Can greenhouse gases in breath be used to genetically improve feed efficiency of dairy cows?

There is considerable interest in improving feed utilization of dairy cattle while limiting losses to the environment (i.e., greenhouse gases, GHG). To breed for feed-efficient or climate-friendly cattle, it is first necessary to obtain accurate estimates of genetic parameters and correlations of feed intake, greenhouse gases, and production traits. Reducing dry matter take (DMI) requirements while maintaining production has high economic value to farmers, but DMI is costly to record and thus limited to small research or nucleus herds. Conversely, enteric methane (CH4) currently has no economic value, is also costly to record, and is limited to small experimental trials. However, breath gas concentrations of methane (CH4c) and carbon dioxide (CO2c) are relatively cheap to measure at high throughput under commercial conditions by installing sniffers in automated milking stations. The objective of this study was to assess the genetic correlations between DMI, body weight (BW), fat- and protein-corrected milk yield (FPCM), and GHG-related traits: CH4c and CO2c from Denmark (DNK) and the Netherlands (NLD). A second objective was to assess the genetic potential for improving feed efficiency and the added benefits of using CH4c and CO2c as indicators. Feed intake data were available on 703 primiparous cows in DNK and 524 in NLD; CH4c and CO2c records were available on 434 primiparous cows in DNK and 656 in NLD. The GHG-related traits were heritable (e.g., CH4c h2: DNK = 0.26, NLD = 0.15) but were differentially genetically correlated with DMI and feed efficiency in both magnitude and sign, depending on the population and the definition of feed efficiency. Across feed efficiency traits and DMI, having bulls with 100 daughters with FPCM, BW, and GHG traits resulted in sufficiently high accuracy to almost negate the need for DMI records. Despite differences in genetic correlation structure, the relatively cheap GHG-related traits showed considerable potential for improving the accuracy of breeding values of highly valuable feed intake and feed efficiency traits.

Combining multi-population datasets for joint genome-wide association and meta-analyses: The case of bovine milk fat composition traits.

In genome-wide association studies (GWAS), sample size is the most important factor affecting statistical power that is under control of the investigator, posing a major challenge in understanding the genetics underlying difficult-to-measure traits. Combining data sets available from different populations for joint or meta-analysis is a promising alternative to increasing sample sizes available for GWAS. Simulation studies indicate statistical advantages from combining raw data or GWAS summaries in enhancing quantitative trait loci (QTL) detection power. However, the complexity of genetics underlying most quantitative traits, which itself is not fully understood, is difficult to fully capture in simulated data sets. In this study, population-specific and combined-population GWAS as well as a meta-analysis of the population-specific GWAS summaries were carried out with the objective of assessing the advantages and challenges of different data-combining strategies in enhancing detection power of GWAS using milk fatty acid (FA) traits as examples. Gas chromatography (GC) quantified milk FA samples and high-density (HD) genotypes were available from 1,566 Dutch, 614 Danish, and 700 Chinese Holstein Friesian cows. Using the joint GWAS, 28 additional genomic regions were detected, with significant associations to at least 1 FA, compared with the population-specific analyses. Some of these additional regions were also detected using the implemented meta-analysis. Furthermore, using the frequently reported variants of the diacylglycerol acyltransferase 1 (DGAT1) and stearoyl-CoA desaturase (SCD1) genes, we show that significant associations were established with more FA traits in the joint GWAS than the remaining scenarios. However, there were few regions detected in the population-specific analyses that were not detected using the joint GWAS or the meta-analyses. Our results show that combining multi-population data set can be a powerful tool to enhance detection power in GWAS for seldom-recorded traits. Detection of a higher number of regions using the meta-analysis, compared with any of the population-specific analyses also emphasizes the utility of these methods in the absence of raw multi-population data sets to undertake joint GWAS.

Multi-population GWAS and enrichment analyses reveal novel genomic regions and promising candidate genes underlying bovine milk fatty acid composition.

BACKGROUND: The power of genome-wide association studies (GWAS) is often limited by the sample size available for the analysis. Milk fatty acid (FA) traits are scarcely recorded due to expensive and time-consuming analytical techniques. Combining multi-population datasets can enhance the power of GWAS enabling detection of genomic region explaining medium to low proportions of the genetic variation. GWAS often detect broader genomic regions containing several positional candidate genes making it difficult to untangle the causative candidates. Post-GWAS analyses with data on pathways, ontology and tissue-specific gene expression status might allow prioritization among positional candidate genes. RESULTS: Multi-population GWAS for 16 FA traits quantified using gas chromatography (GC) in sample populations of the Chinese, Danish and Dutch Holstein with high-density (HD) genotypes detects 56 genomic regions significantly associated to at least one of the studied FAs; some of which have not been previously reported. Pathways and gene ontology (GO) analyses suggest promising candidate genes on the novel regions including OSBPL6 and AGPS on Bos taurus autosome (BTA) 2, PRLH on BTA 3, SLC51B on BTA 10, ABCG5/8 on BTA 11 and ALG5 on BTA 12. Novel genes in previously known regions, such as FABP4 on BTA 14, APOA1/5/7 on BTA 15 and MGST2 on BTA 17, are also linked to important FA metabolic processes. CONCLUSION: Integration of multi-population GWAS and enrichment analyses enabled detection of several novel genomic regions, explaining relatively smaller fractions of the genetic variation, and revealed highly likely candidate genes underlying the effects. Detection of such regions and candidate genes will be crucial in understanding the complex genetic control of FA metabolism. The findings can also be used to augment genomic prediction models with regions collectively capturing most of the genetic variation in the milk FA traits.

Selective breeding for high natural antibody level increases resistance to avian pathogenic Escherichia coli (APEC) in chickens.

Keyhole limpet hemocyanin (KLH)-binding natural antibody (NAb) titers in chickens are heritable, and higher levels have previously been associated with a higher survival. This suggests that selective breeding for higher NAb levels might increase survival by means of improved general disease resistance. Chickens were divergently selected and bred for total NAb levels binding KLH at 16 weeks of age for six generations, resulting in a High NAb selection line and a Low NAb selection line. To for test differences in disease resistance, chickens were challenged with avian pathogenic Escherichia coli (APEC) in two separate experiments. Chickens at 8 days of age received one of four intratracheal inoculations of 0.2 mL phosphate buffered saline (PBS): 1) mock inoculate, 2) with 0.2 mL PBS containing 108.20 colony-forming units (CFU)/mL APEC, 3) with 0.2 mL PBS containing 106.64 CFU/mL APEC, and 4) with 0.2 mL PBS containing 107.55 CFU/mL APEC. Mortality was recorded during 7 days post inoculation. Overall, 50-60% reduced mortality was observed in the High line compared to the Low line for all APEC doses. In addition, morbidity was determined of the surviving chickens at 15 days of age. The High line had lower morbidity scores compared to the Low line. We conclude that selective breeding for high KLH-binding NAb levels at 16 weeks of age increase APEC resistance in early life. This study and previous studies support the hypothesis that KLH-binding NAb might be used as an indicator trait for to selective breed for general disease resistance in an antigen non-specific fashion.

Genome-wide association study for αS1- and αS2-casein phosphorylation in Dutch Holstein Friesian.

Phosphorylation of caseins (CN) is a crucial post-translational modification that allows caseins to form colloid particles known as casein micelles. Both αS1- and αS2-CN show varying degrees of phosphorylation (isoforms) in cow milk and were suggested to be more relevant for stabilizing internal micellar structure than ß- and κ-CN. However, little is known about the genetic background of individual αS2-CN phosphorylation isoforms and the phosphorylation degrees of αS1- and αS2-CN (αS1-CN PD and αS2-CN PD), defined as the proportion of isoforms with higher degrees of phosphorylation in total αS1- and αS2-CN, respectively. We aimed to identify genomic regions associated with these traits using 50K single nucleotide polymorphisms for 1,857 Dutch Holstein Friesian cows. A total of 10 quantitative trait loci (QTL) regions were identified for all studied traits on 10 Bos taurus autosomes (BTA1, 2, 6, 9, 11, 14, 15, 18, 24, and 28). Regions associated with multiple traits were found on BTA1, 6, 11, and 14. We showed 2 QTL regions on BTA1, one affecting αS2-CN production and the other harboring the SLC37A1 gene, which encodes a phosphorus antiporter and affects αS1- and αS2-CN PD. The QTL on BTA6 harbors the casein gene cluster and affects individual αS2-CN phosphorylation isoforms. The QTL on BTA11 harbors the PAEP gene that encodes for ß-lactoglobulin and affects relative concentrations of αS2-CN-10P and αS2-CN-11P as well as αS1-CN PD and αS2-CN PD. The QTL on BTA14 harbors the DGAT1 gene and affects relative concentrations of αS2-CN-10P and αS2-CN-11P as well as αS1-CN PD and αS2-CN PD. Our results suggest that effects of identified genomic regions on phosphorylation of αS1- and αS2-CN are related to changes in milk synthesis and phosphorus secretion in milk. The actual roles of SLC37A1, PAEP, and DGAT1 in αS1- and αS2-CN phosphorylation in Dutch Holstein Friesian require further investigation.

Genetic background of methane emission by Dutch Holstein Friesian cows measured with infrared sensors in automatic milking systems.

International environmental agreements have led to the need to reduce methane emission by dairy cows. Reduction could be achieved through selective breeding. The aim of this study was to quantify the genetic variation of methane emission by Dutch Holstein Friesian cows measured using infrared sensors installed in automatic milking systems (AMS). Measurements of CH4 and CO2 on 1,508 Dutch Holstein Friesian cows located on 11 commercial dairy farms were available. Phenotypes per AMS visit were the mean of CH4, mean of CO2, mean of CH4 divided by mean of CO2, and their log10-transformations. The repeatabilities of the log10-transformated methane phenotypes were 0.27 for CH4, 0.31 for CO2, and 0.14 for the ratio. The log10-transformated heritabilities of these phenotypes were 0.11 for CH4, 0.12 for CO2, and 0.03 for the ratio. These results indicate that measurements taken using infrared sensors in AMS are repeatable and heritable and, thus, could be used for selection for lower CH4 emission. Furthermore, it is important to account for farm, AMS, day of measurement, time of day, and lactation stage when estimating genetic parameters for methane phenotypes. Selection based on log10-transformated CH4 instead of the ratio would be expected to give a greater reduction of CH4 emission by dairy cows.

Genetic parameters for αS1-casein and αS2-casein phosphorylation isoforms in Dutch Holstein Friesian.

Relative concentrations of αS1-casein and αS2-casein (αS1-CN and αS2-CN) phosphorylation isoforms vary considerably among milk of individual cows. We estimated heritabilities for αS2-CN phosphorylation isoforms, determined by capillary zone electrophoresis from 1,857 morning milk samples, and genetic correlations among αS2-CN phosphorylation isoforms in Dutch Holstein Friesian. To investigate if phosphorylation of αS1-CN and αS2-CN are due to the same genetic mechanism, we also estimated genetic correlations between αS1-CN and αS2-CN phosphorylation isoforms as well as the genetic correlations between the phosphorylation degrees (PD) of αS1-CN and αS2-CN defined as the proportion of isoforms with higher degrees of phosphorylation in total αS1-CN and αS2-CN, respectively. The intra-herd heritabilities for the relative concentrations of αS2-CN phosphorylation isoforms were high and ranged from 0.54 for αS2-CN-10P to 0.89 for αS2-CN-12P. Furthermore, the high intra-herd heritabilities of αS1-CN PD and αS2-CN PD imply a strong genetic control of the phosphorylation process, which is independent of casein production. The genetic correlations between αS2-CN phosphorylation isoforms are positive and moderate to high (0.33-0.90). Furthermore, the strong positive genetic correlation (0.94) between αS1-CN PD and αS2-CN PD suggests that the phosphorylation processes of αS1-CN and αS2-CN are related. This study shows the possibility of breeding for specific αS1-CN and αS2-CN phosphorylation isoforms, and relations between the phosphorylation degrees of αS1-CN and αS2-CN and technological properties of milk need to be further investigated to identify potential benefits for the dairy industry.

Fine-mapping of BTA17 using imputed sequences for associations with de novo synthesized fatty acids in bovine milk.

The aim of this study was to fine-map a genomic region associated with milk fatty acids (FA) on Bos taurus autosome (BTA) 17. This genomic region has been discovered with 50,000 (50k) single nucleotide polymorphisms (SNP) imputed to 777,000 (777k) SNP. In this study, high-density genotypes were imputed to whole-genome sequences level to identify candidate gene(s) associated with milk FA composition on BTA17. Phenotypes and genotypes were available for 1,640 cows sampled in winter, and for 1,581 cows sampled in summer. Phenotypes consisted of gas chromatography measurements in winter and in summer milk samples of 6 individual FA and the indicator of de novo synthesis, C6:0-C14:0. Genotypes consisted of imputed 777k SNP, and 89 sequenced ancestors of the population of genotyped cows. In addition, 450 whole-genome sequences from the 1,000 Bull Genome Consortium were available. Using 495 Holstein-Friesian sequences as a reference population, the 777k SNP genotypes of the cows were imputed to sequence level. We then applied single-variant analyses with an animal model, and identified thousands of significant associations with C6:0, C8:0, C10:0, C12:0, C14:0, and C6:0-C14:0. For C8:0 in summer milk samples, the genomic region located between 29 and 34 Mbp on BTA17 revealed a total of 646 significant associations. The most significant associations [-log10(P-value) = 7.82] were 8 SNP in perfect linkage disequilibrium. After fitting one of these 8 SNP as a fixed effect in the model, and re-running the single-variant analyses, no further significant associations were found for any of the 6 FA or C6:0-C14:0. These findings suggest that one polymorphism underlying this QTL on BTA17 influences multiple de novo synthesized milk FA. Thirteen genes in the QTL region were identified and analyzed carefully. Six out of the 8 SNP that showed the strongest associations were located in the La ribonucleoprotein domain family, member 1B (LARP1B) gene, and we suggest LARP1B as a primary candidate gene. Another gene of interest for this QTL region might be PKL4. None of these suggested candidate genes have previously been associated with milk fat synthesis or milk FA composition.

Linseed oil and DGAT1 K232A polymorphism: Effects on methane emission, energy and nitrogen metabolism, lactation performance, ruminal fermentation, and rumen microbial composition of Holstein-Friesian cows.

Complex interactions between rumen microbiota, cow genetics, and diet composition may exist. Therefore, the effect of linseed oil, DGAT1 K232A polymorphism (DGAT1), and the interaction between linseed oil and DGAT1 on CH4 and H2 emission, energy and N metabolism, lactation performance, ruminal fermentation, and rumen bacterial and archaeal composition was investigated. Twenty-four lactating Holstein-Friesian cows (i.e., 12 with DGAT1 KK genotype and 12 with DGAT1 AA genotype) were fed 2 diets in a crossover design: a control diet and a linseed oil diet (LSO) with a difference of 22 g/kg of dry matter (DM) in fat content between the 2 diets. Both diets consisted of 40% corn silage, 30% grass silage, and 30% concentrates (DM basis). Apparent digestibility, lactation performance, N and energy balance, and CH4 emission were measured in climate respiration chambers, and rumen fluid samples were collected using the oral stomach tube technique. No linseed oil by DGAT1 interactions were observed for digestibility, milk production and composition, energy and N balance, CH4 and H2 emissions, and rumen volatile fatty acid concentrations. The DGAT1 KK genotype was associated with a lower proportion of polyunsaturated fatty acids in milk fat, and with a higher milk fat and protein content, and proportion of saturated fatty acids in milk fat compared with the DGAT1 AA genotype, whereas the fat- and protein-corrected milk yield was unaffected by DGAT1. Also, DGAT1 did not affect nutrient digestibility, CH4 or H2 emission, ruminal fermentation or ruminal archaeal and bacterial concentrations. Rumen bacterial and archaeal composition was also unaffected in terms of the whole community, whereas at the genus level the relative abundances of some bacterial genera were found to be affected by DGAT1. The DGAT1 KK genotype was associated with a lower metabolizability (i.e., ratio of metabolizable to gross energy intake), and with a tendency for a lower milk N efficiency compared with the DGAT1 AA genotype. The LSO diet tended to decrease CH4 production (g/d) by 8%, and significantly decreased CH4 yield (g/kg of DM intake) by 6% and CH4 intensity (g/kg of fat- and protein-corrected milk) by 11%, but did not affect H2 emission. The LSO diet also decreased ruminal acetate molar proportion, the acetate to propionate ratio, and the archaea to bacteria ratio, whereas ruminal propionate molar proportion and milk N efficiency increased. Ruminal bacterial and archaeal composition tended to be affected by diet in terms of the whole community, with several bacterial genera found to be significantly affected by diet. These results indicate that DGAT1 does not affect enteric CH4 emission and production pathways, but that it does affect traits other than lactation characteristics, including metabolizability, N efficiency, and the relative abundance of Bifidobacterium. Additionally, linseed oil reduces CH4 emission independent of DGAT1 and affects the rumen microbiota and its fermentative activity.

Genetic and nongenetic factors contributing to differences in αS-casein phosphorylation isoforms and other major milk proteins.

Relative concentrations of αS-casein (αS-CN) phosphorylation isoforms vary considerably among milk of individual cows. We aimed to explore to what extent genetic and other factors contribute to the variation in relative concentrations of αS-CN phosphorylation isoforms and the phosphorylation degree of αS-CN defined as the proportion of isoforms with higher degrees of phosphorylation. We also investigated the associations of genetic variants of milk proteins and casein haplotypes with relative concentrations of αS-CN phosphorylation isoforms and with the phosphorylation degree of αS-CN in French Montbéliarde cattle from the cheese production area of Franche-Comté. Detailed milk protein composition was determined by liquid chromatography coupled with electrospray ionization mass spectrometry from 531 test-day morning milk samples. Parity, lactation stage, and genetic variation of cows contributed to the phenotypic variation in relative concentrations of individual αS-CN phosphorylation isoforms and in the phosphorylation degree of αS-CN. As lactation progressed, we observed a significant increase for relative concentrations of αS-CN isoforms with higher degrees of phosphorylation (αS1-CN-9P, αS2-CN-13P, and αS2-CN-14P) as well as for the phosphorylation degree of both αS1-CN and αS2-CN. Furthermore, the ß-CN I variant was associated with a greater proportion of isoforms with lower degrees of phosphorylation (αS1-CN-8P, αS2-CN-10P, and αS2-CN-11P); the ß-CN B variant was associated with a greater proportion of isoforms with higher degrees of phosphorylation (αS1-CN-9P, αS2-CN-12P to αS2-CN-14P). The heritability estimates were low to moderate for relative concentrations of αS2-CN phosphorylation isoforms (0.07 to 0.32), high for relative concentrations of αS1-CN-8P (0.84) and αS1-CN-9P (0.56), and moderate for phosphorylation degrees of αS1-CN (0.37) and αS2-CN (0.23). Future studies investigating relations between the phosphorylation degree of αS-CN and technological properties of milk will be beneficial for the dairy industry.

The relationships among bovine αS-casein phosphorylation isoforms suggest different phosphorylation pathways.

Casein (CN) phosphorylation is an important posttranslational modification and is one of the key factors responsible for constructing and stabilizing casein micelles. Variation in phosphorylation degree of αS-CN is of great interest because it is suggested to affect milk technological properties. This study aimed to investigate the variation in phosphorylation degree of αS-CN among milk of individual cows and to explore relationships among different phosphorylation isoforms of αS-CN. For this purpose, we analyzed morning milk samples from 529 French Montbéliarde cows using liquid chromatography coupled with electrospray ionization mass spectrometry. We detected 3 new phosphorylation isoforms: αS2-CN-9P, αS2-CN-14P, and αS2-CN-15P in bovine milk, in addition to the known isoforms αS1-CN-8P, αS1-CN-9P, αS2-CN-10P, αS2-CN-11P, αS2-CN-12P, and αS2-CN-13P. The relative concentrations of each αS-CN phosphorylation isoform varied considerably among individual cows. Furthermore, the phenotypic correlations and hierarchical clustering suggest at least 2 regulatory systems for phosphorylation of αS-CN: one responsible for isoforms with lower levels of phosphorylation (αS1-CN-8P, αS2-CN-10P, and αS2-CN-11P), and another responsible for isoforms with higher levels of phosphorylation (αS1-CN-9P, αS2-CN-12P, αS2-CN-13P, and αS2-CN-14P). Identifying all phosphorylation sites of αS2-CN and investigating the genetic background of different αS2-CN phosphorylation isoforms may provide further insight into the phosphorylation mechanism of caseins.

Effects of the diacylglycerol o-acyltransferase 1 (DGAT1) K232A polymorphism on fatty acid, protein, and mineral composition of dairy cattle milk.

Several studies have described associations between the diacylglycerol o-acyltransferase 1 (DGAT1) K232A polymorphism and routinely collected milk production traits but not much is known about effects of the DGAT1 polymorphism on detailed milk composition. The aim of this study was to estimate effects of the DGAT1 polymorphism on milk fatty acid, protein, and mineral composition. We looked for effects that were significant and consistent in Danish Holstein Friesian (HF), Danish Jersey, and Dutch HF as these are likely to be true effects of the DGAT1 K232A polymorphism rather than being effects of linked loci. For fatty acid composition, significant and consistent effects of the DGAT1 polymorphism were detected on C14:0, C16:0, C15:0, C16:1, C18:1 cis-9, conjugated linoleic acid (CLA) cis-9,trans-11, C18:2 cis-9,cis-12, and C18:3 cis-9,cis-12,cis-15 content (percent by weight, wt/wt %). For C16:0, C16:1, and C18:1 cis-9, the DGAT1 polymorphism explained more than 10% of the phenotypic variation. Significant effects on milk protein composition in Dutch HF could not be confirmed in Danish Jersey or Danish HF. For mineral content, significant and consistent effects of the DGAT1 polymorphism on calcium, phosphorus, and zinc were detected. In the Dutch HF population, the contribution of the DGAT1 K232A polymorphism to phenotypic variance was 12.0% for calcium, 8.3% for phosphorus, and 6.1% for zinc. Different from effects on fatty acid composition, effects of the DGAT1 polymorphism on yields of long-chain fatty acids C18:1 cis-9, CLA cis-9,trans-11, C18:2 cis-9,cis-12, and C18:3 cis-9,cis-12,cis-15 were not significant. This indicates that effects of DGAT1 on these fatty acids are indirect, not direct, effects: DGAT1 affects de novo synthesis of fatty acids and, consequently, the contribution of the long-chain fatty acids to total fat is decreased. In addition, effects of the DGAT1 polymorphism on yields of Ca, P, and Zn were not significant, which indicates that effects on these minerals are the result of indirect rather than direct effects of DGAT1: effects on calcium, phosphorus, and zinc content can be explained by effects of DGAT1 on milk volume. The reported effects of the DGAT1 polymorphism on fatty acid and mineral composition of milk are substantial and therefore relevant for milk quality.

Short communication: Genetic study of methane production predicted from milk fat composition in dairy cows.

Dairy cows produce enteric methane, a greenhouse gas with 25 times the global warming potential of CO2. Breeding could make a permanent, cumulative, and long-term contribution to methane reduction. Due to a lack of accurate, repeatable, individual methane measurements needed for breeding, indicators of methane production based on milk fatty acids have been proposed. The aim of the present study was to quantify the genetic variation for predicted methane yields. The milk fat composition of 1,905 first-lactation Dutch Holstein-Friesian cows was used to investigate 3 different predicted methane yields (g/kg of DMI): Methane1, Methane2, and Methane3. Methane1 was based on the milk fat proportions of C17:0anteiso, C18:1 rans-10+11, C18:1 cis-11, and C18:1 cis-13 (R(2)=0.73). Methane2 was based on C4:0, C18:0, C18:1 trans-10+11, and C18:1 cis-11 (R(2)=0.70). Methane3 was based on C4:0, C6:0, and C18:1 trans-10+11 (R(2)=0.63). Predicted methane yields were demonstrated to be heritable traits, with heritabilities between 0.12 and 0.44. Breeding can, thus, be used to decrease methane production predicted based on milk fatty acids.

Effects of the DGAT1 polymorphism on test-day milk production traits throughout lactation.

Several studies have shown that the diacylglycerol O-acyltransferase 1 (DGAT1) K232A polymorphism has a major effect on milk production traits. It is less clear how effects of DGAT1 on milk production traits change throughout lactation, if dominance effects of DGAT1 are relevant, and whether DGAT1 also affects lactose content, lactose yield, and total energy output in milk. Results from this study, using test-day records of 3 subsequent parities of around 1,800 cows, confirm previously reported effects of the DGAT1 polymorphism on milk, fat, and protein yield, as well as fat and protein content. In addition, we found significant effects of the DGAT1 polymorphism on lactose content and lactose yield. No significant effects on somatic cell score were detected. The effect of DGAT1 on total energy excreted in milk was only significant in parity 1 and is mainly due to a higher energy output in milk of heterozygous cows. Significant but relatively small dominance effects of DGAT1 on fat content and yield were detected, which are of little practical relevance. Significant DGAT1 by lactation stage interaction was detected for milk yield, lactose yield, fat content, and protein content, indicating that the effect of the DGAT1 polymorphism changes during lactation. In general, the DGAT1 effect shows a large increase during early lactation (from the start of lactation to d 50 to 150) and tends to decrease later in lactation. No DGAT1 by lactation stage interaction for fat yield was observed. Similar to DGAT1, effects of other genes also might vary throughout lactation and, therefore, using longitudinal models is recommended.

A quantitative trait locus on Bos taurus autosome 17 explains a large proportion of the genetic variation in de novo synthesized milk fatty acids.

A genomic region associated with milk fatty acid (FA) composition has been detected on Bos taurus autosome (BTA)17 based on 50,000 (50K) single nucleotide polymorphism (SNP) genotypes. The aim of our study was to fine-map BTA17 with imputed 777,000 (777 K) SNP genotypes to identify candidate genes associated with milk FA composition. Phenotypes consisted of gas chromatography measurements of 14 FA based on winter and summer milk samples. Phenotypes and genotypes were available on 1,640 animals in winter milk, and on 1,581 animals in summer milk samples. Single-SNP analyses showed that several SNP in a region located between 29.0 and 34.0 Mbp were in strong association with C6:0, C8:0, and C10:0. This region was further characterized based on haplotypes. In summer milk samples, for example, these haplotypes explained almost 10% of the genetic variance in C6:0, 9% in C8:0, 3.5% in C10:0, 1.8% in C12:0, and 0.9% in C14:0. Two groups of haplotypes with distinct predicted effects could be defined, suggesting the presence of one causal variant. Predicted haplotype effects tended to increase from C6:0 to C14:0; however, the proportion of genetic variance explained by the haplotypes tended to decrease from C6:0 to C14:0. This is an indication that the quantitative trait locus (QTL) region is involved either in the elongation process or in early termination of de novo synthesized FA. Although many genes are present in this QTL region, most of these genes on BTA17 have not been characterized yet. The strongest association was found close to the progesterone receptor membrane component 2 (PGRMC2) gene, which has not yet been associated with milk FA composition. Therefore, no clear candidate gene associated with milk FA composition could be identified for this QTL.

Genetic correlation between composition of bovine milk fat in winter and summer, and DGAT1 and SCD1 by season interactions.

Milk fat composition shows substantial seasonal variation, most of which is probably caused by differences in the feeding of dairy cows. The present study aimed to know whether milk fat composition in winter is genetically the same trait as milk fat composition in summer. For this purpose, we estimated heritabilities, genetic correlations, effects of acyl-coenzyme A:diacylglycerol acyltransferase 1 (DGAT1) K232A, and stearoyl-coenzyme A desaturase 1 (SCD1) A293V polymorphisms for milk fat composition in winter and summer, and tested for genotype by season interactions of DGAT1 K232A and SCD1 A293V polymorphisms. Milk samples were obtained from 2,001 first-lactation Dutch Holstein-Friesian cows, most with records in both winter and summer. Summer milk contained higher amounts of unsaturated fatty acids (FA) and lower amounts of saturated FA compared with winter milk. Heritability estimates were comparable between seasons: moderate to high for short- and medium-chain FA (0.33 to 0.74) and moderate for long-chain FA (0.19 to 0.43) in both seasons. Genetic correlations between winter and summer milk were high, indicating that milk fat composition in winter and in summer can largely be considered as genetically the same trait. Effects of DGAT1 K232A and SCD1 A293V polymorphisms were similar across seasons for most FA. Allele DGAT1 232A in winter as well as in summer milk samples was negatively associated with most FA with less than 18 carbons, saturated FA, saturated FA to unsaturated FA ratio, and C10 to C16 unsaturation indices, and was positively associated with C14:0, unsaturated C18, unsaturated FA, and C18 and conjugated linoleic acid unsaturation indices. Allele SCD1 293V in winter as well as in summer milk samples was negatively associated with C18:0, C10:1 to cis-9 C14:1, trans-11 C18:1, and C10 to C14 unsaturation indices, and positively associated with C8:0 to C14:0, cis-9 C16:1, and C16 to conjugated linoleic acid unsaturation indices. In addition, significant DGAT1 K232A by season interaction was found for some FA and SCD1 A293V by season interaction was only found for trans-11 C18:1. These interactions were due to scaling of genotype effects.

Short communication: A new bovine milk-protein variant: α-lactalbumin variant D.

Capillary zone electrophoresis of 1,948 Holstein-Friesian cows suggested the presence of an unknown protein variant of α-lactalbumin (α-LA) in the milk of 1 cow. Sequencing genomic DNA of this cow showed a polymorphism in the α-LA gene (LAA) that appears to be responsible for this protein variant. This single nucleotide polymorphism g.600G > T was located in exon 2 of LAA and causes the amino acid change 65Gln > His in the α-LA protein. This α-LA protein variant is a new protein variant and should be called α-LA protein variant D. This amino acid change is not expected to affect protein function. Genomic DNA of 156 bulls of various dairy cattle breeds was screened to examine the presence of the new α-LA protein variant D. Single nucleotide polymorphism g.600G > T, responsible for α-LA protein variant D, was not found in any of the 156 bulls. However, 10 other polymorphisms in the coding and promoter regions of LAA were detected that were used to construct haplotypes.

Whole-genome association study for milk protein composition in dairy cattle.

Our objective was to perform a genome-wide association study for content in bovine milk of α(S1)-casein (α(S1)-CN), α(S2)-casein (α(S2)-CN), ß-casein (ß-CN), κ-casein (κ-CN), α-lactalbumin (α-LA), ß-lactoglobulin (ß-LG), casein index, protein percentage, and protein yield using a 50K single nucleotide polymorphism (SNP) chip. In total, 1,713 Dutch Holstein-Friesian cows were genotyped for 50,228 SNP and a 2-step association study was performed. The first step involved a general linear model and the second step used a mixed model accounting for all family relationships. Associations with milk protein content and composition were detected on 20 bovine autosomes. The main genomic regions associated with milk protein composition or protein percentage were found on chromosomes 5, 6, 11, and 14. The number of chromosomal regions showing significant (false discovery rate <0.01) effects ranged from 3 for ß-CN and 3 for ß-LG to 12 for α(S2)-CN. A genomic region on Bos taurus autosome (BTA) 6 was significantly associated with all 6 major milk proteins, and a genomic region on BTA 11 was significantly associated with the 4 caseins and ß-LG. In addition, regions were detected that only showed a significant effect on one of the milk protein fractions: regions on BTA 13 and 22 with effects on α(S1)-CN; regions on BTA 1, 9, 10, 17, 19, and 28 with effects on α(S2)-CN; a region on BTA 6 with an effect on ß-CN; regions on BTA 13 and 21 with effects on κ-CN; regions on BTA 1, 5, 9, 16, 17, and 26 with effects on α-LA; and a region on BTA 24 with an effect on ß-LG. The proportion of genetic variance explained by the SNP showing the strongest association in each of these genomic regions ranged from <1% for α(S1)-CN on BTA 22 to almost 100% for casein index on BTA 11. Variation associated with regions on BTA 6, 11, and 14 could in large part but not completely be explained by known protein variants of ß-CN (BTA 6), κ-CN (BTA 6), and ß-LG (BTA 11) or DGAT1 variants (BTA 14). Our results indicate 3 regions with major effects on milk protein composition, in addition to several regions with smaller effects involved in the regulation of milk protein composition.

Association of bovine ß-casein protein variant I with milk production and milk protein composition.

The aim of this study was to detect new polymorphisms in the bovine ß-casein (ß-CN) gene and to evaluate association of (new) ß-CN protein variants with milk production traits and milk protein composition. Screening of the ß-CN gene in genomic DNA from 72 Holstein Friesian (HF) bulls resulted in detection of 19 polymorphisms and revealed the presence of ß-CN protein variant I in the Dutch HF population. Studies of association of ß-CN protein variants with milk composition usually do not discriminate protein variant I from variant A2. Association of ß-CN protein variants with milk composition was studied in 1857 first-lactation HF cows and showed that associations of protein variants A2 and I were quite different for several traits. ß-CN protein variant I was significantly associated with protein percentage and protein yield, and with αs1 -casein (αs1 -CN), αs2 -casein (αs2 -CN), κ-casein (κ-CN), α-lactalbumin (α-LA), ß-lactoglobulin (ß-LG), casein index and casein yield. Inferring ß-κ-CN haplotypes showed that ß-CN protein variant I occurred only with κ-CN variant B. Consequently, associations of ß-κ-CN haplotype IB with protein percentage, κ-CN, α-LA, ß-LG and casein index are likely resulting from associations of κ-CN protein variant B, while associations of ß-κ-CN haplotype IB with αs1 -CN and αs2 -CN seem to be resulting from associations of ß-CN variant I.

Genome-wide scan to detect quantitative trait loci for milk urea nitrogen in Dutch Holstein-Friesian cows.

Studies have reported genetic variation in milk urea nitrogen (MUN) between cows, suggesting genetic differences in nitrogen efficiency between cows. In this paper, the results of a genome-wide scan to identify quantitative trait loci (QTL) that contribute to genetic variation in MUN and MUN yield are presented. Two to 3 morning milk samples were taken from 1,926 cows, resulting in 5,502 test-day records. Test-day records were corrected for systematic environmental effects using a repeatability animal model. Averages of corrected phenotypes of 849 cows, belonging to 7 sire families, were used in an across-family multimarker regression approach to detect QTL. Animals were successfully genotyped for 1,341 single nucleotide polymorphisms. The QTL analysis resulted in 4 chromosomal regions with suggestive QTL: Bos taurus autosomes (BTA) 1, 6, 21, and 23. On BTA 1, 2 suggestive QTL affecting MUN were detected at 60 and 140 cM. On BTA 6, 1 suggestive QTL affecting both MUN and MUN yield was detected at 103 cM. On BTA 21, 1 suggestive QTL affecting MUN yield was detected at 83 cM. On BTA 23, 1 suggestive QTL affecting MUN was detected at 54 cM. Quantitative trait loci for MUN and MUN yield were suggestive and each explained between 2 and 3% of the phenotypic variance.