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.

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.

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.

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.

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.

The genetic and biological basis of feed efficiency in mid-lactation Holstein dairy cows.

The objective of this study was to identify genomic regions and candidate genes associated with feed efficiency in lactating Holstein cows. In total, 4,916 cows with actual or imputed genotypes for 60,671 single nucleotide polymorphisms having individual feed intake, milk yield, milk composition, and body weight records were used in this study. Cows were from research herds located in the United States, Canada, the Netherlands, and the United Kingdom. Feed efficiency, defined as residual feed intake (RFI), was calculated within location as the residual of the regression of dry matter intake (DMI) on milk energy (MilkE), metabolic body weight (MBW), change in body weight, and systematic effects. For RFI, DMI, MilkE, and MBW, bivariate analyses were performed considering each trait as a separate trait within parity group to estimate variance components and genetic correlations between them. Animal relationships were established using a genomic relationship matrix. Genome-wide association studies were performed separately by parity group for RFI, DMI, MilkE, and MBW using the Bayes B method with a prior assumption that 1% of single nucleotide polymorphisms have a nonzero effect. One-megabase windows with greatest percentage of the total genetic variation explained by the markers (TGVM) were identified, and adjacent windows with large proportion of the TGVM were combined and reanalyzed. Heritability estimates for RFI were 0.14 (±0.03; ±SE) in primiparous cows and 0.13 (±0.03) in multiparous cows. Genetic correlations between primiparous and multiparous cows were 0.76 for RFI, 0.78 for DMI, 0.92 for MBW, and 0.61 for MilkE. No single 1-Mb window explained a significant proportion of the TGVM for RFI; however, after combining windows, significance was met on Bos taurus autosome 27 in primiparous cows, and nearly reached on Bos taurus autosome 4 in multiparous cows. Among other genes, these regions contain ß-3 adrenergic receptor and the physiological candidate gene, leptin, respectively. Between the 2 parity groups, 3 of the 10 windows with the largest effects on DMI neighbored windows affecting RFI, but were not in the top 10 regions for MilkE or MBW. This result suggests a genetic basis for feed intake that is unrelated to energy consumption required for milk production or expected maintenance as determined by MBW. In conclusion, feed efficiency measured as RFI is a polygenic trait exhibiting a dynamic genetic basis and genetic variation distinct from that underlying expected maintenance requirements and milk energy output.

Considerations when combining data from multiple nutrition experiments to estimate genetic parameters for feed efficiency.

Prior to genomic selection on a trait, a reference population needs to be established to link marker genotypes with phenotypes. For costly and difficult-to-measure traits, international collaboration and sharing of data between disciplines may be necessary. Our aim was to characterize the combining of data from nutrition studies carried out under similar climate and management conditions to estimate genetic parameters for feed efficiency. Furthermore, we postulated that data from the experimental cohorts within these studies can be used to estimate the net energy of lactation (NE(L)) densities of diets, which can provide estimates of energy intakes for use in the calculation of the feed efficiency metric, residual feed intake (RFI), and potentially reduce the effect of variation in energy density of diets. Individual feed intakes and corresponding production and body measurements were obtained from 13 Midwestern nutrition experiments. Two measures of RFI were considered, RFI(Mcal) and RFI(kg), which involved the regression of NE(L )intake (Mcal/d) or dry matter intake (DMI; kg/d) on 3 expenditures: milk energy, energy gained or lost in body weight change, and energy for maintenance. In total, 677 records from 600 lactating cows between 50 and 275 d in milk were used. Cows were divided into 46 cohorts based on dietary or nondietary treatments as dictated by the nutrition experiments. The realized NE(L) densities of the diets (Mcal/kg of DMI) were estimated for each cohort by totaling the average daily energy used in the 3 expenditures for cohort members and dividing by the cohort's total average daily DMI. The NE(L) intake for each cow was then calculated by multiplying her DMI by her cohort's realized energy density. Mean energy density was 1.58 Mcal/kg. Heritability estimates for RFI(kg), and RFI(Mcal) in a single-trait animal model did not differ at 0.04 for both measures. Information about realized energy density could be useful in standardizing intake data from different climate conditions or management systems, as well as investigating potential genotype by diet interactions.