Inbreeding depression for producer-recorded udder, metabolic, and reproductive diseases in US dairy cattle

Authors: LOZADA SOTO, EMMANUEL - North Carolina State University; PARKER GADDIS, KRISTEN - Council On Dairy Cattle Breeding; TIEZZI, FRANCESCO - Collaborator; JIANG, JICAI - North Carolina State University; MA, LI - University Of Maryland; Toghiani, Sajjad; Vanraden, Paul; MALTECCA, CHRISTIAN - North Carolina State University

Submitted to: Journal of Dairy Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/7/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary: Increased rates of inbreeding can negatively affect genetic diversity and long-term sustainability of dairy populations. We performed a simulation study consisting of ten generations of selection using genotypes from US Holstein bulls from three distinct breeding companies. A penalty on genomic inbreeding of progeny helped reduce average homozygosity while providing genetic gains similar to selecting on breeding values alone. Germplasm exchange generally provided long-term benefits to all cooperating populations. Germplasm exchange combined with an inbreeding penalty provided on average 13% more cumulative genetic progress than no exchange and provided long-term benefits to all companies and populations. Breeding strategies can balance genetic progress with genetic diversity and benefit from cooperation between companies to ensure sustainability of each private breeding program.

Technical Abstract: While genomic selection has led to considerable improvements in genetic gain, it has also seemingly led to increased rates of inbreeding, 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 ten generations of selection with each breeding population consisting 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 PEN-EBV, low genomic future inbreeding of progeny (GFI), or randomly (RAND). Variation of several parameters, such as the number of QTL, 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. Germplasm exchange using the PEN-EBV strategy provided on average approximately 13% more cumulative genetic progress than no exchange; the amount of genetic progress achieved with the PEN-EBV germplasm exchange strategy was higher for scenarios with the highest number of QTL, a higher genetic correlation between the selection objectives of studs, and for a larger size of exchange. Both the PEN-EBV and GFI exchange strategies allowed decreases to homozygosity and the latter provided significant benefits to across-population measures of genetic diversity, including increased average minor allele frequencies and decreased proportions of markers near fixation. Overall, this study showed the value in breeding strategies to balance genetic progress and genetic diversity and the benefits of cooperation between studs to ensure sustainability of their respective breeding programs.