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dc.contributorGorjanc, Gregoren_US
dc.contributorVarshney, Rajeeven_US
dc.contributorNettelblad, Carlen_US
dc.creatorHickey, Johnen_US
dc.date2015-12-29en_US
dc.date.accessioned2017-05-15T21:21:15Z
dc.date.available2017-05-15T21:21:15Z
dc.identifierhttps://mel.cgiar.org/reporting/download/hash/aYq5fxAXen_US
dc.identifier.citationJohn Hickey, Gregor Gorjanc, Rajeev Varshney, Carl Nettelblad. (29/12/2015). Imputation of single nucleotide polymorphism genotypes in biparental, backcross, and topcross populations with a hidden Markov model. Crop Science, 55, pp. 1-13.en_US
dc.identifier.urihttps://hdl.handle.net/20.500.11766/7007
dc.description.abstractGenomic selection offers great potential to increase the rate of genetic improvement in plant breeding programs. The ability to accurately impute missing genotypes for a large number of individuals, screened with low marker density, at low cost is crucial for achieving this. In this research an existing general algorithm for tracing allele inheritance in known pedigrees was modified to enable genotype imputation in specific crosses (biparental, backcross, and topcross) that are common in plant breeding. The extension was tested with a series of representative simulated examples of these crosses. The results show success of imputation is affected by many factors including the number of low-density markers per cM, level of inbreeding or intercrossing of the individuals to have genotypes imputed, level of inbreeding of the parents of a cross, and genome length; but not by the number of high-density markers or by the interaction between the genome length and the number of low-density markers. With as few as one or two markers per 20 cM genotype imputation was successful when parents were inbred. Therefore, genotyping strategies in which inbred parents of a cross are genotyped at high-density and their descendants are genotyped with 200 to 400 markers genome wide may be cost effective and useful in practical plant breeding programs that utilize genomic selection.en_US
dc.formatPDFen_US
dc.languageenen_US
dc.publisherCrop Science Society of Americaen_US
dc.rightsCC-BY-NC-4.0en_US
dc.sourceCrop Science;55,(2015) Pagination 1,13en_US
dc.subjecthidden markov modelsen_US
dc.titleImputation of single nucleotide polymorphism genotypes in biparental, backcross, and topcross populations with a hidden Markov modelen_US
dc.typeJournal Articleen_US
cg.subject.agrovocplant breedingen_US
cg.subject.agrovocplant genetic resourcesen_US
cg.subject.agrovocgenomic selectionen_US
cg.subject.agrovocgenetic improvementen_US
cg.subject.agrovocgenotypesen_US
cg.contributor.centerUniversity of Edinburgh, College of Medicine & Veterinary Medicine, Royal (Dick) School of Veterinary Studies - ED - CoM&VM - VETen_US
cg.contributor.centerUniversity of Edinburgh - EDen_US
cg.contributor.centerInternational Crops Research Institute for the Semi-Arid Tropics - ICRISATen_US
cg.contributor.centerSwedish University of Agricultural Sciences - SLUen_US
cg.contributor.crpCGIAR Research Program on Grain Legumes - GLen_US
cg.contributor.funderNot Applicableen_US
cg.coverage.regionGlobalen_US
cg.contactjohn.hickey@roslin.ed.ac.uken_US
cg.identifier.doihttps://dx.doi.org/10.2135/cropsci2014.09.0648en_US
dc.identifier.statusOpen accessen_US
mel.impact-factor1.550en_US


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