Epistatic effects on abdominal fat content in chickens: results from a genome-wide SNP-SNP interaction analysis.
We performed a pairwise epistatic interaction test using the chicken 60 K single nucleotide polymorphism (SNP) chip for the 11(th) generation of the Northeast Agricultural University broiler lines divergently selected for abdominal fat content. A linear mixed model was used to test two dimensions of...
Main Authors: | , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Public Library of Science (PLoS)
2013-01-01
|
Series: | PLoS ONE |
Online Access: | http://europepmc.org/articles/PMC3855290?pdf=render |
id |
doaj-aa4041e4114b47b1ade4f40ac010755d |
---|---|
record_format |
Article |
spelling |
doaj-aa4041e4114b47b1ade4f40ac010755d2020-11-25T01:18:49ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-01812e8152010.1371/journal.pone.0081520Epistatic effects on abdominal fat content in chickens: results from a genome-wide SNP-SNP interaction analysis.Fangge LiGuo HuHui ZhangShouzhi WangZhipeng WangHui LiWe performed a pairwise epistatic interaction test using the chicken 60 K single nucleotide polymorphism (SNP) chip for the 11(th) generation of the Northeast Agricultural University broiler lines divergently selected for abdominal fat content. A linear mixed model was used to test two dimensions of SNP interactions affecting abdominal fat weight. With a threshold of P<1.2×10(-11) by a Bonferroni 5% correction, 52 pairs of SNPs were detected, comprising 45 pairs showing an Additive×Additive and seven pairs showing an Additive×Dominance epistatic effect. The contribution rates of significant epistatic interactive SNPs ranged from 0.62% to 1.54%, with 47 pairs contributing more than 1%. The SNP-SNP network affecting abdominal fat weight constructed using the significant SNP pairs was analyzed, estimated and annotated. On the basis of the network's features, SNPs Gga_rs14303341 and Gga_rs14988623 at the center of the subnet should be important nodes, and an interaction between GGAZ and GGA8 was suggested. Twenty-two quantitative trait loci, 97 genes (including nine non-coding genes), and 50 pathways were annotated on the epistatic interactive SNP-SNP network. The results of the present study provide insights into the genetic architecture underlying broiler chicken abdominal fat weight.http://europepmc.org/articles/PMC3855290?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Fangge Li Guo Hu Hui Zhang Shouzhi Wang Zhipeng Wang Hui Li |
spellingShingle |
Fangge Li Guo Hu Hui Zhang Shouzhi Wang Zhipeng Wang Hui Li Epistatic effects on abdominal fat content in chickens: results from a genome-wide SNP-SNP interaction analysis. PLoS ONE |
author_facet |
Fangge Li Guo Hu Hui Zhang Shouzhi Wang Zhipeng Wang Hui Li |
author_sort |
Fangge Li |
title |
Epistatic effects on abdominal fat content in chickens: results from a genome-wide SNP-SNP interaction analysis. |
title_short |
Epistatic effects on abdominal fat content in chickens: results from a genome-wide SNP-SNP interaction analysis. |
title_full |
Epistatic effects on abdominal fat content in chickens: results from a genome-wide SNP-SNP interaction analysis. |
title_fullStr |
Epistatic effects on abdominal fat content in chickens: results from a genome-wide SNP-SNP interaction analysis. |
title_full_unstemmed |
Epistatic effects on abdominal fat content in chickens: results from a genome-wide SNP-SNP interaction analysis. |
title_sort |
epistatic effects on abdominal fat content in chickens: results from a genome-wide snp-snp interaction analysis. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2013-01-01 |
description |
We performed a pairwise epistatic interaction test using the chicken 60 K single nucleotide polymorphism (SNP) chip for the 11(th) generation of the Northeast Agricultural University broiler lines divergently selected for abdominal fat content. A linear mixed model was used to test two dimensions of SNP interactions affecting abdominal fat weight. With a threshold of P<1.2×10(-11) by a Bonferroni 5% correction, 52 pairs of SNPs were detected, comprising 45 pairs showing an Additive×Additive and seven pairs showing an Additive×Dominance epistatic effect. The contribution rates of significant epistatic interactive SNPs ranged from 0.62% to 1.54%, with 47 pairs contributing more than 1%. The SNP-SNP network affecting abdominal fat weight constructed using the significant SNP pairs was analyzed, estimated and annotated. On the basis of the network's features, SNPs Gga_rs14303341 and Gga_rs14988623 at the center of the subnet should be important nodes, and an interaction between GGAZ and GGA8 was suggested. Twenty-two quantitative trait loci, 97 genes (including nine non-coding genes), and 50 pathways were annotated on the epistatic interactive SNP-SNP network. The results of the present study provide insights into the genetic architecture underlying broiler chicken abdominal fat weight. |
url |
http://europepmc.org/articles/PMC3855290?pdf=render |
work_keys_str_mv |
AT fanggeli epistaticeffectsonabdominalfatcontentinchickensresultsfromagenomewidesnpsnpinteractionanalysis AT guohu epistaticeffectsonabdominalfatcontentinchickensresultsfromagenomewidesnpsnpinteractionanalysis AT huizhang epistaticeffectsonabdominalfatcontentinchickensresultsfromagenomewidesnpsnpinteractionanalysis AT shouzhiwang epistaticeffectsonabdominalfatcontentinchickensresultsfromagenomewidesnpsnpinteractionanalysis AT zhipengwang epistaticeffectsonabdominalfatcontentinchickensresultsfromagenomewidesnpsnpinteractionanalysis AT huili epistaticeffectsonabdominalfatcontentinchickensresultsfromagenomewidesnpsnpinteractionanalysis |
_version_ |
1725140117514878976 |