Using genomic relationship likelihood for parentage assignment

Genetics, Selection, Evolution : GSE
Kim E GrasheiTheo H E Meuwissen

Abstract

Parentage assignment is usually based on a limited number of unlinked, independent genomic markers (microsatellites, low-density single nucleotide polymorphisms (SNPs), etc.). Classical methods for parentage assignment are exclusion-based (i.e. based on loci that violate Mendelian inheritance) or likelihood-based, assuming independent inheritance of loci. For true parent-offspring relations, genotyping errors cause apparent violations of Mendelian inheritance. Thus, the maximum proportion of such violations must be determined, which is complicated by variable call- and genotype error rates among loci and individuals. Recently, genotyping using high-density SNP chips has become available at lower cost and is increasingly used in genetics research and breeding programs. However, dense SNPs are not independently inherited, violating the assumptions of the likelihood-based methods. Hence, parentage assignment usually assumes a maximum proportion of exclusions, or applies likelihood-based methods on a smaller subset of independent markers. Our aim was to develop a fast and accurate trio parentage assignment method for dense SNP data without prior genotyping error- or call rate knowledge among loci and individuals. This genomic relat...Continue Reading

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Citations

Oct 18, 2018·Journal of Animal Science·Kirsty Lee MooreMike Coffey
Dec 24, 2018·Molecular Ecology·Sarah P Flanagan, Adam G Jones
Aug 7, 2019·G3 : Genes - Genomes - Genetics·Ken G DoddsShannon M Clarke
Oct 15, 2019·Molecular Ecology Resources·Ronan GriotMarc Vandeputte
Apr 18, 2019·Genetics, Selection, Evolution : GSE·Hanne DvergedalGunnar Klemetsdal
Mar 20, 2020·Genetics, Selection, Evolution : GSE·Kim Erik GrasheiTheo H E Meuwissen
Aug 14, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Jared CrainJesse Poland
Dec 15, 2018·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Andrew WhalenJohn M Hickey
Sep 10, 2021·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·Ryota KomiyaMasahiro Satoh
Nov 9, 2021·Frontiers in Plant Science·Felipe Bitencourt MartinsAnete Pereira de Souza

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Methods Mentioned

BETA
chip
genotyping

Software Mentioned

Colony2
GRL
R
Linux
QMSim
custom

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