Single nucleotide polymorphism calling and imputation strategies for cost-effective genotyping in a tropical maize breeding program.

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dc.contributorAmanda Avelar de Oliveira, Escola Superior de Agricultura "Luiz de Queiroz"
dc.contributorLAURO JOSE MOREIRA GUIMARAES, CNPMS
dc.contributorCLAUDIA TEIXEIRA GUIMARAES, CNPMS
dc.contributorPAULO EVARISTO DE O GUIMARAES, CNPMS
dc.contributorMARCOS DE OLIVEIRA PINTO, CNPMS
dc.contributorMARIA MARTA PASTINA, CNPMS
dc.contributorGabriel Rodrigues Alves Margarido, Escola Superior de Agricultura "Luiz de Queiroz".
dc.creatorOLIVEIRA, A. A. de
dc.creatorGUIMARAES, L. J. M.
dc.creatorGUIMARÃES, C. T.
dc.creatorGUIMARAES, P. E. de O.
dc.creatorPINTO, M. de O.
dc.creatorPASTINA, M. M.
dc.creatorMARGARIDO, G. R. A.
dc.date2020-11-12T14:20:26Z
dc.date2020-11-12T14:20:26Z
dc.date2020-09-18
dc.date2020
dc.date.accessioned2026-07-07T05:24:36Z
dc.descriptionGenotyping-by-sequencing (GBS) datasets typically feature high rates of missingness and heterozygote undercalling, prompting the use of data imputation. We compared the accuracy of four imputation methods?NPUTE, Beagle, knearest neighbors imputation (KNNI), and fast inbreed line library imputation (FILLIN)?using GBS data of maize (Zea mays L.) inbred lines, genotyped using different multiplexing levels. Two strategies for SNP-calling and genotype imputation were evaluated. First, only lines genotyped through 96-plex were used for single nucleotide polymorphism (SNP) discovery, whereas both 96- and 384-plex were simultaneously used in the second strategy. In the first genotype imputation strategy, only the 96-plex lines were imputed, then the remaining lines were appended (96-plex-imputed plus 384-plex) and then imputed. In the second imputation strategy, we jointly imputed both datasets. We also investigated the impacts of including heterozygous genotypes and distinct rates of missing genotypes per locus. The different SNP-calling strategies and percentage of missing data did not substantially affect the imputation accuracy. However, the different imputation strategies showed a substantial effect. Generally, imputations were less accurate for heterozygotes. The scenario 96-plex-imputed plus 384-plex showed accuracies similar to the 96-plex scenario. Beagle and NPUTE produced the highest accuracies. Our results indicate that combining SNP-calling and imputation strategies can enhance genotyping in a cost-effective manner, resulting in higher imputation accuracies.
dc.identifierCrop Science, v. 60, n. 6, p. 3066-3082, 2020.
dc.identifierhttp://www.alice.cnptia.embrapa.br/alice/handle/doc/1125019
dc.identifier10.1002/csc2.20255
dc.identifier.urihttp://hdl.handle.net/123456789/490197
dc.languageeng
dc.rightsopenAccess
dc.subjectGenotipagem
dc.subjectImputação
dc.subjectGenética Vegetal
dc.subjectSeleção Genótipa
dc.subjectGenótipo
dc.subjectMelhoramento Genético Vegetal
dc.subjectMilho
dc.subjectPolimorfismo
dc.titleSingle nucleotide polymorphism calling and imputation strategies for cost-effective genotyping in a tropical maize breeding program.
dc.typeArtigo de periódico

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