Assessment of genetic diversity, inbreeding and collection completeness of Jersey bulls in the US National Animal Germplasm Program.

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. While 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.

Inheritance of a mutation causing neuropathy with splayed forelimbs in Jersey cattle.

A new undesirable genetic factor, neuropathy with splayed forelimbs (JNS), has been identified recently in the Jersey breed. Calves affected with JNS are unable to stand on splayed forelimbs that exhibit significant extensor rigidity and excessive lateral abduction at birth. Affected calves generally are alert at birth but exhibit neurologic symptoms, including spasticity of head and neck and convulsive behavior. Other symptoms reported include dislocated shoulders, congenital craniofacial anomalies, and degenerative myelopathy. Inheritance of an undesirable genetic factor was determined from a study of 16 affected calves reported by Jersey breeders across the United States. All of their pedigrees traced back on both paternal and maternal sides to a common ancestor born in 1995. Genotypes revealed that JNS is attributable to a specific haplotype on Bos taurus autosome 6. Currently 8.2% of the genotyped US Jersey population are carriers of the haplotype. Sequencing of the region of shared homozygosity revealed missense variant rs1116058914 at base 60,158,901 of the ARS-UCD1.2 reference map as the most concordant with the genetic condition and the most likely cause. The single-base G to A substitution is in the coding region of the last exon of UCHL1, which is conserved across species. Mutations in humans and gene knockouts in mice cause similar recessive symptoms and muscular degeneration. Since December 2020, carrier status has been tracked using the identified haplotype and reported for all 459,784 genotyped Jersey animals. With random mating, about 2,200 affected calves per year with losses of about $250,000 would result from the 1.3 million US Jersey cows in the national population. Selection and mating programs can reduce numbers of JNS-affected births using either the haplotype status or a direct gene test in the future. Breeders should report calf abnormalities to their breed association to help discover new defects such as JNS.

Genome-wide association study for ketosis in US Jerseys using producer-recorded data.

Ketosis is one of the most frequently reported metabolic health events in dairy herds. Several genetic analyses of ketosis in dairy cattle have been conducted; however, few have focused specifically on Jersey cattle. The objectives of this research included estimating variance components for susceptibility to ketosis and identification of genomic regions associated with ketosis in Jersey cattle. Voluntary producer-recorded health event data related to ketosis were available from Dairy Records Management Systems (Raleigh, NC). Standardization was implemented to account for the various acronyms used by producers to designate an incidence of ketosis. Events were restricted to the first reported incidence within 60 d after calving in first through fifth parities. After editing, there were a total of 42,233 records from 23,865 cows. A total of 1,750 genotyped animals were used for genomic analyses using 60,671 markers. Because of the binary nature of the trait, a threshold animal model was fitted using THRGIBBS1F90 (version 2.110) using only pedigree information, and genomic information was incorporated using a single-step genomic BLUP approach. Individual single nucleotide polymorphism (SNP) effects and the proportion of variance explained by 10-SNP windows were calculated using postGSf90 (version 1.38). Heritability of susceptibility to ketosis was 0.083 [standard deviation (SD) = 0.021] and 0.078 (SD = 0.018) in pedigree-based and genomic analyses, respectively. The marker with the largest associated effect was located on chromosome 10 at 66.3 Mbp. The 10-SNP window explaining the largest proportion of variance (0.70%) was located on chromosome 6 beginning at 56.1 Mbp. Gene Ontology (GO) and Medical Subject Heading (MeSH) enrichment analyses identified several overrepresented processes and terms related to immune function. Our results indicate that there is a genetic component related to ketosis susceptibility in Jersey cattle and, as such, genetic selection for improved resistance to ketosis is feasible.

Effects of inbreeding on production and survival in Jerseys.

Responses of registered Jersey cows to various levels of inbreeding were examined with pedigree data supplied by the American Jersey Cattle Association and test-day production data from 1970 through 1998 obtained from the Animal Breeding Center at Cornell University. Rate of increase in level of inbreeding is accelerating with time, making it more difficult for producers to make matings that avoid the potentially deleterious effects of inbreeding. Production losses caused by inbreeding were significant and curvilinear for all traits studied except somatic cell linear score, with the greatest losses at higher levels of inbreeding. Inbreeding was found to have the greatest effect on production at early ages and early in lactation. Early onset of the deleterious effects of inbreeding resulted in larger net present value losses than if effects of inbreeding occurred later in the life of an animal. Losses were probably enhanced because of the need to freshen animals as early as possible to maximize net present value returns. Survival decreased as level of inbreeding increased and was likely to have a greater negative impact on the financial health of the dairy enterprise than production losses.

Comparison of United States and Danish strains of Jerseys for yield traits.

Eleven US and 11 Danish young bulls were AI sampled in the US and Denmark. The milking daughters of these sires provided an opportunity for comparison of the US and Danish Jersey populations. Danish age and month of calving and DIM adjustment factors were developed so that Danish and US records could be compared on a standardized basis (305-d lactation, mature equivalent). Least squares and animal model analyses were used to estimate strain differences and effects of heterosis. Jerseys from the US had superiority over Danish Jerseys of approximately 1000 kg for milk and 17 kg for protein. However, Danish Jersey had an advantage of 20 kg for fat. Estimates of heterosis from crosses of US and Danish Jerseys were 1.5 to 3% of the mean for milk, fat, and protein yields. Correlations of EBV from official genetic evaluations of the US and Denmark were high, > or = .78, for the project bulls, providing little evidence of an interaction of genotype and environment.

Application of canonical transformation with missing values to multitrait evaluation of Jersey type.

A multitrait animal model was used to calculate predicted transmitting ability and reliabilities for final score and 15 linear type traits of 225,632 US Jersey cows. Records were adjusted for age and stage of lactation before analysis. The model contained effects for interactions of herd and date scored; year scored, parity, and age; and herd and sire; effects of permanent environment and additive genetics were also included. Of the 381,511 records included, some observations were missing for final score (8%), body depth (43%), and teat length (33%). The evaluation system used a canonical transformation, included several random effects, and estimated missing values with each iteration. Inbreeding was considered in the computations. Convergence was achieved in approximately 50 rounds of iteration. Correlations between animal and sire model predicted transmitting ability ranged from 0.56 to 0.95 and generally were higher for bulls than for cows and for more recent birth years. Genetic trend was strongly positive for dairy form, final score, and rear udder traits (height and width) and negative for udder depth. For other traits, genetic trend was small. This methodology should improve the accuracy of genetic evaluations for type traits of US Jerseys.

Estimation of (co)variance components for Jersey type traits using a repeatability model.

(Co)variance components for final score and 15 linear types traits of Jersey cows were estimated by multitrait REML using multiple diagonalization and a repeatability model with 34,999 records of 22,354 cows. Multiple diagonalization gave relative off-diagonals (ratio of squared off-diagonals to the product of diagonals) of < 0.1%. Heritabilities and repeatabilities, respectively, were estimated as 0.29 and 0.48 for final score, 0.40 and 0.57 for stature, 0.26 and 0.39 for strength, 0.28 and 0.43 for dairy form, 0.13 and 0.25 for foot angle, 0.13 and 0.25 for rear legs (side view), 0.27 and 0.41 for body depth, 0.31 and 0.52 for rump angle, 0.22 and 0.33 for thurl width, 0.22 and 0.36 for fore under attachment, 0.28 and 0.46 for rear udder height, 0.26 and 0.42 for rear udder width, 0.32 and 0.48 for udder depth, 0.20 and 0.36 for udder cleft, 0.29 and 0.46 for front teat placement, and 0.31 and 0.48 for teat length. Estimates of heritability generally were higher, and estimates of repeatability were lower, than values used previously for USDA genetic evaluations, which were based on data from the 1970s and early 1980s. Final score was highly correlated both genetically and phenotypically with dairy form and rear udder traits. These estimates of heritabilities and (co)variance components are necessary for multitrait genetic evaluation of linear type traits of US Jerseys.