Exclusion and Genomic Relatedness Methods for Assignment of Parentage Using Genotyping-by-Sequencing Data

G3 : Genes - Genomes - Genetics
K G DoddsShannon M Clarke

Abstract

Genotypes are often used to assign parentage in agricultural and ecological settings. Sequencing can be used to obtain genotypes but does not provide unambiguous genotype calls, especially when sequencing depth is low in order to reduce costs. In that case, standard parentage analysis methods no longer apply. A strategy for using low-depth sequencing data for parentage assignment is developed here. It entails the use of relatedness estimates along with a metric termed excess mismatch rate which, for parent-offspring pairs or trios, is the difference between the observed mismatch rate and the rate expected under a model of inheritance and allele reads without error. When more than one putative parent has similar statistics, bootstrapping can provide a measure of the relatedness similarity. Putative parent-offspring trios can be further checked for consistency by comparing the offspring's estimated inbreeding to half the parent relatedness. Suitable thresholds are required for each metric. These methods were applied to a deer breeding operation consisting of two herds of different breeds. Relatedness estimates were more in line with expectation when the herds were analyzed separately than when combined, although this did not alte...Continue Reading

References

Jun 20, 1998·Molecular Ecology·T C MarshallJ M Pemberton
Nov 4, 2004·Molecular Phylogenetics and Evolution·Christian PitraP Colin Groves
Oct 15, 2008·PloS One·Nathan A BairdEric A Johnson
Nov 17, 2009·Nature Genetics·Sarah B NgMichael J Bamshad
Sep 30, 2010·Nature Reviews. Genetics·Joseph E PowellMichael E Goddard
May 17, 2011·PloS One·Robert J ElshireSharon E Mitchell
Nov 26, 2014·BMC Bioinformatics·Thorfinn KorneliussenRasmus Nielsen
Feb 28, 2015·GigaScience·Christopher C ChangJames J Lee
Nov 15, 2015·Plant Science : an International Journal of Experimental Plant Biology·Changsoo KimAndrew H Paterson
Dec 15, 2015·BMC Genomics·Ken G DoddsShannon M Clarke
Jan 6, 2016·Nature Reviews. Genetics·Kimberly R AndrewsPaul A Hohenlohe
Sep 21, 2016·Ecology and Evolution·Veronika Städele, Linda Vigilant
May 28, 2017·Genetics·Bruce S Weir, Jérôme Goudet
Oct 17, 2017·Nucleic Acids Research·Alina OttPatrick S Schnable
May 20, 2018·Genetics, Selection, Evolution : GSE·Kim E GrasheiTheo H E Meuwissen
Oct 18, 2018·Journal of Animal Science·Kirsty Lee MooreMike Coffey
Apr 9, 2019·Animal Genetics·T P BiltonS J Rowe

❮ Previous
Next ❯

Citations

Apr 22, 2020·G3 : Genes - Genomes - Genetics·Christos PalaiokostasDirk-Jan De Koning
Aug 8, 2020·Ecology and Evolution·Shi-Yi ChenWei Wang
Apr 4, 2021·Animals : an Open Access Journal From MDPI·Fotis Pappas, Christos Palaiokostas

❮ Previous
Next ❯

Methods Mentioned

BETA
genotyping
chip
PCR

Software Mentioned

PLINK
R

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.