New mutation within a common haplotype is associated with calf muscle weakness in Holsteins.

A recessive haplotype resulting in elevated calf mortality but with apparent incomplete penetrance was previously linked to the end of chromosome 16 (78.7-80.7 Mbp). Genotype analysis of 5.6 million Holsteins indicated that the haplotype was common and traced back to 1952, with a key ancestor born in 1984 (HOUSA1964484, Southwind) identified from chip genotypes as homozygous for the suspect haplotype. Sequence data from Southwind (an affected calf) and the sire of the affected calf were scanned for candidate mutations. A missense mutation with a deleterious projected impact at 79,613,592 bp was homozygous in the affected calf and heterozygous in the calf's sire and Southwind. Sequence data available from the Cooperative Dairy DNA Repository for 299 other Holsteins indicated a 97% concordance with the haplotype and an 89% call rate. The exon amino acid sequence appears to be broadly conserved in the CACNA1S gene, and mutations in humans and mice can cause phenotypes of temporary or permanent paralysis analogous to those in calves with the haplotype causing muscle weakness (HMW). Improved methods for using pedigree to track new mutations within existing haplotypes were developed and applied to the haplotypes for both muscle weakness and Holstein cholesterol deficiency (HCD). For HCD, concordance of the gene test with its haplotype status was greatly improved. For both defects, haplotype status was matched to heifer livability records for 558,000 calves. For HMW, only 46 heifers with livability records were homozygous and traced only to Southwind on both sides. Of those, 52% died before 18 mo at an average age of 1.7 ± 1.6 mo, but that death rate may be underestimated if only healthier calves were genotyped. The death rate was 2.4% for noncarriers. Different reporting methods or dominance effects may be needed to include HMW and other partially lethal effects in selection and mating. Direct tests are needed for new mutations within existing common haplotypes because tracking can be difficult even with accurate pedigrees when the original haplotype has a high frequency.

The impact of beef sire breed on dystocia, stillbirth, gestation length, health, and lactation performance of cows that carry beef × dairy calves.

In the United States, it is becoming common for dairy herds to mate a portion of cows to beef semen to create a value-added calf. The objectives of this study were to determine if dystocia risk, stillbirth (SB) risk, gestation length (GL), probability of early-lactation clinical disease events, early-lactation culling risk, or subsequent milk production differ between cows that carried calves sired by different beef breeds and those that carried Holstein-sired calves. Records from 10 herds contained 75,256 lactations from 39,249 cows that had calves with known Holstein or beef breed sires from the years 2010 to 2023. Calf sire breeds with ≥150 records included in analyses were Holstein, Angus, Simmental, Limousin, crossbred beef, and Charolais. Additional beef sire breeds that existed in lower frequency (n < 150 records) were condensed together and classified as "other." Because GL is a continuous variable, sire breed inclusion criteria were reduced to n ≥ 100 records; thus, Wagyu sires were included as their own breed group. Some records did not contain all variables of interest, thus models included fewer lactations depending on variable. Binomial generalized mixed models evaluated dystocia risk (defined as calving ease score ≥4 or calving ease score ≥3), SB risk, clinical health event risk (defined as lameness, mastitis, metabolic, reproductive, other, or any health events occurring within 60 d in milk [DIM]), and early culling risk (defined as death or culling within 60 DIM). Gestation length and test-date milk, fat, and protein yields were evaluated with mixed models. Calves sired by crossbred beef bulls had a greater probability of being stillborn (5%; 95% confidence interval lower = 2.9% upper = 9.0%) than those sired by Holstein bulls (2%; 95% confidence interval lower = 1.5%, upper = 2.7%). All beef-sired calves increased GL from that of Holstein-sired calves (277 ± 0.15 d) with Limousin (282 ± 0.81 d) and Wagyu-sired calves (285 d ± 0.79) resulting in the longest GL. The risk of dystocia, clinical health events, and early-lactation culling did not differ by calf sire breed nor did subsequent milk and component yield. Generally, carrying a calf sired by the beef breeds included in this study did not negatively affect the dairy cow.

Genetic evaluation of health costs in US organic Holstein calves and cows.

Minimizing the incidence of disease on organic dairy farms is important for both economic and animal welfare purposes. The objective of this study was to estimate genetic parameters for total disease treatment costs using producer-recorded treatments in organic Holstein dairy calves and cows. Individual cow and calf health data were collected from 16 USDA certified organic farms from across the United States. Eleven of these farms provided treatment costs for some or all of the following cow health issues (mean cost): mastitis ($46.10), milk fever ($39.05), ketosis ($29.81), metritis ($28.66), retained placenta ($45.59), displaced abomasum ($439.71), lameness ($66.36), indigestion ($22.94), respiratory ($48.35), and died ($64.98). These farms also provided the following health costs for calves (mean cost): respiratory ($56.37) and scours ($25.21). Costs included consultant fees, therapeutics, and producer labor. The total lactational health cost (HCOST) was analyzed using animal models adjusted for the fixed effects of lactation and herd and the random effect of herd-year-season of calving with animal relationships based on the blending of pedigree and genomic relationships established from 2,347 genotyped cows. Along with HCOST, the binary traits stayability and presence of disease were included in a trivariate model such that lactations absent of disease were considered to be missing HCOST. To estimate the genetic relationship between nulliparous and primiparous health costs, a 2-trait linear model was fitted for total nulliparous health costs (NHCOST) and first lactation HCOST. The most expensive cow-lactation was $643.86 and 26.5% of lactations encountered disease. The heritability for HCOST was 0.03 ± 0.01, and the repeatability was 0.21 ± 0.01. The heritability of NHCOST was 0.06 ± 0.01, and the genetic correlation between NHCOST and HCOST was 0.98 ± 0.51. Traits representing the repeated nature of disease have a genetic component that should foster improved disease resistance among organic Holstein dairy cows. However, total cost of disease did not lead to gains in genetic variation over consideration of disease traits considered as binary variables and is a more laborious phenotype to obtain, diminishing its appeal for use in routine genetic evaluations.

Relationships of beta-casein genetics with production, fertility, and survival of purebred organic Holstein dairy cows.

The objective of this study was to compare ß-casein genotype of purebred certified-organic Holstein cows, and their effect on production, fertility, and survival. Holstein cows (n = 1,982) from 13 certified-organic dairy herds from the western, midwestern, and northeastern United States were genomically tested with CLARIFIDE Plus (Zoetis) for ß-casein genotype. Two hundred fourteen cows were A1A1 (11%), 848 cows were A1A2 (43%), and 920 cows were A2A2 (46%). In total, 2,249 lactation records, 1,025 from the first parity and 1,224 records during second and greater parities were used. Test-day milk, fat, and protein production (305-d) and somatic cell score were obtained from the Dairy Herd Improvement Association. A lower limit of 50 d for days open was applied, and cows with more than 250 d open had days open set to 250 d. Independent variables for statistical analysis were the fixed effects of herd, parity, ß-casein genotype (A1A1, A1A2, A2A2), and ß-casein genotype by parity interaction. Cow nested within parity was the random effect in the statistical models for fertility and production traits. Herd had a significant effect on all fertility, production, and survival variables. Parity affected the number of times bred per pregnancy and days open, milk, fat, and protein production, and somatic cell score. Beta-casein genotype and herd influenced the percentage of cows surviving to first and second lactation. Results indicate no difference in production and fertility regarding ß-casein genotype for organic dairy herds. Survival was biased against the A1 allele, which is indicated by lower survival rates during first lactation. These results may offer organic producers more flexibility in breeding and culling decisions to produce A2A2 milk.

Association between hyperketolactia and production in early-lactating dairy cows.

Study aims were to investigate associations of hyperketolactia (HYKL) status of Holstein dairy cows between 6 and 60 d in milk (DIM), defined by milk acetone (mACE) and ß-hydroxybutyrate (mBHB) content, with daily milk yield and composition. Milk samples (∼5.0 million) were collected over a 5-yr period (2014-2019) within the milk recording system in Poland. Concentrations of mACE and mBHB determined by Fourier-transform infrared spectroscopy were used to categorize samples into 4 ketolactia groups. Based on threshold values of ≥0.15 mmol/L mACE and ≥0.10 mmol/L mBHB, ketolactia groups were normoketolactia (NKL; mACE <0.15 mmol/L and mBHB <0.10 mmol/L), BHB hyperketolactia (HYKLBHB; mACE <0.15 mmol/L and mBHB ≥0.10 mmol/L), ACE hyperketolactia (HYKLACE; mACE ≥0.15 mmol/L and mBHB <0.10 mmol/L), and ACE and BHB hyperketolactia (HYKLACEBHB; mACE ≥0.15 mmol/L and mBHB ≥0.10 mmol/L). To investigate ketolactia association with production outcomes, a linear model was developed, including ketolactia group, DIM, parity, their interactions, year-season as fixed effects, and random effects of herd and cow. Among all milk samples, 31.2% were classified as HYKL, and of these, 52.6%, 39.6%, and 7.8% were HYKLACEBHB, HYKLBHB, and HYKLACE, respectively. Ketolactia groups differed for all traits studied in all parities and DIM. Among HYKL groups, lowest milk yield was found in HYKLACEBHB cows, except for 6 to 30 DIM in first- and second-lactation cows. Milk yield of HYKLBHB cows was higher than that of NKL cows until 20 to 30 DIM, and then it was lower than NKL cows. Milk yield of HYKLACE cows was mostly lower than NKL cows. Energy-corrected milk (ECM) yield of HYKLACEBHB cows was higher than that of NKL cows until 30 to 35 DIM for second lactation and third lactation or greater, and in the whole study period for first lactation. The yield of ECM for HYKLBHB cows was mostly higher than that of NKL cows, whereas HYKLACE cows had higher ECM than NKL cows until 15 to 25 DIM and then was lower for the HYKLACE group. Milk composition differed among HYKL groups. Highest milk fat (MF) and lowest milk lactose (ML) contents were observed in HYKLACEBHB cows. Cows in HYKLACEBHB and HYKLBHB groups had higher MF and lower milk protein (MP; except in 6-8 DIM in first lactation) and ML content than NKL cows. Milk fat content was higher in HYKLACE than NKL cows in first lactation and during the first 30 to 40 DIM in older cows. Lactose content was lower in HYKLACE than in NKL cows within 30 to 40 DIM; afterward it was higher in NKL cows. Lower MP content was found in HYKLACE than in NKL cows, except during 6 to 9 DIM for cows in first lactation and third lactation or greater. In conclusion, HYKL is associated with altered milk production in all parities, but a range of these negative relations depends on ketone status addressing both ACE and BHB contents. Further research is needed to ascertain underpinning biochemical defects of HYKL from elevated ACE, alone or in combination with BHB, during early lactation.

Interaction of DGAT1 polymorphism, parity, and acetate supplementation on feeding behavior, milk synthesis, and plasma metabolites.

Acetate supplementation increases milk fat production, but interactions with animal-related factors have not been investigated. The objective of this study was to characterize the interaction of acetate supplementation with parity and genetic potential for milk fat synthesis including the DGAT1 K232A polymorphism (AA and KA genotypes). In total, 47 primiparous and 49 multiparous lactating cows were used in 2 blocks in a crossover design. The basal diet was formulated to have a low risk of biohydrogenation-induced milk fat depression and had 32.8% and 32.0% neutral detergent fiber and 21.7% and 23.6% starch [all on a dry matter (DM) basis] in block 1 and 2, respectively. The control treatment received the basal diet, and the acetate supplementation treatment included anhydrous sodium acetate supplemented to the basal diet at 3.2% and 3.1% of DM of the diet for block 1 and 2, respectively (targeting 10 mol/d of acetate). The DGAT1 genotype frequency of the experimental cows was 45% AA and 51% KA, with 4% cows with either a KK or unimputable genotype. Acetate supplementation increased DM intake (DMI) in KA multiparous cows, but acetate did not change DMI in AA multiparous or primiparous cows of either genotype. Acetate supplementation increased the frequency of meals by 8% and decreased the length of each meal by ∼5 min compared with control. There was no effect of acetate on milk yield. Acetate supplementation increased milk fat yield and concentration by 117 g/d and 0.31 percentage units, respectively, regardless of DGAT1 polymorphism or parity. The increase in milk fat yield was mostly due to an increase in yield of 16C mixed-sourced fatty acids, suggesting that acetate supplementation drives mammary de novo synthesis toward completion. Response to acetate supplementation was not related to genomic predicted transmitting ability of milk fat concentration and yield or to pretrial milk fat percent and yield, suggesting that acetate increases milk fat production regardless of genetic potential for milk fat yield and level of milk fat synthesis. Interestingly, analyzing the temporal effect on the interaction between treatment and DGAT1 polymorphism on milk fat yield suggested that DGAT1 polymorphism may affect the short-term response to acetate supplementation during the first ≤7 d on treatment. Acetate supplementation also increased plasma ß-hydroxybutyrate concentration and decreased plasma glucose concentration. In conclusion, acetate supplementation consistently increased milk fat synthesis regardless of parity or genetic potential for milk fat synthesis.

Microbial composition, rumen fermentation parameters, enteric methane emissions, and lactational performance of phenotypically high and low methane-emitting dairy cows.

This experiment was designed to investigate the relation of high and low methane-yield phenotypes with body weight (BW), dry matter intake (DMI), lactation performance, enteric CH4 emissions, and rumen fermentation parameters in lactating dairy cows. A total of 130 multi- and primiparous Holstein cows were screened for enteric CH4 emissions using the GreenFeed system (C-Lock Inc.). Out of these 130 cows, 5 were identified as phenotypically high (HM) and 5 as phenotypically low (LM) CH4 emitters. Cows in the LM group had lower daily enteric CH4 emissions than cows in the HM group (on average 346 vs. 439 g/d, respectively), lower CH4 yield (15.5 vs. 20.4 g of CH4/kg of DMI), and CH4 intensity (13.2 vs. 17.0 g of CH4/ kg of energy-corrected milk yield). Enteric emissions of CO2 and H2 did not differ between HM and LM cows. These 10 cows were blocked by parity, days in milk, and milk production, and were used in a 5-wk randomized complete block design experiment. Milk composition, production, and BW were also not different between LM and HM cows. The concentration of total volatile fatty acids in ruminal contents did not differ between CH4 phenotypes, but LM cows had a lower molar proportion of acetate (57 vs. 62.1%), a higher proportion of propionate (27.5 vs. 21.6%, respectively), and therefore a lower acetate-to-propionate ratio than HM cows. Consistently, the 16S cDNA analysis revealed the abundance of Succinivibrionaceae and unclassified Veillonellaceae to be higher in LM cows compared with HM cows, bacteria that were positively correlated with ruminal propionate concentration. Notably, Succinivibrionaceae trigger the formation of propionate via oxaloacetate pathway from phosphoenolpyruvate via Enzyme Commission: 4.1.1.49, which showed a trend to be higher in LM cows compared with HM cows. Additionally, LM cows possessed fewer transcripts of a gene encoding for methyl-CoM reductase enzyme compared with HM. In this study, low and high CH4-yield cows have similar production performance and milk composition, but total-tract apparent digestibility of organic matter and fiber fractions was lower in the former group of animals.

Identification of a putative haplotype associated with recumbency in Holstein calves.

Thirty-four Holstein calves from multiple farms were found recumbent during the neonatal period with no detectable neurologic, infectious, or metabolic abnormalities. Most calves did not survive beyond 6 wk of age. The objective of this study was to conduct a genome-wide association and pedigree analysis to determine if a genetic origin was plausible. There were 101,917 DNA markers for 18 affected calves and 26 unaffected family controls available for analysis. Genome-wide association, homozygosity screening, and a parental based transmission disequilibrium test were conducted in PLINK. A genomic region on the end of chromosome 16 that contained 78 markers based on a recessive inheritance model and that spanned 5.1 million bp was considered the most probable region for a genetic defect; the region was narrowed to 2.1 million bp following homozygosity screening and the transmission disequilibrium test with all affected calves homozygous in the candidate region and 1 homozygous control. A genotyped sire and 2 dams with imputed genotypes were heterozygous in the candidate region. A common sire born in 2008 was identified that was present for both paternal and maternal lineages of all affected calves; nearly all lineages traced through a prolific son born in 2010 who was genotyped and was heterozygous for the candidate region. Therefore, a possible genetic defect with incomplete penetrance on chromosome 16 that results in recumbency has been identified. Further efforts with an increase in families represented are needed to confirm a genetic basis, and identify the mutation and mode of inheritance.

Genetic parameters and association of national evaluations with breeding values for health traits in US organic Holstein cows.

Among other regulations, organic cows in the United States cannot receive antibiotics and preserve their organic status, emphasizing the importance of prevention of illness and benefit of high genetic merit for disease resistance. At the same time, data underlying national genetic evaluations primarily come from conventional cows, drawing concern to the possibility of a genotype by environment interaction whereby the value of a genotype varies depending on the environment, and potentially limits the relevance of these evaluations to organic cows. The objectives of this study were to characterize the genetics of and determine the presence of genotype by environment interaction for health traits in US organic dairy cows. Individual cow health data were obtained from 16 US Department of Agriculture certified organic dairy farms from across the United States that used artificial insemination and maintained detailed records. Data were obtained for the following traits: died, lameness, mastitis, metabolic diseases (displaced abomasum, ketosis, and milk fever), reproductive diseases (abortion, metritis, and retained placenta), transition health events (any health event occurring 21 d before or after parturition), and all health events. Binary phenotypes (1 = diseased, 0 = otherwise) for 38,949 lactations on 19,139 Holstein cows were used. Genotypes from 2,347 cows with 87.5% or greater Holstein breed-based representation were incorporated into single-step multitrait threshold animal models that included stayability (1 = completed lactation, 0 = otherwise). Gibbs sampling was used. Genomic predicted transmitting abilities (gPTA) from national genetic evaluations were obtained for sires for production, fitness, health, and conformation traits. We approximated genetic correlations for sires using these gPTA and our estimated breeding values. We also regressed health phenotypes on cow estimated breeding values and sire gPTA. Heritabilities (± standard error) ranged from 0.03 ± 0.01 (reproductive diseases) to 0.11 ± 0.03 (metabolic diseases). Most genetic correlations among health traits were positive, though the genetic correlation between metabolic disease and mastitis was -0.42 ± 0.17. Approximate genetic correlations between disease resistance for our health trait categories and disease resistance for the nationally-evaluated health traits generally carried the expected sign with the strongest correlation for mastitis (0.72 ± 0.084). Regression coefficients carried the expected sign and were mostly different from zero, indicating that evaluations from primarily conventional herd data predicted health on organic farms. In conclusion, use of national evaluations for health traits should afford genetic improvement for health in US organic herds.

Characterization of ketolactia in dairy cows during early lactation.

Fourier transform infrared spectroscopy (FTIR) allows for the determination of milk acetone (mACE) and ß-hydroxybutyrate (mBHB) concentrations, providing a potential herd monitoring tool for hyperketolactia, defined as elevated milk ketone bodies. The study aim was to characterize mACE and mBHB concentration dynamics during early lactation in Polish Holstein-Friesian cows. Milk samples (n = 3,867,390) were collected within 6 to 60 days in milk (DIM) over a 4-yr period (April 1, 2013 to March 31, 2017) from approximately 21,300 dairy herds (average 38.7 cows/herd). Fixed effects of parity, DIM, and their interaction on mACE and mBHB concentrations were determined using a mixed model with a herd-year-season fixed effect and random cow effect. Published hyperketolactic mACE (≥0.15 mmol/L) and mBHB (≥0.10 mmol/L) threshold concentrations were used to classify study milk samples into ketolactia groups of normal (mACE <0.15 mmol/L and mBHB <0.10 mmol/L) and hyperketolactic (HYKL; either mACE ≥0.15 mmol/L or mBHB ≥0.10 mmol/L). Additionally, HYKL samples were categorized into subpopulations as having elevated mBHB and mACE (HYKLACEBHB, mACE ≥0.15 mmol/L and mBHB ≥0.10 mmol/L), only elevated mBHB (HYKLBHB; mACE <0.15 mmol/L and mBHB ≥0.10 mmol/L), or only elevated mACE (HYKLACE; mACE ≥0.15 mmol/L and mBHB <0.10 mmol/L). Effects of parity, DIM, ketolactia group or subpopulation, and their interactions on mACE and mBHB concentrations were also determined using the mixed model that included ketolactia group or subpopulation as an independent variable. Across all data, mACE and mBHB concentrations were influenced by effects of parity, DIM, and their interaction as well as parity, DIM, ketolactia group or subpopulation, and their interactions. For all samples, mACE and mBHB concentrations decreased with increasing DIM, with mACE concentration declining more rapidly compared with mBHB. In the data set, 68% and 32% of all samples were defined as normal or HYKL, respectively. Among HYKL samples, mACE was elevated soon after calving and declined over time. In contrast, mBHB started lower after calving and increased reaching peak concentrations around 30 DIM, and then decreased. Within HYKL samples, 50.8, 41.3, and 7.9% were categorized as HYKLACEBHB, HYKLBHB, and HYKLACE respectively. Between 6 and 21 DIM, 11.3% of HYKL were classified as HYKLACE. Primiparous cows had greater (14.8%) HYKLACE samples in this time period. In conclusion, this study has characterized mACE and mBHB concentrations during early lactation and determined effects of parity, DIM, and their interaction. Using published criteria interpreting mACE and mBHB concentrations, it was intriguing to identify a unique population of samples having elevated mACE without mBHB in early lactation, especially in primiparous cows. Further research is needed to determine if this sample population represents an unhealthy metabolic status that adversely affects cow health and performance.

Genetic parameters and genomic regions associated with horn fly resistance in organic Holstein cattle.

Horn flies (Haematobia irritans [L.]) contribute to major economic losses of pastured cattle operations, particularly in organic herds because of limitations on control methods that can be used. The objectives of this research were to determine if resistance to horn flies is a heritable trait in organic Holstein cattle, determine associations with yield traits, and to detect genomic regions associated with fly infestation. Observations of fly load were recorded from 1,667 pastured Holstein cows, of which 640 were genotyped, on 13 organic dairies across the United States. Fly load score was determined using a 0 to 4 scale based on fly coverage from chine to loin on one side of the body, with 0 indicating few to no flies and 4 indicating high infestation. The scoring system was validated by counting flies from photographs taken at the time of scoring from 252 cows. To mitigate the effect of our data structure on potential selection bias effects on genetic parameter estimates, survival to subsequent lactations of scored animals and herd-mates that had been culled before the trial was accounted for as the trait stayability. Genetic parameters were estimated using single-step genomic analysis with 3-trait mixed models that included fly score, stayability, and a third phenotype. Model effects differed by variable, but fixed effects generally included a contemporary group, scorer, parity, and stage of lactation; random effects included animal, permanent environment, and residual error. A genome-wide association study was performed by decomposing estimated breeding values into marker effects to detect significant genomic regions associated with fly score. The rank correlation between the subjective fly score and the objective count was 0.79. The average heritability of fly score (± standard error) estimated across multiple models was 0.25 ± 0.04 when a known Holstein maternal grandsire was required and 0.19 ± 0.03 when only a known Holstein sire was required. Genetic correlation estimates with yield traits were moderately positive, but a greater fly load was associated with reduced yield after accounting for genetic merit. Lower fly loads were associated with white coat coloration; a significant genomic region on Bos taurus autosome 6 was identified that contains the gene KIT, which was the most plausible candidate gene for fly resistance because of its role in coat pattern and coloration. The magnitude of heritable variation in fly infestation is similar to other traits included in selection programs, suggesting that producers can select for resistance to horn flies.

Genetic parameters of calf morbidity and stayability for US organic Holstein calves.

The objectives of this study were to estimate genetic parameters of calf health in organic US Holstein calves. Calves were born on farms across the United States from 2006 to 2019. Three calf health traits were evaluated in the study: calf respiratory disease until 365 d of age, calf scours until 60 d of age, and heifer stayability until 365 d of age. For respiratory disease and scours, animals were assigned a phenotype of 0 if they were healthy and a phenotype of 1 if they were diseased. For stayability, animals were assigned a phenotype of 0 if they were removed from the herd by 365 d of age and 1 if they remained in the herd at 365 d of age. Genetic parameters were estimated from threshold models that included the fixed effects of mean, year-season of birth, and dam age (respiratory disease and scours only) as well as the random effects of herd-year of birth and additive genetics. Heritability estimates were 0.100, 0.075, and 0.085 for respiratory disease, scours, and stayability, respectively. Solutions for estimated breeding values for respiratory disease and scours were transformed from disease risk to disease resistance by reversing the signs before calculating genetic correlations such that higher values of scours, respiratory disease, and stayability were favored. There was a moderate favorable genetic correlation estimate between respiratory disease resistance and stayability of 0.675. However, genetic correlation estimates between respiratory disease resistance and scours resistance (0.148) and between scours resistance and stayability (0.165) were low. Estimated breeding value correlations between calf health traits and other traits evaluated nationally were generally low in magnitude. The strongest correlation estimates were with longevity, particularly between stayability and heifer livability (0.217) and between stayability and cow livability (0.288); respiratory disease resistance was also favorably correlated with heifer (0.190) and cow (0.178) livability. Correlations with cow health traits were generally low and unfavorable. Linear models including the random effect of herd-by-sire indicated that herd-by-sire accounted for approximately 2% of phenotypic variance for scours and stayability, which may indicate a genotype by environment interaction effect for these traits. In conclusion, there is significant genetic variation in organic calf health, and there was evidence of genotype by environment interaction.

Review: Perspective on high-performing dairy cows and herds.

Milk and dairy products provide highly sustainable concentrations of essential amino acids and other required nutrients for humans; however, amount of milk currently produced per dairy cow globally is inadequate to meet future needs. Higher performing dairy cows and herds produce more milk with less environmental impact per kg than lower performing cows and herds. In 2018, 15.4% of the world's dairy cows produced 45.4% of the world's dairy cow milk, reflecting the global contribution of high-performing cows and herds. In high-performing herds, genomic evaluations are utilized for multiple trait selection, welfare is monitored by remote sensing, rations are formulated at micronutrient levels, health care is focused on prevention and reproduction is managed with precision. Higher performing herds require more inputs and generate more waste products per cow, thus innovations in environmental management on such farms are essential for lowering environmental impacts. Our focus is to provide perspectives on technologies and practices that contribute most to sustainable production of milk from high-performing dairy cows and herds.

Determination of relationships between rumination and milk fat concentration and fatty acid profile using data from commercial rumination sensing systems.

Milk fat production is highly influenced by nutrition and rumen fermentation. Rumination is an essential part of the ruminant digestive process and can serve as an indicator of rumen fermentation. The objective of this research was to quantify variation in rumination time between and within dairy herds and test for relationships between rumination time and milk fat production and fatty acid (FA) profile as a proxy of rumen fermentation. Our hypothesis was that rumination may indicate disruptions to rumen fermentation and that cows that spent less time ruminating would have lower milk fat due to these rumen disruptions. Data were collected from 1,733 Holstein cows on 5 commercial dairy farms (4 in Pennsylvania and 1 in New York) of 200 to 700 head using 1 of 2 commercially-available rumination sensing systems, CowManager SensOor ear tags (Agis Automatisering BV) or SCR model HR-LDn neck collars (SCR Engineers). Rumination data were collected for 7 consecutive days leading up to a DHIA test, summed within day, then averaged to obtain mean daily minutes of rumination time. Milk samples from the DHIA test were analyzed for fat content by mid-infrared spectroscopy and for milk FA profile by gas chromatography. Rumination data were analyzed using multiple linear regression models. Rumination time was related to concentration of specific odd- and branched-chain and trans FA in milk but was not directly related to milk fat concentration. Rumination time also did not contribute to models predicting milk fat concentration after accounting for other cow-level variables. There was a linear relationship between trans-10 C18:1 and rumination time that was positive after accounting for the effect of farm (partial R2 of 2.97% across all data, 4.24% in SCR data, and 2.22% in CowManager data). Although rumination time was not related directly to milk fat, it was associated with differences in trans and odd- and branched-chain FA that have been demonstrated to change during subacute ruminal acidosis or biohydrogenation-induced milk fat depression, which may affect milk fat and other production variables. These associations suggest that further investigation into using rumination data from commercial systems to predict or identify the presence of these conditions is warranted.

Genetic parameters for stayability of Holsteins in US organic herds.

The objectives of this study were to estimate genetic parameters for stayability in US organic Holstein dairy cows and estimate genetic correlations with nationally evaluated traits of interest. Stayability is the binary trait for success or failure to remain in the herd until a given time point. We used birth, calving, and cull dates from 16 USDA certified organic farms recommended by industry personnel as herds maintaining individual cow records and using artificial insemination. Stayability at 5 time points was assigned based on the presence of a calving date for each parity up to 5 (STAY1 to STAY5). We also considered livebirth (vs. stillbirth), stayability from a successful first calving to second calving (STAY12), stayability from a successful second calving to third calving (STAY23), and stayability as a repeated measure encompassing STAY1 to STAY5. In total, 44,995 females were used in this study. Ninety-six percent were born alive and of these, 64% reached first parity. Animals with Holstein sires and no other identified breed for 3 generations on the maternal side were included. Heritabilities for stayability to each parity on the underlying scale were estimated using a threshold model with the fixed effect of herd and the random effects of animal and herd-year-season of birth. Genetic correlations were estimated among livebirth, STAY1, STAY12, and STAY23 with a 4-trait linear model with fixed herd-year-season of birth and random effects of animal, dam of the calf (livebirth), and herd calving date (STAY12 and STAY23). Heritabilities for stayability ranged from 0.07 to 0.15 and was 0.08 for the direct effect of livebirth and 0.06 for the maternal effect of livebirth. The repeatability for stayability was 0.60. Genetic correlations ranged from 0.11 between livebirth and STAY1 to 0.83 between STAY12 and STAY23. Excluding livebirth, stayability to all time points was significantly correlated with productive life and with cow livability. In general, stayability was positively associated with milk yield and negatively associated with fat percent and stillbirth. In conclusion, stayability in organic herds is heritable and positively associated with nationally evaluated longevity traits suggesting that improvement for stayability in organic herds can be achieved with current national evaluations for longevity.

Genetic parameters of passive transfer of immunity for US organic Holstein calves.

Passive transfer of immunity is important for calf health and survival. The objectives of this study were to estimate genetic parameters for calf passive transfer of immunity through producer-recorded serum total protein (STP) and to determine associations with other routinely evaluated traits in organic Holstein calves (n = 16,725) that were born between July 2013 to June 2018; a restricted subset (n = 7,518) of calves with known Holstein maternal grandsires was analyzed separately. Producers measured STP on farm, and STP was extracted from farm management software. Failure of passive transfer of immunity (FPT) was declared for calves with STP ≤5.2 g/dL. Calves that had the opportunity to reach 1 yr of age were recorded as either staying in the herd or leaving the herd (STAY365). Univariate and threshold models were fitted for STP and FPT, respectively, and included the fixed effects of herd-year-month of birth, calf age in days at STP measurement, dam age in years, and random effects of animal and birthdate within herd. Model effects for STAY365 included the fixed effects of herd-year-month of birth and random effects of animal and birthdate within herd. Multivariate analyses of STP with FPT or STAY365 were conducted to determine the genetic correlation between traits and STP was also regressed on gestation length. Heritability estimates of STP were 0.06 and 0.08 for full and restricted data, respectively. Heritability estimates for FPT were 0.04 and 0.06 for full and restricted data, respectively. The genetic correlation between STP and FPT was near unity. Heritability estimates for STAY365 ranged from 0.08 to 0.11 with genetic correlation estimates between STP and STAY365 ranging from 0.19 and 0.25. Approximate genetic correlations were estimated for sires (n = 302 and n = 256 for full and restricted data, respectively) with at least 10 daughters for STP and predicted transmitting abilities for health, calving traits, and production. Positive approximate genetic correlations were estimated for STP with cow livability, productive life, net merit dollars, and milk yield; favorable approximate genetic correlations were observed for daughter and sire calving ease, and sire stillbirth. Longer gestation length was associated with reduced STP genetically and phenotypically. These results suggest that passive transfer as measured through STP is heritable and favorably correlated with current measures of health, calving, and production.

Relationship of daily total somatic cell output with somatic cell concentration and clinical mastitis.

Somatic cell count (SCC) measures the concentration of somatic cells in milk and is used as a mastitis diagnostic tool. It is plausible that variation in milk yield could alter the relationship between SCC and mastitis status. Our objective was to evaluate total daily SCC output as a predictor of clinical mastitis. Data included 37,035 test-day records from 4,179 lactations of 1,679 cows and 1,286 mastitis events from an experimental herd. Daily total SCC was derived by multiplying SCC by daily milk yield in milliliters and transformed to daily total somatic cell score (DTSCS) via a log2 transformation. Milk yield, SCS, and DTSCS were evaluated with mixed models that included the proximity of a mastitis event to the test date and days in milk as the main fixed effects. A second series of logistic regression was conducted that considered mastitis (1 = mastitis occurred during a test interval; 0 = no mastitis) as the dependent variable with milk yield, SCS, and DTSCS the main independent effects. Least squares means for test dates associated with mastitis-free lactations were 2.43 and 2.25 for SCS and DTSCS, respectively. The corresponding values were 5.96 for SCS and 5.66 for DTSCS for the week of a mastitis event. Whereas SCS declined rapidly in early lactation and then increased steadily thereafter, DTSCS was lowest in early lactation and increased by a proportionally smaller amount throughout lactation. Including both SCS and DTSCS in the same model improved the logistic regression model fit over a model with SCS only. Dilution effects from milk yield influence SCS, and consideration of DTSCS in management and genetic selection schemes could improve mastitis detection and resistance.

Relationship of body weight at first calving with milk yield and herd life.

The objectives of this study were to investigate the association of body weight (BW) at first calving (BWFC) and maturity rate (MR; BWFC as a percentage of mature BW) with first-lactation 305-d milk yield (FLMY), milk yield (MY) in the 24 mo following first calving (24MMY), herd life, and BW change (BWC) through the first month of lactation in Holstein heifers. We retrieved daily milk production records and daily BW records from AfiFarm (S. A. E. Afikim, Kibbutz Afikim, Israel). The data set included daily records for 1,110 Holstein cows from The Pennsylvania State University (n = 435,002 records) and 1,229 Holstein cows from University of Florida (n = 462,013 records) that calved from 2001 to 2016. Body weight at first calving was defined as mean BW from 5 to 10 d in milk of the first lactation, whereas BWC represented change from BWFC to average BW from 30 to 40 d in milk. First-lactation 305-d MY and 24MMY were analyzed with a linear model that included effects of farm-year-season of calving, age at calving, and quintiles of BWFC, MR, or BWC. Body weight change was analyzed with the same model to determine associations with BWFC. Survival analysis was performed to estimate the effect of BWFC on survival. Heifers in the top 60% of BWFC had significantly higher FLMY (10,041 to 10,084 kg) than lighter heifers (9,683 to 9,917 kg), but there was wide variation in every quintile, and no relationship of BWFC and FLMY existed within the top 60%. Relationships between BWFC and 24MMY were not significant. Heifers with higher BWFC or MR lost significantly more BW in early lactation. Although BWFC and MR were significant predictors of FLMY, they accounted for <3% of variation in FLMY or 24MMY, suggesting that BWFC and MR are not primary contributors to variation in MY. Compared with the lightest heifers, the heaviest heifers were 49% more likely to be culled at a given time. These data indicated that, among heifers managed similarly, heavier heifers produced more milk in first lactation than lighter heifers but lost more BW, faced a higher risk of being culled, and did not produce more milk in the long term. Based on our data, heifers that reach between 73 and 77% MR at first calving can produce more milk in their first lactation without sacrificing long-term MY and herd life.

Genetic, farm, and lactation effects on behavior and performance of US Holsteins in automated milking systems.

Selecting for favorable behavior and performance could enhance the efficiency of production in automated milking systems (AMS). The objectives of this study were to describe AMS behavior and performance in Holsteins, estimate genetic parameters among AMS traits, and determine genetic relationships of AMS traits with other routinely recorded traits. The edited data included 1,101,651 individual milking records and 394,636 daily records from 2,531 lactations and 1,714 cows that resided on 3 farms; data were obtained from the Dairy Data Warehouse (Assen, Netherlands) cloud. Traits considered were individual milking and daily totals for milk yield, milking time, milk harvest rate (the ratio of milk yield to milking time), milk flow rate, electrical conductivity, machine kickoffs, incomplete milkings, and blood in milk; the number of milkings per day and 305-d mature-equivalent milk yield (305ME) were also evaluated. Individual milkings were evaluated with mixed models that included fixed effects of week of lactation, lactation group (1, 2, ≥3), hour of day, and farm; random effects included cow within lactation, lactation group by week of lactation, and interactions of farm with date, hour, week of lactation, and year-season of calving. Daily records were evaluated with 3-trait animal models that included 305ME and 2 AMS traits with random additive genetic and permanent environment effects. Estimated breeding values were extracted and correlated with yield, conformation, and udder health genetic evaluations. Farm specific robot access policies had notable effects on week of lactation patterns for milk yield and number of milkings. Mature cows had higher milk harvest rates (2.05 kg/min) than first-lactation cows (1.73 kg/min) with larger differences in early lactation. First-lactation cows were more likely to kick off the machine (15.04%) than mature cows (8.62%), particularly in early lactation. Heritability estimates were generally lower for behavior traits (0.03 for incomplete milkings and 0.08 for kickoffs) than for milk harvest rate (0.30) and flow rate (0.55). Udder conformation traits did not have favorable genetic correlations with AMS traits, with the exception that longer teats were correlated with fewer kickoffs (-0.34) and incomplete milkings (-0.49); increased milk harvest rate and flow rate were unfavorably associated with genetic merit for udder health. There is genetic variation for milking efficiency and behavioral traits, suggesting genetic selection to enhance efficiency in AMS systems is possible. Genetic associations with udder conformation indicate that selection for udder morphology is unlikely to substantially improve milking efficiency. This calls for more direct selection of traits related to AMS efficiency.

Relationships between milk fat and rumination time recorded by commercial rumination sensing systems.

Low rumination in the dairy cow is often assumed to result in reduction of saliva flow, rumen buffering, and milk fat, which is a major contributor to milk value in many pricing systems. Rumination time (RT) of individual cows can be measured with commercial rumination sensing systems, but our understanding of how daily RT (minutes per day) is related to milk fat production is limited. Our hypothesis was that between cows within a herd, greater RT would be associated with lower milk fat concentration. Data from 1,823 cows on 2 commercial dairy farms in Pennsylvania over 8 DHIA tests were analyzed for a total of 8,587 cow test-days. Rumination was measured on farm A with CowManager SensoOr ear tags (Agis Automatisering BV, Harmelen, the Netherlands) and on farm B with SCR Hi-Tag neck collars (SCR Engineers, Netanya, Israel). Rumination data were collected for 7 consecutive days leading up to each DHIA test, summed within day, and averaged across days. Data were analyzed using linear mixed models with a repeated effect of test day. Daily RT reported by commercial rumination systems varied across and within cows and was strongly influenced by a cow effect. Greater RT tended to be associated with a small decrease in milk fat concentration in farm A, but was not related to milk fat in farm B. The reason for this difference is unclear, but may be related to a potentially greater prevalence of biohydrogenation-induced milk fat depression on farm A. The significant, but small, model coefficients for milk fat and RT indicate that the relationship between these variables may not be strong enough to permit identification of cows with biohydrogenation-induced milk fat depression based on RT from commercial systems alone. Research assessing changes in rumination before, during, and after onset of altered rumen fermentation is necessary to determine whether RT could be used to identify cows with altered rumen fermentation.