Skip to main content
ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #402560
Research Project: Increasing Accuracy of Genomic Prediction, Developing Algorithms, Selecting Markers, and Evaluating New Traits to Improve Dairy Cattle

Location: Animal Genomics and Improvement Laboratory

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

Author
item LOZADA-SOTO, EMMANUEL - North Carolina State University
item TIEZZI, FRANCESCO - University Of Florence
item JIANG, JICAI - North Carolina State University
item COLE, JOHN - Former ARS Employee
item Vanraden, Paul
item Toghiani, Sajjad
item MALTECCA, CHRISTIAN - North Carolina State University

Submitted to: European Association of Animal Production Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 5/20/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: This study aimed to determine the effect of different germplasm exchange strategies on short- and long-term genetic gain, inbreeding, and genetic diversity metrics. Actual genotypes from U.S. Holstein animals born between 2010 and 2020 and belonging to 3 distinct stud populations were used as a basis for a simulated breeding program. Ten generations of selection were simulated within each population by mating 200 bulls and 5000 cows. Three traits were simulated (one for each population) with the same underlying genetic architecture (either 10 or 100 QTL/per chromosome) and an additive genetic correlation between traits determined by a parameter epsilon (r_12 = epsilon , r_13 = epsilon , r_23 = epsilon^2; where epsilon=0.10, 0.50, or 0.90). Animals within a given population were selected either randomly, using true breeding value (TBV), estimated breeding value (EBV), or an estimated breeding value penalized for kinship (pEBV) with females (cows were selected based on EBV for this scenario). To evaluate the effect of germplasm exchange between populations, we simulated scenarios where sires (25 or 100) from the other two populations were used for mating instead of a portion of within-population sires. These sires were chosen either randomly, using pEBV, or solely based on minimizing the population's genomic future inbreeding (GFI). The study monitored cumulative genetic progress, genomic homozygosity, pedigree inbreeding, genetic differentiation (across populations), and average MAF (across populations). The simulation was replicated ten times. A mixed-linear model using the fixed effects of within- and across-population selection scenarios, population, number of QTL, epsilon parameter, and all the two-order interactions, and the random effect of replicate was used. Least-squares means were obtained for each level of the main effects. Using sires from other populations (specifically the PEBV and GFI scenarios) provided higher genetic gain (up to 34.39% more), lower average homozygosity (up to 725.3% less), lower average pedigree inbreeding (up to 34.45% less), higher average MAF (up to 2.44% more), and lower F_ST (up to 64.63 % less).