Detection of potential functional variants based on systems-biology: the case of feed efficiency in beef cattle

dc.contributor.authorRibeiro, Gabriela
dc.contributor.authorBaldi, Fernando [UNESP]
dc.contributor.authorCesar, Aline S. M.
dc.contributor.authorAlexandre, Pâmela A.
dc.contributor.authorPeripolli, Elisa [UNESP]
dc.contributor.authorFerraz, José B. S.
dc.contributor.authorFukumasu, Heidge
dc.contributor.institutionUniversidade de São Paulo (USP)
dc.contributor.institutionUniversidade Estadual Paulista (UNESP)
dc.contributor.institutionCSIRO Agriculture & Food
dc.description.abstractBackground: Potential functional variants (PFVs) can be defined as genetic variants responsible for a given phenotype. Ultimately, these are the best DNA markers for animal breeding and selection, especially for polygenic and complex phenotypes. Herein, we described the identification of PFVs for complex phenotypes (in this case, Feed Efficiency in beef cattle) using a systems-biology driven approach based on RNA-seq data from physiologically relevant organs. Results: The systems-biology coupled with deep molecular phenotyping by RNA-seq of liver, muscle, hypothalamus, pituitary, and adrenal glands of animals with high and low feed efficiency (FE) measured by residual feed intake (RFI) identified 2,000,936 uniquely variants. Among them, 9986 variants were significantly associated with FE and only 78 had a high impact on protein expression and were considered as PFVs. A set of 169 significant uniquely variants were expressed in all five organs, however, only 27 variants had a moderate impact and none of them a had high impact on protein expression. These results provide evidence of tissue-specific effects of high-impact PFVs. The PFVs were enriched (FDR < 0.05) for processing and presentation of MHC Class I and II mediated antigens, which are an important part of the adaptive immune response. The experimental validation of these PFVs was demonstrated by the increased prediction accuracy for RFI using the weighted G matrix (ssGBLUP+wG; Acc = 0.10 and b = 0.48) obtained in the ssGWAS in comparison to the unweighted G matrix (ssGBLUP; Acc = 0.29 and b = 1.10). Conclusion: Here we identified PFVs for FE in beef cattle using a strategy based on systems-biology and deep molecular phenotyping. This approach has great potential to be used in genetic prediction programs, especially for polygenic phenotypes.en
dc.description.affiliationDepartment of Veterinary Medicine Faculty of Animal Science and Food Engineering University of Sao Paulo, Pirassununga
dc.description.affiliationDepartment of Animal Science São Paulo State University (UNESP), Jaboticabal
dc.description.affiliationEscola Superior de Agricultura “Luiz de Queiroz” University of Sao Paulo, Piracicaba
dc.description.affiliationCSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia
dc.description.affiliationUnespDepartment of Animal Science São Paulo State University (UNESP), Jaboticabal
dc.identifier.citationBMC Genomics, v. 23, n. 1, 2022.
dc.relation.ispartofBMC Genomics
dc.subjectFeed efficiency
dc.subjectFunctional variants
dc.titleDetection of potential functional variants based on systems-biology: the case of feed efficiency in beef cattleen
unesp.departmentZootecnia - FCAVpt