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.     

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.     

Short communication: Genome-wide scan for bovine milk-fat composition. II. Quantitative trait loci for long-chain fatty acids

We present the results of a genome-wide scan to identify quantitative trait loci (QTL) that contribute to genetic variation in long-chain milk fatty acids. Milk-fat composition phenotypes were available on 1,905 Dutch Holstein-Friesian cows. A total of 849 cows and their 7 sires were genotyped for 1,341 single nucleotide polymorphisms across all Bos taurus autosomes (BTA). We detected significant QTL on BTA14, BTA15, and BTA16: for C18:1 cis-9, C18:1 cis-12, C18:2 cis-9,12, CLA cis-9,trans-11, C18:3 cis-9,12,15, the C18 index, the total index, total saturated fatty acids, total unsaturated fatty acids (UFA), and the ratio of saturated fatty acids:unsaturated fatty acids on BTA14; for C18:1 trans fatty acids on BTA15; and for the C18 and CLA indices on BTA16. The QTL explained 3 to 19% of the phenotypic variance. Suggestive QTL were found on 16 other chromosomes. The diacylglycerol acyltransferase 1 (DGAT1) K232A polymorphism on BTA14, which is known to influence fatty acid composition, most likely explains the QTL that was detected on BTA14.     

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 α_S1- and α_S2-CN show varying degrees of phosphorylation (isoforms) in cow milk and were suggested to be more relevant for stabilizing internal micellar structure than β- and κ-CN. However, little is known about the genetic background of individual α_S2-CN phosphorylation isoforms and the phosphorylation degrees of α_S1- and α_S2-CN (α_S1-CN PD and α_S2-CN PD), defined as the proportion of isoforms with higher degrees of phosphorylation in total α_S1- and α_S2-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 α_S2-CN production and the other harboring the SLC37A1 gene, which encodes a phosphorus antiporter and affects α_S1- and α_S2-CN PD. The QTL on BTA6 harbors the casein gene cluster and affects individual α_S2-CN phosphorylation isoforms. The QTL on BTA11 harbors the PAEP gene that encodes for β-lactoglobulin and affects relative concentrations of α_S2-CN-10P and α_S2-CN-11P as well as α_S1-CN PD and α_S2-CN PD. The QTL on BTA14 harbors the DGAT1 gene and affects relative concentrations of α_S2-CN-10P and α_S2-CN-11P as well as α_S1-CN PD and α_S2-CN PD. Our results suggest that effects of identified genomic regions on phosphorylation of α_S1- and α_S2-CN are related to changes in milk synthesis and phosphorus secretion in milk. The actual roles of SLC37A1, PAEP, and DGAT1 in α_S1- and α_S2-CN phosphorylation in Dutch Holstein Friesian require further investigation.     

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

Relative concentrations of α_S1-casein and α_S2-casein (α_S1-CN and α_S2-CN) phosphorylation isoforms vary considerably among milk of individual cows. We estimated heritabilities for α_S2-CN phosphorylation isoforms, determined by capillary zone electrophoresis from 1,857 morning milk samples, and genetic correlations among α_S2-CN phosphorylation isoforms in Dutch Holstein Friesian. To investigate if phosphorylation of α_S1-CN and α_S2-CN are due to the same genetic mechanism, we also estimated genetic correlations between α_S1-CN and α_S2-CN phosphorylation isoforms as well as the genetic correlations between the phosphorylation degrees (PD) of α_S1-CN and α_S2-CN defined as the proportion of isoforms with higher degrees of phosphorylation in total α_S1-CN and α_S2-CN, respectively. The intra-herd heritabilities for the relative concentrations of α_S2-CN phosphorylation isoforms were high and ranged from 0.54 for α_S2-CN-10P to 0.89 for α_S2-CN-12P. Furthermore, the high intra-herd heritabilities of α_S1-CN PD and α_S2-CN PD imply a strong genetic control of the phosphorylation process, which is independent of casein production. The genetic correlations between α_S2-CN phosphorylation isoforms are positive and moderate to high (0.33–0.90). Furthermore, the strong positive genetic correlation (0.94) between α_S1-CN PD and α_S2-CN PD suggests that the phosphorylation processes of α_S1-CN and α_S2-CN are related. This study shows the possibility of breeding for specific α_S1-CN and α_S2-CN phosphorylation isoforms, and relations between the phosphorylation degrees of α_S1-CN and α_S2-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.     

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), β-casein (β-CN), κ-casein (κ-CN), α-lactalbumin (α-LA), β-lactoglobulin (β-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 β-CN and 3 for β-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 β-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 β-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 β-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 β-CN (BTA 6), κ-CN (BTA 6), and β-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.     

Genome-wide scan for bovine milk-fat composition. I. Quantitative trait loci for short- and medium-chain fatty acids

A genome-wide scan was performed to identify quantitative trait loci (QTL) for short- and medium-chain fatty acids (expressed in wt/wt %). Milk samples were available from 1,905 cows from 398 commercial herds in the Netherlands, and milk-fat composition was measured by gas chromatography. DNA was available from 7 of the paternal half-sib families: 849 cows and their 7 sires. A genetic map was constructed comprising 1,341 SNP and 2,829 cM, with an average information content of 0.83. Multimarker interval mapping was used in an across-family regression on corrected phenotypes for the 7 half-sib families. Four QTL were found: on Bos taurus autosome (BTA) 6, a QTL was identified for C6:0 and C8:0; on BTA14, a QTL was identified for fat percentage, all odd-chain fatty acids, and C14:0, C16:0, C16:1, and their unsaturation indices; on BTA19, a QTL affected C14:0; and on BTA26, a QTL was identified for the monounsaturated fatty acids and their unsaturation indices. The QTL explained 3 to 19% of phenotypic variance. Furthermore, 49 traits with suggestive evidence for linkage were found on 21 chromosomes. Additional analyses revealed that the QTL on BTA14 was most likely caused by a mutation in DGAT1, whereas the QTL on BTA26 was most likely caused by a mutation in the SCD1 gene. Quantitative trait loci that affect specific fatty acids might increase the understanding of physiological processes regarding fat synthesis and the position of the causal genes.