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ABSTRACT: Genomic selection and extensive use of a few elite bulls through artificial insemination are leading to reduced genetic diversity in Jersey cattle. Conservation of genetic diversity through gene banks can protect a breed's genetic diversity and genetic gain, ensuring continued genetic advancement in the future. The availability of genomic information in the US National Animal Germplasm Program (NAGP) facilitates characterization of Jersey bulls in the germplasm collection. Therefore, in this study, we compared the genetic diversity and inbreeding between Jersey bulls in the NAGP and the National Cooperator Database (NCD). The NCD is maintained and curated by the Council on Dairy Cattle Breeding (CDCB). We found the genetic diversity to be marginally higher in NAGP (Ho = 0.34 ± 0.17) relative to the NCD population (Ho = 0.33 ± 0.16). The average pedigree and genomic inbreeding (FPED, FGRM, FROH > 2Mb) were similar between the groups, with estimates of 7.6% with FPED, 11.07% with FGRM and 20.13% with FROH > 2Mb. An increasing trend in inbreeding was detected, and a significantly higher level of inbreeding was estimated among the older bulls in the NAGP collection, suggesting an overrepresentation of the genetics from elite bulls. Results from principal component analyses (PCA) provided evidence that the NAGP collection is representative of the genetic variation found in the NCD population and a broad majority of the loci segregating (98.2%) in the NCD population were also segregating in the NAGP. Ward's clustering was used to assess collection completeness of Jerseys in the NAGP by comparison with top 1000 sires of bulls, top 1000 sires of cow, and bulls with high Lifetime Net Merit (NM$). All the clusters were represented in the NAGP suggesting that most of the genetic diversity in the US Jersey population is represented in the NAGP and confirmed the PCA results. The decade of birth was the major driver grouping bulls into clusters, suggesting the importance of selection over time. Selection signature analysis between the historic bulls in the NAGP with the newer bulls, born in the decade after implementation of genomic selection, identified selection for milk production, fat and protein yield, fertility, health, and reproductive traits. Cluster analysis revealed that the NAGP has captured allele frequency changes over time associated with selection, validating the strategy of repeated sampling and suggests that the continuation of a repeated sampling policy is essential for the germplasm collection to maintain its future utility. Although NAGP should continue to collect bulls that have large influence on the population due to selection, care should be taken to include the entire breadth of bulls, including low merit bulls.

ABSTRACT: The aim of this study was to evaluate the effect of therapeutically administered tildipirosin or florfenicol + flunixin meglumine for the treatment of bovine respiratory disease (BRD) accompanied by fever in calves before weaning compared with diseased and untreated animals. As specific objectives, we evaluated the composition of the bacterial microbiota of the upper respiratory tract (URT) and blood and health parameters of the animals. Preweaning Holstein female calves diagnosed with naturally acquired pneumonia were randomly assigned to one of the following experimental groups on the day of diagnosis (d 0): (1) TLD (n = 36): single subcutaneous injection with 4 mg/kg tildipirosin; (2) FLF (n = 33): single subcutaneous injection with an antimicrobial (40 mg/kg florfenicol) combined with a nonsteroidal anti-inflammatory drug (2.2 mg/kg flunixin meglumine); and (3) NEG (n = 35): no treatment within the first 5 d following enrollment. The NEG treatment group was closely monitored for 5 d, and calves were removed from the study following a standardized late treatment protocol, when necessary, to minimize health concerns. Healthy untreated calves (CTR; n = 31) were also selected for the study and used as controls. Blood samples used for biochemical analysis and nasopharyngeal swabs used for evaluation of URT microbiota were collected daily from d 0 until d 5 and then weekly until weaning. Next-generation sequencing of the 16S rRNA gene was used to assess the URT microbiota at the phylum and genus levels. Clinical signs associated with pneumonia and otitis media were assessed daily, as was the need for antibiotic interventions. Calves in the TLD and FLF groups had faster recovery from fever within the first 5 d after enrollment. In addition, antibiotic-treated calves reached the same serum haptoglobin levels as healthy calves on d 2 after diagnosis, whereas calves in the NEG group had higher haptoglobin levels than the CTR group until at least d 5 after BRD diagnosis. Calves in the TLD and FLF groups had a lower risk of treatment for pneumonia (FLF = 22.8%; TLD = 27.7%) from d 5 to weaning than calves in the NEG group (54.7%). Furthermore, FLF treatment had a significantly lower risk of nasal discharge, otitis media, and treatment failure compared with the NEG group, but did not differ from the TLD group. Differences in the composition of the URT microbiota were found between groups, and the genus Mycoplasma was the most abundant in samples collected from the URT of calves with and without pneumonia. Both drugs were effective in reducing the mean relative abundance (MRA) of important genera associated with pneumonia (Mannheimia and Pasteurella), although an increase in Mycoplasma MRA was observed for tildipirosin-treated calves. In conclusion, both drugs were effective in reducing the inflammatory signs of pneumonia and the need for antimicrobial treatment after enrollment compared with no treatment. In addition, both TLD and FLF were effective in reducing the MRA of important bacterial genera associated with pneumonia; however, TLD treatment was associated with increased Mycoplasma MRA compared with healthy and untreated calves.