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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #381706
Research Project: Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals

Location: Animal Genomics and Improvement Laboratory

Title: Genetic mechanisms of reproductive heterosis in crossbred dairy cows involve genome-wide additive and nonadditive effects

Author
item PRAKAPENKA, DZIANIS - University Of Minnesota
item LIANG, ZUOXIANG - University Of Minnesota
item Vanraden, Paul
item SANTOS, DANIEL - University Of Maryland
item JIANG, JICAI - North Carolina State University
item MA, LI - University Of Maryland
item GARBE, JOHN - University Of Minnesota
item MELTICCA, CHRISTIAN - North Carolina State University
item HANSEN, PETER - University Of Florida
item DA, YANG - University Of Minnesota

Submitted to: Journal of Dairy Science
Publication Type: Abstract Only
Publication Acceptance Date: 4/2/2021
Publication Date: 6/28/2021
Citation: Prakapenka, D., Liang, Z., Van Raden, P.M., Santos, D., Jiang, J., Ma, L., Garbe, J.R., Melticca, C., Hansen, P.J., Da, Y. 2021. Genetic mechanisms of reproductive heterosis in crossbred dairy cows involve genome-wide additive and nonadditive effects [abstract]. Journal of Dairy Science. 104(Suppl. 1):224(abstr. P169).

Interpretive Summary:

Technical Abstract: Reproduction is one of the areas with strong heterosis in crossbred dairy cows. To identify the genetic mechanism of reproductive heterosis, we conducted a genome-wide association study for daughter pregnancy rate (DPR) using 79,294 SNPs and 9565 crossbred dairy cows. For the cut-off significance level of log(1/p) = 8 with the Bonferroni correction, the number of significant SNP effects was 16,449 for additive effects, and 10,449 for dominance effects, compared to only 112 additive and 2 dominance effects for DPR from a large-scale Holstein GWAS. The most significant additive effect had a log(1/p) of 53, whereas the most significant dominance effects had a log(1/p) of 203, and 481 dominance effects had log(1/p)>53. For pairwise epistasis effects, the cut-off significance level with the Bonferroni correction was log(1/p) = 12. This study only focused on the top 50,000 pairwise effects with minimal log(1/p) value of 29. Of these 50,000 effects, 50.2% were A×A effects, 37.6% A×D and D×A, and 12.2% D×D, with 30% intra-chromosome and 70% inter-chromosome epistasis effects. Of the A×A effects, 82% were inter-chromosome and 18% were intra-chromosome effects. These results indicated that the genetic mechanism of reproductive heterosis involved both additive and nonadditive effects, and inter-chromosome A×A effects had a major role in reproductive heterosis. The large number of significant additive effects indicated a larger collection of favorable alleles for DPR in crossbred cows than in purebred Holsteins in comparison with previous GWAS results for Holsteins, and the large numbers of significant dominance and epistasis effects indicated a major role of nonadditive effects underlying reproductive heterosis in crossbred dairy cows. The intra-chromosome and inter-chromosome epistasis effects as well as the significant additive and dominance effects involved all chromosomes, indicating that the entire genome contributed to reproductive heterosis.