Dissection of additive, dominance, and imprinting effects for production and reproduction traits in Holstein cattle

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dc.contributor.authorJiang, Jicai
dc.contributor.authorShen, Botong
dc.contributor.authorO’Connell, Jeffrey R.
dc.contributor.authorVanRaden, Paul M.
dc.contributor.authorCole, John B.
dc.contributor.authorMa, Li
dc.date.accessioned2021-07-21T18:07:55Z
dc.date.available2021-07-21T18:07:55Z
dc.date.issued2017-05-30
dc.description.abstractAlthough genome-wide association and genomic selection studies have primarily focused on additive effects, dominance and imprinting effects play an important role in mammalian biology and development. The degree to which these non-additive genetic effects contribute to phenotypic variation and whether QTL acting in a non-additive manner can be detected in genetic association studies remain controversial. To empirically answer these questions, we analyzed a large cattle dataset that consisted of 42,701 genotyped Holstein cows with genotyped parents and phenotypic records for eight production and reproduction traits. SNP genotypes were phased in pedigree to determine the parent-of-origin of alleles, and a three-component GREML was applied to obtain variance decomposition for additive, dominance, and imprinting effects. The results showed a significant non-zero contribution from dominance to production traits but not to reproduction traits. Imprinting effects significantly contributed to both production and reproduction traits. Interestingly, imprinting effects contributed more to reproduction traits than to production traits. Using GWAS and imputation-based fine-mapping analyses, we identified and validated a dominance association signal with milk yield near RUNX2, a candidate gene that has been associated with milk production in mice. When adding non-additive effects into the prediction models, however, we observed little or no increase in prediction accuracy for the eight traits analyzed. Collectively, our results suggested that non-additive effects contributed a non-negligible amount (more for reproduction traits) to the total genetic variance of complex traits in cattle, and detection of QTLs with non-additive effect is possible in GWAS using a large dataset.en_US
dc.description.urihttps://doi.org/10.1186/s12864-017-3821-4
dc.identifierhttps://doi.org/10.13016/v275-txnx
dc.identifier.citationJiang, J., Shen, B., O’Connell, J.R. et al. Dissection of additive, dominance, and imprinting effects for production and reproduction traits in Holstein cattle. BMC Genomics 18, 425 (2017).en_US
dc.identifier.urihttp://hdl.handle.net/1903/27554
dc.language.isoen_USen_US
dc.publisherSpringer Natureen_US
dc.relation.isAvailableAtCollege of Agriculture & Natural Resourcesen_us
dc.relation.isAvailableAtAnimal & Avian Sciencesen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us
dc.subjectVariance decompositionen_US
dc.subjectAdditiveen_US
dc.subjectImprintingen_US
dc.subjectDominanceen_US
dc.subjectCattleen_US
dc.subjectDairy traitsen_US
dc.subjectQtlen_US
dc.titleDissection of additive, dominance, and imprinting effects for production and reproduction traits in Holstein cattleen_US
dc.typeArticleen_US

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