novel traits, such as milk fatty acids profile, are scarce in the literature. Aim We aimed to evaluate the impact of inbreeding levels on milk fatty acids profile measured in a Brazilian Holstein cattle population. Methods Monthly records of the percentages (%) of palmitic, stearic, oleic, total saturated, unsaturated, monounsaturated and polyunsaturated fatty acids in milk were collected from 2047 Holstein cows between May and December 2012. The pedigree file contained 7963 animals over seven generations. The inbreeding trend was evaluated by linear regression of inbreeding coefficients on generations. The inbreeding impacts on breeding and phenotypic values were evaluated by linear regression of breeding values and phenotypic values on generations respectively. Breeding values were obtained by a Bayesian approach based on an animal model that included the systematic effect of contemporary group, cubic effect of days in milk as a covariate, and the random direct additive genetic and animal permanent environmental effects. Key results The average inbreeding coefficient was 0.28% for all animals, and 1.39% for inbred animals. Inbreeding tended to increase 0.24% per generation (P-value &lt;0.0001). The regression coefficients of phenotypic values on inbreeding were not significant for saturated, unsaturated, monounsaturated, palmitic, stearic and oleic fatty acids (P-values &gt;0.18, 0.10, 0.16, 0.26, 0.51 and 0.09 respectively); whereas for polyunsaturated fatty acids, they were significant (P-value &lt;0.04), with an increase of –0.000978% on phenotypic values for each 1% increase in inbreeding. The regression coefficients of breeding values on inbreeding were not significant for unsaturated, monounsaturated, polyunsaturated, stearic and oleic fatty acids (P-values &gt;0.33, 0.78, 0.48, 0.32 and 0.07 respectively). However, they were significant for saturated and palmitic fatty acids (P-values &lt;0.03 and 0.0001 respectively), presenting an increase of 0.000689% and 0.000283% respectively on breeding values for each 1% increase in inbreeding. Conclusions There was a significant increase in inbreeding coefficients over the studied generations; however, the impacts on both breeding and phenotypic values were small, when significant. Implications Our study may contribute to the understanding of how inbreeding levels may affect the fatty acids profile in a Brazilian Holstein cattle population, as well as encourage future research on this subject.

Enhancing Omega-3 Long-Chain Polyunsaturated Fatty Acid Content of Dairy-Derived Foods for Human Consumption

Omega-3 polyunsaturated fatty acids (n-3 PUFA) are termed essential fatty acids because they cannot be synthesized de novo by humans due to the lack of delta-12 and delta-15 desaturase enzymes and must therefore be acquired from the diet. n-3 PUFA include α-linolenic acid (ALA, 18:3n-3), eicosapentaenoic (EPA, 20:5n-3), docosahexaenoic (DHA, 22:6n-3), and the less recognized docosapentaenoic acid (DPA, 22:5n-3). The three long-chain (≥C20) n-3 PUFA (n-3 LC-PUFA), EPA, DHA, and DPA play an important role in human health by reducing the risk of chronic diseases. Up to the present time, seafood, and in particular, fish oil-derived products, have been the richest sources of n-3 LC-PUFA. The human diet generally contains insufficient amounts of these essential FA due largely to the low consumption of seafood. This issue provides opportunities to enrich the content of n-3 PUFA in other common food groups. Milk and milk products have traditionally been a major component of human diets, but are also among some of the poorest sources of n-3 PUFA. Consideration of the high consumption of milk and its processed products worldwide and the human health benefits has led to a large number of studies targeting the enhancement of n-3 PUFA content in dairy products. The main objective of this review was to evaluate the major strategies that have been employed to enhance n-3 PUFA content in dairy products and to unravel potential knowledge gaps for further research on this topic. Nutritional manipulation to date has been the main approach for altering milk fatty acids (FA) in ruminants. However, the main challenge is ruminal biohydrogenation in which dietary PUFA are hydrogenated into monounsaturated FA and/or ultimately, saturated FA, due to rumen microbial activities. The inclusion of oil seed and vegetable oil in dairy animal diets significantly elevates ALA content, while the addition of rumen-protected marine-derived supplements is the most effective way to increase the concentration of EPA, DHA, and DPA in dairy products. In our view, the mechanisms of n-3 LC-PUFA biosynthesis pathway from ALA and the biohydrogenation of individual n-3 LC-PUFA in ruminants need to be better elucidated. Identified knowledge gaps regarding the activities of candidate genes regulating the concentrations of n-3 PUFA and the responses of ruminants to specific lipid supplementation regimes are also critical to a greater understanding of nutrition-genetics interactions driving lipid metabolism.

Comparative milk metabolite profiling for exploring superiority of indigenous Indian cow milk over exotic and crossbred counterparts

This study was planned to identify differences in the milk metabolite composition of Indian (Sahiwal), exotic (Holstein-Friesian) and their crossbred cows in intensive system of management. To mimic the management system of ancient India, indigenous cattle under extensive system (zero input) were also included. Holstein-Friesian (HF) had significantly higher amount of saturated fatty acids (SFA, 76.3%) as compared to the crossbred (73.3%) and Sahiwal (68.0%). HF had the highest concentration (42.7%) of hypercholesterolemic fatty acids and the maximum value (68.5) of athrogenecity index (AI). Sahiwal had the highest proportion (32.1%) of total unsaturated fatty acids (UFA). Mineral, vitamin, n-3 fatty acids and total amount of essential amino acids did not vary across the three groups. Milk of indigenous cattle maintained only on grazing had more favorable nutrient profile. It had low SFA (61.4%), high UFA (38.6%) and higher concentrations of both monounsaturated fatty acids (31.4%) and polyunsaturated fatty acids (7.2%). The n-6/n-3 ratio (2.7) and the AI (33.9) were significantly lower. Significantly higher concentrations of minerals (Zn, Fe, P and Cu) and vitamins except vitamin B5 were recorded in their milk. The study revealed that milk metabolite characteristics can be used to promote indigenous cattle.

Role of Fatty Acids in Milk Fat and the Influence of Selected Factors on Their Variability-A Review

Fatty acids (FAs) of milk fat are considered to be important nutritional components of the diets of a significant portion of the human population and substantially affect human health. With regard to dairy farming, the FA profile is also seen as an important factor in the technological quality of raw milk. In this sense, making targeted modifications to the FA profile has the potential to significantly contribute to the production of dairy products with higher added value. Thus, FAs also have economic importance. Current developments in analytical methods and their increasing efficiency enable the study of FA profiles not only for scientific purposes but also in terms of practical technological applications. It is important to study the sources of variability of FAs in milk, which include population genetics, type of farming, and targeted animal nutrition. It is equally important to study the health and technological impacts of FAs. This review summarizes current knowledge in the field regarding sources of FA variability, including the impact of factors such as: animal nutrition, seasonal feed changes, type of animal farming (conventional and organic), genetic parameters (influence of breed), animal individuality, lactation, and milk yield. Potential practical applications (to improve food technology and consumer health) of FA profile information are also reviewed.

SNP co-association and network analyses identify E2F3, KDM5A and BACH2 as key regulators of the bovine milk fatty acid profile

The fatty acid (FA) profile has a considerable impact on the nutritional and technological quality of milk and dairy products. The molecular mechanism underlying the regulation of fat metabolism in bovine mammary gland have been not completely elucidated. We conducted genome-wide association studies (GWAS) across 65 milk FAs and fat percentage in 1,152 Brown Swiss cows. In total, we identified 175 significant single nucleotide polymorphism (SNPs) spanning all chromosomes. Pathway analyses revealed that 12:0 was associated with the greatest number of overrepresented categories/pathways (e.g. mitogen-activated protein kinase (MAPK) activity and protein phosphorylation), suggesting that it might play an important biological role in controlling milk fat composition. An Associated Weight Matrix approach based on SNP co-associations predicted a network of 791 genes related to the milk FA profile, which were involved in several connected molecular pathways (e.g., MAPK, lipid metabolism and hormone signalling) and undetectable through standard GWAS. Analysis of transcription factors and their putative target genes within the network identified BACH2, E2F3 and KDM5A as key regulators of milk FA metabolism. These findings contribute to increasing knowledge of FA metabolism and mammary gland functionality in dairy cows and may be useful in developing targeted breeding practices to improve milk quality.

Seasonal Variation of Triacylglycerol Profile of Bovine Milk

Milk contains 3–6% of fat, of which the dominant component is triacylglycerol (TAG). Over 100 TAG groups can be readily detected in any non-enriched milk sample by LC-MS; most TAG groups contain several isomers (TAG molecules with different fatty acid composition), which cannot be fully resolved chromatographically by any single stationary phase. TAG profile of mature milk from 19 cows was surveyed in this study for eight consecutive months using RP-LC-Orbitrap MS. It was found that TAG profile of milk was not constant throughout the milking season and the seasonal pattern varied with TAG groups. The overall unsaturation level of TAG was stable from October 2013 to January 2014, decreased in February/March 2014 and then increased from April and peaked in May 2014. In addition to the seasonal fluctuation in TAG profile, the proportion of different isomeric species within a TAG group also changed substantially across seasons. However, the proportion of different positional isomers within a given TAG group does not seem to vary during the milking season. To our knowledge, this is the first report on the seasonal change of milk lipid at the TAG group and isomer level.

Genetic analysis of groups of mid-infrared predicted fatty acids in milk

The objective of this study was to investigate genetic variability of mid-infrared predicted fatty acid groups in Canadian Holstein cattle. Genetic parameters were estimated for 5 groups of fatty acids: short-chain (4 to 10 carbons), medium-chain (11 to 16 carbons), long-chain (17 to 22 carbons), saturated, and unsaturated fatty acids. The data set included 49,127 test-day records from 10,029 first-lactation Holstein cows in 810 herds. The random regression animal test-day model included days in milk, herd-test date, and age-season of calving (polynomial regression) as fixed effects, herd-year of calving, animal additive genetic effect, and permanent environment effects as random polynomial regressions, and random residual effect. Legendre polynomials of the third degree were selected for the fixed regression for age-season of calving effect and Legendre polynomials of the fourth degree were selected for the random regression for animal additive genetic, permanent environment, and herd-year effect. The average daily heritability over the lactation for the medium-chain fatty acid group (0.32) was higher than for the short-chain (0.24) and long-chain (0.23) fatty acid groups. The average daily heritability for the saturated fatty acid group (0.33) was greater than for the unsaturated fatty acid group (0.21). Estimated average daily genetic correlations were positive among all fatty acid groups and ranged from moderate to high (0.63-0.96). The genetic correlations illustrated similarities and differences in their origin and the makeup of the groupings based on chain length and saturation. These results provide evidence for the existence of genetic variation in mid-infrared predicted fatty acid groups, and the possibility of improving milk fatty acid profile through genetic selection in Canadian dairy cattle.

Genome-wide association mapping for milk fat composition and fine mapping of a QTL for de novo synthesis of milk fatty acids on bovine chromosome 13

Background

Bovine milk is widely regarded as a nutritious food source for humans, although the effects of individual fatty acids on human health is a subject of debate. Based on the assumption that genomic selection offers potential to improve milk fat composition, there is strong interest to understand more about the genetic factors that influence the biosynthesis of bovine milk and the molecular mechanisms that regulate milk fat synthesis and secretion. For this reason, the work reported here aimed at identifying genetic variants that affect milk fatty acid composition in Norwegian Red cattle. Milk fatty acid composition was predicted from the nation-wide recording scheme using Fourier transform infrared spectroscopy data and applied to estimate heritabilities for 36 individual and combined fatty acid traits. The recordings were used to generate daughter yield deviations that were first applied in a genome-wide association (GWAS) study with 17,343 markers to identify quantitative trait loci (QTL) affecting fatty acid composition, and next on high-density and sequence-level datasets to fine-map the most significant QTL on BTA13 (BTA for Bos taurus chromosome).

Results

The initial GWAS revealed 200 significant associations, with the strongest signals on BTA1, 13 and 15. The BTA13 QTL highlighted a strong functional candidate gene for de novo synthesis of short- and medium-chained saturated fatty acids; acyl-CoA synthetase short-chain family member 2. However, subsequent fine-mapping using single nucleotide polymorphisms (SNPs) from a high-density chip and variants detected by resequencing showed that the effect was more likely caused by a second nearby gene; nuclear receptor coactivator 6 (NCOA6). These findings were confirmed with results from haplotype studies. NCOA6 is a nuclear receptor that interacts with transcription factors such as PPARγ, which is a major regulator of bovine milk fat synthesis.

Conclusions

An initial GWAS revealed a highly significant QTL for de novo-synthesized fatty acids on BTA13 and was followed by fine-mapping of the QTL within NCOA6. The most significant SNPs were either synonymous or situated in introns; more research is needed to uncover the underlying causal DNA variation(s).

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-017-0294-5) contains supplementary material, which is available to authorized users.

Effect of Calf Gender on Milk Yield and Fatty Acid Content in Holstein Dairy Cows

The scale of sexed semen use to avoid the birth of unwanted bull calves in the UK dairy industry depends on several economic factors. It has been suggested in other studies that calf gender may affect milk yield in Holsteins- something that would affect the economics of sexed semen use. The present study used a large milk recording data set to evaluate the effect of calf gender (both calf born and calf in utero) on both milk yield and saturated fat content. Linear regression was used to model data for first lactation and second lactation separately. Results showed that giving birth to a heifer calf conferred a 1% milk yield advantage in first lactation heifers, whilst giving birth to a bull calf conferred a 0.5% advantage in second lactation. Heifer calves were also associated with a 0.66kg reduction in saturated fatty acid content of milk in first lactation, but there was no significant difference between the genders in second lactation. No relationship was found between calf gender and milk mono- or polyunsaturated fatty acid content. The observed effects of calf gender on both yield and saturated fatty acid content was considered minor when compared to nutritional and genetic influences.

Changes throughout lactation in phenotypic and genetic correlations between methane emissions and milk fatty acid contents predicted from milk mid-infrared spectra

The aim of this study was to estimate phenotypic and genetic correlations between methane production (Mp) and milk fatty acid contents of first-parity Walloon Holstein cows throughout lactation. Calibration equations predicting daily Mp (g/d) and milk fatty acid contents (g/100 dL of milk) were applied on milk mid-infrared spectra related to Walloon milk recording. A total of 241,236 predictions of Mp and milk fatty acids were used. These data were collected between 5 and 305 d in milk in 33,555 first-parity Holstein cows from 626 herds. Pedigree data included 109,975 animals. Bivariate (i.e., Mp and a fatty acid trait) random regression test-day models were developed to estimate phenotypic and genetic parameters of Mp and milk fatty acids. Individual short-chain fatty acids (SCFA) and groups of saturated fatty acids, SCFA, and medium-chain fatty acids showed positive phenotypic and genetic correlations with Mp (from 0.10 to 0.16 and from 0.23 to 0.30 for phenotypic and genetic correlations, respectively), whereas individual long-chain fatty acids (LCFA), and groups of LCFA, monounsaturated fatty acids, and unsaturated fatty acids showed null to positive phenotypic and genetic correlations with Mp (from -0.03 to 0.13 and from -0.02 to 0.32 for phenotypic and genetic correlations, respectively). However, these correlations changed throughout lactation. First, de novo individual and group fatty acids (i.e., C4:0, C6:0, C8:0, C10:0, C12:0, C14:0, SCFA group) showed low phenotypic or genetic correlations (or both) in early lactation and higher at the end of lactation. In contrast, phenotypic and genetic correlations between Mp and C16:0, which could be de novo synthetized or derived from blood lipids, were more stable during lactation. This fatty acid is the most abundant fatty acid of the saturated fatty acid and medium-chain fatty acid groups of which correlations with Mp showed the same pattern across lactation. Phenotypic and genetic correlations between Mp and C17:0 and C18:0 were low in early lactation and increased afterward. Phenotypic and genetic correlations between Mp and C18:1 cis-9 originating from the blood lipids were negative in early lactation and increased afterward to become null from 18 wk until the end of lactation. Correlations between Mp and groups of LCFA, monounsaturated fatty acids, and unsaturated fatty acids showed a similar or intermediate pattern across lactation compared with fatty acids that compose them. Finally, these results indicate that correlations between Mp and milk fatty acids vary following lactation stage of the cow, a fact still often ignored when trying to predict Mp from milk fatty acid profile.

A post-GWAS confirming the SCD gene associated with milk medium- and long-chain unsaturated fatty acids in Chinese Holstein population

The stearoyl-CoA desaturase (delta-9-desaturase) gene encodes a key enzyme in the cellular biosynthesis of monounsaturated fatty acids. In our initial genome-wide association study (GWAS) of Chinese Holstein cows, 19 SNPs fell in a 1.8-Mb region (20.3-22.1 Mb) on chromosome 26 underlying the SCD gene and were highly significantly associated with C14:1 or C14 index. The aims of this study were to verify whether the SCD gene has significant genetic effects on milk fatty acid composition in dairy cattle. By resequencing the entire coding region of the bovine SCD gene, a total of six variations were identified, including three coding variations (g.10153G>A, g.10213T>C and g.10329C>T) and three intronic variations (g.6926A>G, g.8646G>A and g.16158G>C). The SNP in exon 3, g.10329C>T, was predicted to result in an amino acid replacement from alanine (GCG) to valine (GTG) in the SCD protein. An association study for 16 milk fatty acids using 346 Chinese Holstein cows with accurate phenotypes and genotypes was performed using the mixed animal model with the proc mixed procedure in sas 9.2. All six detected SNPs were revealed to be associated with six medium- and long-chain unsaturated fatty acids (P = 0.0457 to P < 0.0001), specifically for C14:1 and C14 index (P = 0.0005 to P < 0.0001). Subsequently, strong linkage disequilibrium (D' = 0.88-1.00) was observed among all six SNPs in SCD and the five SNPs (rs41623887, rs109923480, rs42090224, rs42092174 and rs42091426) within the 1.8-Mb region identified in our previous GWAS, indicating that the significant association of the SCD gene with milk fatty acid content traits reduced the observed significant 1.8-Mb chromosome region in GWAS. Haplotype-based analysis revealed significant associations of the haplotypes encompassing the six SCD SNPs and one SNP (rs109923480) in a GWAS with C14:1, C14 index, C16:1 and C16 index (P = 0.0011 to P < 0.0001). In summary, our findings provide replicate evidence for our previous GWAS and demonstrate that variants in the SCD gene are significantly associated with milk fatty acid composition in dairy cattle, which provides clear evidence for an increased understanding of milk fatty acid synthesis and enhances opportunities to improve milk-fat composition in dairy cattle.

Genetic and environmental relationships of detailed milk fatty acids profile determined by gas chromatography in Brown Swiss cows

The aim of this study was to characterize the profile of 47 fatty acids, including conjugated linoleic acid (CLA), 13 fatty acid groups, and 5 Δ(9)-desaturation indices in milk samples from Brown Swiss cows. The genetic variation was assessed and the statistical relevance of the genetic background for each trait was evaluated using the Bayes factor test. The additive genetic, herd-date, and residual relationships were also estimated among all single fatty acids and groups of fatty acids. Individual milk samples were collected from 1,158 Italian Brown Swiss cows and a detailed analysis of fat percentages and milk fatty acid compositions was performed by gas chromatography. Bayesian animal models were used for (co)variance components estimation. Exploitable genetic variation was observed for most of the de novo synthesized fatty acids and saturated fatty acids, except for C4:0 and C6:0, whereas long-chain fatty acids and unsaturated fatty acids (including CLA) were mainly influenced by herd-date effects. Herd-date effect explained large portions of the total phenotypic variance for C18:2 cis-9,cis-12 (0.668), C18:3 cis-9,cis-12,cis-15 (0.631), and the biohydrogenation and elongation products of these fatty acids. The desaturation ratios showed higher heritability estimates than the individual fatty acids, except for CLA desaturation index (0.098). Among the medium-chain fatty acids, C12:0 had greater heritability than C14:0 (0.243 vs. 0.097, respectively). Both C14:0 and C16:0 showed negative additive genetic correlations with the main monounsaturated and polyunsaturated fatty acids of milk fat, suggesting that their synthesis in the mammary gland may be influenced by the presence of unsaturated fatty acids. No correlation was observed between C4:0 and the other short-chain fatty acids (except for C6:0), confirming the independence of C4:0 from de novo mammary fatty acid synthesis. Among the genetic correlations dealing with potentially beneficial fatty acids, C18:0 was positively correlated with vaccenic and rumenic acids and negatively with linoleic acid. Finally, fatty acids C6:0 through C14:0 showed relevant correlations due to unknown environmental effects, suggesting the potential existence of genetic variances in micro-environmental sensitivity. This study allowed us to acquire new knowledge about the genetic and the environmental relationships among fatty acids. Likewise, the existence of genetic variation for most of de novo synthetized fatty acids and saturated fatty acids was also observed. Overall, these results provide useful information to combine feeding with genetic selection strategies for obtaining a desirable milk fatty acids profile, depending on the origin of fatty acids in milk.

Predictions of Daily Milk and Fat Yields, Major Groups of Fatty Acids, and C18:1 cis-9 from Single Milking Data without a Milking Interval

Reducing the frequency of milk recording would help reduce the costs of official milk recording. However, this approach could also negatively affect the accuracy of predicting daily yields. This problem has been investigated in numerous studies. In addition, published equations take into account milking intervals (MI), and these are often not available and/or are unreliable in practice. The first objective of this study was to propose models in which the MI was replaced by a combination of data easily recorded by dairy farmers. The second objective was to further investigate the fatty acids (FA) present in milk. Equations to predict daily yield from AM or PM data were based on a calibration database containing 79,971 records related to 51 traits [milk yield (expected AM, expected PM, and expected daily); fat content (expected AM, expected PM, and expected daily); fat yield (expected AM, expected PM, and expected daily; g/day); levels of seven different FAs or FA groups (expected AM, expected PM, and expected daily; g/dL milk), and the corresponding FA yields for these seven FA types/groups (expected AM, expected PM, and expected daily; g/day)]. These equations were validated using two distinct external datasets. The results obtained from the proposed models were compared to previously published results for models which included a MI effect. The corresponding correlation values ranged from 96.4% to 97.6% when the daily yields were estimated from the AM milkings and ranged from 96.9% to 98.3% when the daily yields were estimated from the PM milkings. The simplicity of these proposed models should facilitate their use by breeding and milk recording organizations.

The use of 2-dimensional gas chromatography to investigate the effect of rumen-protected conjugated linoleic acid, breed, and lactation stage on the fatty acid profile of sheep milk

In this study, 2-dimensional gas chromatography (GC × GC) was used to obtain a detailed fatty acid (FA) profile of sheep milk and to evaluate the effects of a rumen-protected conjugated linoleic acid (rpCLA) supply, breed, days in milk (DIM), sampling period, and number of lambs suckling on the FA profile. Twenty-four ewes, from 3 autochthonous breeds of the Veneto Alps (Brogna, Foza, and Lamon), were housed in 6 pens (2 pens/breed), according to DIM (38 ± 23 d) and body weight (61 ± 13 kg). The ewes and their offspring of 3 pens (1 pen/breed) were fed ad libitum a total mixed ration (control), and the other animals received the same diet supplemented with 12 g/d per ewe, plus 4 g/d for each lamb older than 30 d, of an rpCLA mixture. The study lasted 63 d. Two composite milk samples for each ewe were prepared during the first and second months of the trial. The pooled milk samples were analyzed in duplicate for FA profile by 2-dimensional gas chromatography, which allowed us to obtain a detailed FA profile of sheep milk, with 170 different FA detected, including many that were present in small concentrations. The milk relative proportions of individual FA, groups of FA, or FA indices were analyzed by PROC MIXED of SAS (SAS Institute Inc., Cary, NC), considering diet, breed, DIM, and sampling period as sources of variation. The random effect of animal was used to test diet, breed, and DIM, whereas the effects of period were tested on the residual. Breed had a small influence on milk FA profile, mainly on branched- and odd-chain FA. Within breed, animal repeatability for the relative proportions of milk FA was notable for almost all monounsaturated FA and for saturated FA with 14 to 19 carbon atoms, except C16:0, and less so for polyunsaturated FA. The inclusion of rpCLA (CLA cis-9,trans-11 and CLA trans-10,cis-12) increased the presence of the same CLA isomers in the milk as well as that of CLA trans-9,trans-11, and decreased the proportions of de novo-synthesized short-chain FA. From a cluster analysis based on the matrix of correlation coefficients among all FA relative proportions, 3 main FA groups were observed: the first included mainly odd- or branched-chain saturated FA, C18:0, C16:0 and CLA trans-10,cis-12; the second included monounsaturated FA or polyunsaturated FA with 16 to 20 carbons, CLA cis-9,trans-11, and CLA trans-9,trans-11; and the third included short- to medium-chain saturated FA, polyunsaturated FA with 2 to 5 double bonds, and 3 CLA isomers not affected by rpCLA addition (CLA trans-11,cis-13, CLA cis-9,cis-11, and CLA cis-10,cis-12).