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.

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 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 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.

Genomic predictions for crossbred dairy cattle.

Genomic evaluations are useful for crossbred as well as purebred populations when selection is applied to commercial herds. Dairy farmers had already spent more than $1 million to genotype over 32,000 crossbred animals before US genomic evaluations became available for those animals. Thus, new tools were needed to provide accurate genomic predictions for crossbreds. Genotypes for crossbreds are imputed more accurately when the imputation reference population includes purebreds. Therefore, genotypes of 6,296 crossbred animals were imputed from lower-density chips by including either 3,119 ancestors or 834,367 genotyped animals in the reference population. Crossbreds in the imputation study included 733 Jersey × Holstein F1 animals, 55 Brown Swiss × Holstein F1 animals, 2,300 Holstein backcrosses, 2,026 Jersey backcrosses, 27 Brown Swiss backcrosses, and 502 other crossbreds of various breed combinations. Another 653 animals appeared to be purebreds that owners had miscoded as a different breed. Genomic breed composition was estimated from 60,671 markers using the known breed identities for purebred, progeny-tested Holstein, Jersey, Brown Swiss, Ayrshire, and Guernsey bulls as the 5 traits (breed fractions) to be predicted. Estimates of breed composition were adjusted so that no percentages were negative or exceeded 100%, and breed percentages summed to 100%. Another adjustment set percentages above 93.5% equal to 100%, and the resulting value was termed breed base representation (BBR). Larger percentages of missing alleles were imputed by using a crossbred reference population rather than only the closest purebred reference population. Crossbred predictions were averages of genomic predictions computed using marker effects for each pure breed, which were weighted by the animal's BBR. Marker and polygenic effects were estimated separately for each breed on the all-breed scale instead of within-breed scales. For crossbreds, genomic predictions weighted by BBR were more accurate than the average of parents' breeding values and slightly more accurate than predictions using only the predominant breed. For purebreds, single-trait predictions using only within-breed data were as accurate as multi-trait predictions with allele effects in different breeds treated as correlated effects. Crossbred genomic predicted transmitting abilities were implemented by the Council on Dairy Cattle Breeding in April 2019 and will aid producers in managing their breeding programs and selecting replacement heifers.