Use este identificador para citar ou linkar para este item: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1137227
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dc.contributor.authorMARTINS, F. B.eng
dc.contributor.authorMORAES, A. C. L.eng
dc.contributor.authorAONO, A. H.eng
dc.contributor.authorFERREIRA, R. C. U.eng
dc.contributor.authorCHIARI, L.eng
dc.contributor.authorSIMEÃO, R. M.eng
dc.contributor.authorBARRIOS, S. C. L.eng
dc.contributor.authorSANTOS, M. F.eng
dc.contributor.authorJANK, L.eng
dc.contributor.authorVALLE, C. B. doeng
dc.contributor.authorVIGNA, B. B. Z.eng
dc.contributor.authorSOUZA, A. P. DEeng
dc.date.accessioned2021-12-07T14:00:42Z-
dc.date.available2021-12-07T14:00:42Z-
dc.date.created2021-12-07
dc.date.issued2021
dc.identifier.citationFrontiers in Plant Science, v.12, article 737919, 2021.
dc.identifier.urihttp://www.alice.cnptia.embrapa.br/alice/handle/doc/1137227-
dc.descriptionArtificial hybridization plays a fundamental role in plant breeding programs since it generates new genotypic combinations that can result in desirable phenotypes. Depending on the species and mode of reproduction, controlled crosses may be challenging, and contaminating individuals can be introduced accidentally. In this context, the identification of such contaminants is important to avoid compromising further selection cycles, as well as genetic and genomic studies. The main objective of this work was to propose an automated multivariate methodology for the detection and classification of putative contaminants, including apomictic clones (ACs), self-fertilized individuals, half-siblings (HSs), and full contaminants (FCs), in biparental polyploid progenies of tropical forage grasses. We established a pipeline to identify contaminants in genotyping-by-sequencing (GBS) data encoded as allele dosages of single nucleotide polymorphism (SNP) markers by integrating principal component analysis (PCA), genotypic analysis (GA) measures based on Mendelian segregation, and clustering analysis (CA). The combination of these methods allowed for the correct identification of all contaminants in all simulated progenies and the detection of putative contaminants in three real progenies of tropical forage grasses, providing an easy and promising methodology for the identification of contaminants in biparental progenies of tetraploid and hexaploid species. The proposed pipeline was made available through the polyCID Shiny app and can be easily coupled with traditional genetic approaches, such as linkage map construction, thereby increasing the efficiency of breeding programs.
dc.language.isoeng
dc.rightsopenAccesseng
dc.subjectGBS
dc.subjectApomictic clones
dc.subjectSelf fertilization
dc.subjectHalf sibling
dc.subjectAllele dosage
dc.subjectClustering analysis
dc.subjectShiny
dc.titleA semi-automated SNP-based approach for contaminant identification in biparental Polyploid Populations of tropical forage grasses.
dc.typeArtigo de periódico
dc.subject.nalthesaurusPrincipal component analysis
dc.format.extent219 p.
riaa.ainfo.id1137227
riaa.ainfo.lastupdate2021-12-07
dc.identifier.doihttps://doi.org/10.3389/fpls.2021.737919
dc.contributor.institutionFELIPE BITENCOURT MARTINS, Center for Molecular Biology and Genetic Engineeringeng
dc.contributor.institutionALINE COSTA LIMA MORAES, Center for Molecular Biology and Genetic Engineeringeng
dc.contributor.institutionALEXANDRE HILD AONO, Center for Molecular Biology and Genetic Engineeringeng
dc.contributor.institutionREBECCA CAROLINE ULBRICHT FERREIRA, Center for Molecular Biology and Genetic Engineeringeng
dc.contributor.institutionLUCIMARA CHIARI, CNPGCeng
dc.contributor.institutionROSANGELA MARIA SIMEAO, CNPGCeng
dc.contributor.institutionSANZIO CARVALHO LIMA BARRIOS, CNPGCeng
dc.contributor.institutionMATEUS FIGUEIREDO SANTOS, CNPGCeng
dc.contributor.institutionLIANA JANK, CNPGCeng
dc.contributor.institutionCACILDA BORGES DO VALLE, CNPGCeng
dc.contributor.institutionBIANCA BACCILI ZANOTTO VIGNA, CPPSEeng
dc.contributor.institutionANETE PEREIRA DE SOUZA, Center for Molecular Biology and Genetic Engineeringeng
dc.contributor.institutionUNICAMP.eng
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