Effect of germplasm exchange strategies on genetic gain, homozygosity, and genetic diversity in dairy stud populations: A simulation study

Authors: LOZADA-SOTO, EMMANUEL - North Carolina State University; MALTECCA, CHRISTIAN - North Carolina State University; JIANG, JICAI - North Carolina State University; COLE, JOHN - Council On Dairy Cattle Breeding; Vanraden, Paul; TIEZZI, FRANCESCO - University Of Florence

Submitted to: Journal of Dairy Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/25/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary: Improvements in genetic selection methods have resulted in significant genetic improvement in dairy cattle populations while increasing homozygosity and decreasing genetic diversity. In this study, we simulated selection and germplasm exchange strategies between populations on genetic gain, homozygosity, and genetic diversity. Germplasm exchange with the intent to broaden the genetic variability was found to be a viable strategy for genetic progress within studs and across-population genetic diversity. The genetic correlation between stud breeding objectives, size of the exchange, and the strategy used to identify bulls for exchange were found to impact the success of germplasm exchange.

Technical Abstract: While genomic selection has led to considerable improvements in genetic gain, it has also seemingly led to increased rates of inbreeding and homozygosity, which can negatively affect genetic diversity and the long-term sustainability of dairy populations. Using genotypes from US Holstein animals from three distinct stud populations, we performed a simulation study consisting of twenty generations of selection, with each breeding population composed of 200 males and 5000 females. Selection strategies investigated consisted of selection using true breeding values (TBV), estimated breeding values (EBV), estimated breeding values penalized for the average future genomic inbreeding of progeny (PEN-EBV), or random selection (RAND). We also simulated several germplasm exchange strategies where the germplasm of males from other populations was used for breeding. These strategies included exchanging males based on EBV, PEN-EBV, low genomic future inbreeding of progeny (GFI), or randomly (RAND). Variations of several parameters, such as the correlation between the selection objectives of populations and the size of the exchange, were simulated. Penalizing genetic merit to minimize genomic inbreeding of progeny provided similar genetic gain and reduced the average homozygosity of populations compared to the EBV strategy. Germplasm exchange was found to generally provide long-term benefits to all stud populations. In both the short and long term, germplasm exchange using the EBV or PEN-EBV strategies provided more cumulative genetic progress than the no-exchange strategy; the amount of long-term genetic progress achieved with germplasm exchange using these strategies was higher for scenarios with a higher genetic correlation between the traits selected by the studs and for a larger size of the exchange. Both the PEN-EBV and GFI exchange strategies allowed decreases in homozygosity and provided significant benefits to genetic diversity compared to other strategies, including larger average minor allele frequencies and smaller proportions of markers near fixation. Overall, this study showed the value of breeding strategies to balance genetic progress and genetic diversity and the benefits of cooperation between studs to ensure the sustainability of their respective breeding programs.