Bovine tuberculosis (bTB) is an infectious disease of cattle generally caused by Mycobacterium bovis , a bacterium that can elicit disease humans. Since the 1950s, the objective of the national bTB eradication program in Republic of Ireland was the biological extinction of bTB; that purpose has yet to be achieved. Objectives of the present study were to develop the statistical methodology and variance components to undertake routine genetic evaluations for resistance to bTB; also of interest was the detection of regions of the bovine genome putatively associated with bTB infection in dairy and beef breeds. The novelty of the present study, in terms of research on bTB infection, was the use of beef breeds in the genome-wide association and the utilization of imputed whole genome sequence data. Phenotypic bTB data on 781,270 animals together with imputed whole genome sequence data on 7,346 of these animals’ sires were available. Linear mixed models were used to quantify variance components for bTB and EBVs were validated. Within-breed and multi-breed genome-wide associations were undertaken using a single-SNP regression approach. The estimated genetic standard deviation (0.09), heritability (0.12), and repeatability (0.30) substantiate that genetic selection help to eradicate bTB. The multi-breed genome-wide association analysis identified 38 SNPs and 64 QTL regions associated with bTB infection; two QTL regions (both on BTA23) identified in the multi-breed analysis overlapped with the within-breed analyses of Charolais, Limousin, and Holstein-Friesian. Results from the association analysis, coupled with previous studies, suggest bTB is controlled by an infinitely large number of loci, each having a small effect. The methodology and results from the present study will be used to develop national genetic evaluations for bTB in the Republic of Ireland. In addition, results can also be used to help uncover the biological architecture underlying resistance to bTB infection in cattle.

While several studies in cattle have confirmed the improved performance achievable from selection on total merit indexes, these studies have solely been confined to specific-purpose beef or dairy total merit indexes. Validation studies of total merit indexes used to select beef sires for use on dairy females are lacking. The objective here was to fill this void by quantifying the performance of beef × dairy progeny where the sire excels in either a total merit index encompassing calving performance and beef performance traits (dairy-beef index; DBI) or excels in a subindex based solely on calving performance (CLV); for comparative purposes, these beef × dairy progeny were also compared with dairy × dairy progeny. A total of 123,785 calving records from 101,773 dairy cows calving in 3,065 dairy herds were used; of these, 48,875 progeny also had carcass information. The beef sires were stratified into 5 equally sized groups based separately on their DBI or CLV. Linear and threshold mixed models were used to compare calving and carcass performance of all 3 sire genotypes. Of the 415 sires that ranked in the highest of the 5 strata on the CLV subindex, only 52% of them ranked in the highest stratum for the DBI. The percentage of primiparae requiring any assistance at calving was 2 to 3 percentage units greater for the higher DBI sires relative to both the higher CLV beef sires and the dairy sires (not ranked on anything); no difference existed in multiparae. The extent of calving difficulty in primiparae was, however, less in higher DBI beef sires relative to both the higher CLV beef sires and the dairy sires, although the differences were biologically small. Perinatal mortality was greatest in the beef sires relative to the dairy sires, but no difference existed between the high CLV or high DBI beef sires. No difference in progeny gestation length was evident between the high DBI or high CLV beef sires, although both were >2 d longer than progeny from dairy sires. The higher DBI sires produced progeny with heavier, more conformed carcasses relative to the progeny from both high CLV beef sires and dairy sires. No differences existed between the progeny of the beef sires ranked highly on the CLV versus those ranked highly on the DBI for the probability of achieving the specification for carcass weight (between 270 and 380 kg) or fat score; the higher DBI animals, however, had a 4 to 10% greater probability of achieving the minimum carcass conformation required. In all instances, the beef sires had a greater probability of achieving all specifications relative to the progeny from the dairy sires with the difference for conformation being particularly large. Results indicate that more balanced progeny can be generated using a DBI, helping meet the requirements of both dairy and beef producers. Ignoring market failure across sectors, using higher DBI sires could increase dairy herd profit by 3 to 5% over and above the status quo approach to selection in dairy (i.e., CLV subindex).

Animal mortality is indicative of animal health and welfare standards, which are of growing concern to the agricultural industry. The objective of the present study was to ascertain risk factors associated with mortality at multiple life stages in pasture-based, seasonal-calving dairy and beef herds. Males and females were stratified into seven life stages based on age (0 to 2 d, 3 to 7 d, 8 to 30 d, 31 to 182 d, 183 to 365 d, 366 to 730 d, and 731 to 1,095 d) whereas females with ≥1 calving event were further stratified into five life stages based on cow parity number (1, 2, 3, 4, and 5). Mortality was defined as whether an animal died during each life stage; only animals that either survived the entire duration or died during a life stage were considered. The data, following edits, consisted of 4,404,122 records from 1,358,712 animals. Multivariable logistic regression was used to estimate the logit of the probability of mortality in each life stage separately. The odds of a young animal (i.e., aged ≤ 1,095 d) dying was generally greater if veterinary assistance was required at their birth relative to no assistance (odds ratio [OR]: 3.10 to 31.85), if the animal was a twin relative to a singleton (OR: 1.46 to 2.31) or if the animal was male relative to female (OR: 1.14 to 6.15). Moreover, the odds of a cow (i.e., females with ≥1 calving event) dying were greater when she required veterinary assistance at calving (OR: 2.69 to 7.55) compared with a cow that did not require any assistance, if she produced twin relative to singleton progeny (OR: 1.59 to 2.03) or male relative to female progeny (OR: 1.09 to 1.20). Additionally, the odds of a first or second parity cow dying when she herself had received veterinary assistance at birth were only 0.63 to 0.66 times that of a cow that was provided no assistance at birth. For both young animals and cows, the odds of dying generally increased with herd size, whereas animals residing in expanding herds had lower odds of dying. Results from the present study indicate that the risk factors associated with mortality in pasture-based, seasonal-calving herds are similar to those reported in literature in confinement, nonseasonal-calving herds. Moreover, the present study identifies that these risk factors are similar in both dairy and beef herds, yet the magnitude of the association often differs and also changes with life stage.