A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep.

Accurate pedigree information is critical to animal breeding systems to ensure the highest rate of genetic gain and management of inbreeding. The abundance of available genomic data, together with development of high throughput genotyping platforms, means that single nucleotide polymorphisms (SNPs)...

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Main Authors: Shannon M Clarke, Hannah M Henry, Ken G Dodds, Timothy W D Jowett, Tim R Manley, Rayna M Anderson, John C McEwan
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2014-01-01
Series:PLoS ONE
Online Access:http://europepmc.org/articles/PMC3989167?pdf=render
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spelling doaj-16f44b6ad91a4436a81036dee47dc8552020-11-25T01:25:06ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0194e9339210.1371/journal.pone.0093392A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep.Shannon M ClarkeHannah M HenryKen G DoddsTimothy W D JowettTim R ManleyRayna M AndersonJohn C McEwanAccurate pedigree information is critical to animal breeding systems to ensure the highest rate of genetic gain and management of inbreeding. The abundance of available genomic data, together with development of high throughput genotyping platforms, means that single nucleotide polymorphisms (SNPs) are now the DNA marker of choice for genomic selection studies. Furthermore the superior qualities of SNPs compared to microsatellite markers allows for standardization between laboratories; a property that is crucial for developing an international set of markers for traceability studies. The objective of this study was to develop a high throughput SNP assay for use in the New Zealand sheep industry that gives accurate pedigree assignment and will allow a reduction in breeder input over lambing. This required two phases of development--firstly, a method of extracting quality DNA from ear-punch tissue performed in a high throughput cost efficient manner and secondly a SNP assay that has the ability to assign paternity to progeny resulting from mob mating. A likelihood based approach to infer paternity was used where sires with the highest LOD score (log of the ratio of the likelihood given parentage to likelihood given non-parentage) are assigned. An 84 "parentage SNP panel" was developed that assigned, on average, 99% of progeny to a sire in a problem where there were 3,000 progeny from 120 mob mated sires that included numerous half sib sires. In only 6% of those cases was there another sire with at least a 0.02 probability of paternity. Furthermore dam information (either recorded, or by genotyping possible dams) was absent, highlighting the SNP test's suitability for paternity testing. Utilization of this parentage SNP assay will allow implementation of progeny testing into large commercial farms where the improved accuracy of sire assignment and genetic evaluations will increase genetic gain in the sheep industry.http://europepmc.org/articles/PMC3989167?pdf=render
collection DOAJ
language English
format Article
sources DOAJ
author Shannon M Clarke
Hannah M Henry
Ken G Dodds
Timothy W D Jowett
Tim R Manley
Rayna M Anderson
John C McEwan
spellingShingle Shannon M Clarke
Hannah M Henry
Ken G Dodds
Timothy W D Jowett
Tim R Manley
Rayna M Anderson
John C McEwan
A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep.
PLoS ONE
author_facet Shannon M Clarke
Hannah M Henry
Ken G Dodds
Timothy W D Jowett
Tim R Manley
Rayna M Anderson
John C McEwan
author_sort Shannon M Clarke
title A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep.
title_short A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep.
title_full A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep.
title_fullStr A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep.
title_full_unstemmed A high throughput single nucleotide polymorphism multiplex assay for parentage assignment in New Zealand sheep.
title_sort high throughput single nucleotide polymorphism multiplex assay for parentage assignment in new zealand sheep.
publisher Public Library of Science (PLoS)
series PLoS ONE
issn 1932-6203
publishDate 2014-01-01
description Accurate pedigree information is critical to animal breeding systems to ensure the highest rate of genetic gain and management of inbreeding. The abundance of available genomic data, together with development of high throughput genotyping platforms, means that single nucleotide polymorphisms (SNPs) are now the DNA marker of choice for genomic selection studies. Furthermore the superior qualities of SNPs compared to microsatellite markers allows for standardization between laboratories; a property that is crucial for developing an international set of markers for traceability studies. The objective of this study was to develop a high throughput SNP assay for use in the New Zealand sheep industry that gives accurate pedigree assignment and will allow a reduction in breeder input over lambing. This required two phases of development--firstly, a method of extracting quality DNA from ear-punch tissue performed in a high throughput cost efficient manner and secondly a SNP assay that has the ability to assign paternity to progeny resulting from mob mating. A likelihood based approach to infer paternity was used where sires with the highest LOD score (log of the ratio of the likelihood given parentage to likelihood given non-parentage) are assigned. An 84 "parentage SNP panel" was developed that assigned, on average, 99% of progeny to a sire in a problem where there were 3,000 progeny from 120 mob mated sires that included numerous half sib sires. In only 6% of those cases was there another sire with at least a 0.02 probability of paternity. Furthermore dam information (either recorded, or by genotyping possible dams) was absent, highlighting the SNP test's suitability for paternity testing. Utilization of this parentage SNP assay will allow implementation of progeny testing into large commercial farms where the improved accuracy of sire assignment and genetic evaluations will increase genetic gain in the sheep industry.
url http://europepmc.org/articles/PMC3989167?pdf=render
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