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

Authors: SRIKANTH, K - Cornell University; JAAFAR, M - Cornell University; Neupane, Mahesh; ZAABZA, H - US Department Of Agriculture (USDA); MCKAY, S - University Of Missouri; WOLFE, C - American Jersey Cattle Association; METZGER, J - American Jersey Cattle Association; HUSON, H - Cornell University; Van Tassell, Curtis - Curt; Blackburn, Harvey

Submitted to: Journal of Dairy Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/21/2024
Publication Date: 9/28/2024
Citation: Srikanth, K., Jaafar, M.A., Neupane, M., Zaabza, H.B., Mckay, S.D., Wolfe, C.W., Metzger, J.S., Huson, H.J., Van Tassell, C.P., Blackburn, H.D. 2024. Assessment of genetic diversity, inbreeding and collection completeness of Jersey bulls in the US National Animal Germplasm Program. Journal of Dairy Science. https://doi.org/10.3168/jds.2024-25032.
DOI: https://doi.org/10.3168/jds.2024-25032

Interpretive Summary: The U.S. National Animal Germplasm Program (NAGP) conserves genetic diversity of livestock through cryopreservation. The NAGP employed a pedigree-based clustering approach, to build its collection. In this study, we assessed genetic diversity, inbreeding, and collection completeness using genotypic data from Jersey bulls. Comparing Jersey bulls in the NAGP with those in the National Cooperator Database (NCD) maintained by the Council on Dairy Cattle Breeding (CDCB), we found similar inbreeding and genetic diversity, confirming the effectiveness of pedigree-based clustering for building the collection. Additionally, we validated NAGP’s strategy of repeated sampling over time, for capturing allele frequency changes due to selection. The collection of Jersey germplasm closely mirrors the live population.

Technical 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 = 0.343 ± 0.17) relative to the NCD population (Ho 0.328 ± 0.16). The average pedigree and genomic inbreeding (FPED, FGRM, FROH) were similar between the groups with estimates of 7.6% with FPED, 11.07% with FGRM and 20.13% with FROH. 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 over representation 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, sires of cow, and bulls with high Lifetime Net Merit (NM$). All of 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.