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dc.contributor.authorKASARAPU, P.eng
dc.contributor.authorPORTO NETO, L. R.eng
dc.contributor.authorFORTES, M. R. S.eng
dc.contributor.authorLEHNERT, S. A.eng
dc.contributor.authorMUDADU, M. de A.eng
dc.contributor.authorCOUTINHO, L. L.eng
dc.contributor.authorREGITANO, L. C. de A.eng
dc.contributor.authorGEORGE, A.eng
dc.contributor.authorREVERTER, A.eng
dc.date.accessioned2019-05-22T01:09:28Z-
dc.date.available2019-05-22T01:09:28Z-
dc.date.created2017-09-04
dc.date.issued2017
dc.identifier.citationPLOS one, v. 12, n. 8, p. 1-20, 2017.eng
dc.identifier.urihttp://www.alice.cnptia.embrapa.br/alice/handle/doc/1074938-
dc.descriptionNumerical approaches to high-density single nucleotide polymorphism (SNP) data are often employed independently to address individual questions. We linked independent approaches in a bioinformatics pipeline for further insight. The pipeline driven by heterozygosity and Hardy-Weinberg equilibrium (HWE) analyses was applied to characterize Bos taurus and Bos indicus ancestry. We infer a gene co-heterozygosity network that regulates bovine fertility, from data on 18,363 cattle with genotypes for 729,068 SNP. Hierarchical clustering separated populations according to Bos taurus and Bos indicus ancestry. The weights of the first principal component were subjected to Normal mixture modelling allowing the estimation of a gene?s contribution to the Bos taurus-Bos indicus axis. We used deviation from HWE, contribution to Bos indicus content and association to fertility traits to select 1,284 genes. With this set, we developed a co-heterozygosity network where the group of genes annotated as fertility-related had significantly higher Bos indicus content compared to other functional classes of genes, while the group of genes associated with milk production had significantly higher Bos taurus content. The network analysis resulted in capturing novel gene associations of relevance to bovine domestication events. We report transcription factors that are likely to regulate genes associated with cattle domestication and tropical adaptation. Our pipeline can be generalized to any scenarios where population structure requires scrutiny at the molecular level, particularly in the presence of a priori set of genes known to impact a phenotype of evolutionary interest such as fertility.eng
dc.language.isoengeng
dc.rightsopenAccesseng
dc.subjectHardy-Weinberg equilibriumeng
dc.titleThe Bos taurus-Bos indicus balance in fertility and milk related genes.eng
dc.typeArtigo de periódicoeng
dc.date.updated2019-05-22T01:09:28Z
dc.subject.thesagroBos Indicuseng
dc.subject.thesagroBos Tauruseng
riaa.ainfo.id1074938eng
riaa.ainfo.lastupdate2019-05-21
dc.identifier.doihttps://doi.org/10.1371/journal.pone.0181930eng
dc.contributor.institutionParthan Kasarapu, Agriculture and Food/CSIRO; Laercio Ribeiro Porto Neto, Agriculture and Food/CSIRO; Marina R. S. Fortes, The University of Queensland; Sigrid A. Lehnert, Agriculture and Food/CSIRO; MAURICIO DE ALVARENGA MUDADU, CNPTIA; Luiz Lehmann Coutinho, ESALQ/USP; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE; Andrew George, Agriculture and Food/CSIRO; Antonio Reverter, Agriculture and Food/CSIRO.eng
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