Linked Life Data

18765852

Source:http://linkedlifedata.com/resource/pubmed/id/18765852

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
12
pubmed:dateCreated
2008-11-27
pubmed:abstractText
Interplay between genetic and environmental factors, genotype x environment interactions (G x E), affect phenotypes of complex traits. A methodology for assessing G x E was investigated by detecting hygiene (low and high) environment-specific SNP subsets associated with broiler chicken mortality, followed by an examination of consistency between SNP subsets selected from the 2 environments. The trait was mean progeny mortality rate in 253 sire families, after adjusting records for nuisance effects affecting mortality at the individual bird level. Over 5,000 whole-genome SNP were narrowed down via a machine-learning (filter-wrapper) feature selection procedure applied to mortality rates in each of the 2 environments. For both early and late mortality, it was found that the selected SNP subsets differed across hygiene environments, in terms of either across-environment predictive ability or extent of linkage disequilibrium between the subsets. Reduction in predictive ability due to G x E was assessed by the ratio of 2 predicted residual sum of squares statistics, one associated with SNP selected from the same hygiene environment and the other associated with the SNP subset from a different environment. Reduction was 30 and 20% for early and late mortality, respectively. An extremely low level of linkage disequilibrium between SNP subsets selected under low and high hygiene also indicated G x E. Findings suggest that there may not be a universally optimal SNP subset for predicting mortality and that interactions between genome and environmental factors need to be considered in association analysis of complex traits.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Dec
pubmed:issn
1525-3163
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
86
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
3358-66
pubmed:meshHeading
pubmed:year
2008
pubmed:articleTitle
Marker-assisted assessment of genotype by environment interaction: a case study of single nucleotide polymorphism-mortality association in broilers in two hygiene environments.
pubmed:affiliation
Department of Animal Sciences, University of Wisconsin, Madison 53706, USA.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, Non-P.H.S.