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dc.creatorHamilton, M.G.en_US
dc.date.accessioned2021-04-05T07:22:18Z
dc.date.available2021-04-05T07:22:18Z
dc.date.issued2021
dc.identifier.citationHamilton, M. G. (2021). Maximum likelihood parentage assignment using quantitative genotypes. Heredity, online 10 Mar https://doi.org/10.1038/s41437-021-00421-0en_US
dc.identifier.issn0018-067Xen_US
dc.identifier.urihttps://hdl.handle.net/20.500.12348/4585
dc.description.abstractThe cost of parentage assignment precludes its application in many selective breeding programs and molecular ecology studies, and/or limits the circumstances or number of individuals to which it is applied. Pooling samples from more than one individual, and using appropriate genetic markers and algorithms to determine parental contributions to pools, is one means of reducing the cost of parentage assignment. This paper describes and validates a novel maximum likelihood (ML) parentage assignment method, that can be used to accurately assign parentage to pooled samples of multiple individuals – previously published ML methods are applicable to samples of single individuals only – using low-density single nucleotide polymorphism (SNP) ‘quantitative’ (also referred to as ‘continuous’) genotype data.. It is demonstrated with simulated data that, when applied to pools, this ‘quantitative maximum likelihood’ method assigns parentage with greater accuracy than established maximum likelihood parentage assignment approaches, which rely on accurate discrete genotype calls; exclusion methods; and estimating parental contributions to pools by solving the weighted least squares problem. Quantitative maximum likelihood can be applied to pools generated using either a ‘pooling-for-individual-parentage-assignment’ approach, whereby each individual in a pool is tagged or traceable and from a known and mutually exclusive set of possible parents; or a ‘pooling-by-phenotype’ approach, whereby individuals of the same, or similar, phenotype/s are pooled. Although computationally intensive when applied to large pools, quantitative maximum likelihood has the potential to substantially reduce the cost of parentage assignment, even if applied to pools comprised of few individuals.en_US
dc.formatPDFen_US
dc.languageenen_US
dc.publisherSpringer Natureen_US
dc.rightsCC-BY-NC-ND-4.0en_US
dc.sourceHeredity;(2021)en_US
dc.subjectsingle nucleotide polymorphism (snp)en_US
dc.subjectdna poolingen_US
dc.subjectcontinuous genotypeen_US
dc.subjectpedigree reconstructionen_US
dc.subjectparentage analysisen_US
dc.subjectgene poolsen_US
dc.titleMaximum likelihood parentage assignment using quantitative genotypesen_US
dc.typeJournal Articleen_US
cg.contributor.crpFISHen_US
cg.contributor.funderCGIAR System Organizationen_US
cg.coverage.regionGlobalen_US
cg.subject.agrovocaquacultureen_US
cg.subject.agrovocsingle nucleotide polymorphismen_US
cg.subject.agrovocgenotypesen_US
cg.subject.agrovocgenetic markersen_US
cg.subject.agrovocgeneticsen_US
cg.subject.agrovocselective breedingen_US
cg.subject.agrovocquantitative geneticsen_US
cg.contributor.affiliationWorldFishen_US
cg.identifier.statusTimeless limited accessen_US
cg.identifier.ISIindexedISI indexeden_US
cg.contribution.worldfishauthorHamilton, M.G.en_US
cg.description.themeSustainable aquacultureen_US
dc.identifier.doihttps://dx.doi.org/10.1038/s41437-021-00421-0en_US
cg.creator.idMatthew Gray Hamilton: 0000-0001-8098-8845en_US


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