A time-dependent genome-wide SNP-SNP interaction analysis of chicken body weight
Abstract Background The important property of the quantitative traits of model organisms is time-dependent. However, the methodology for investigating the genetic interaction network over time is still lacking. Our study aims to provide insights into the mechanistic basis of epistatic interactions a...
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doaj-80cae55fcd26485687aa333ef4b57ebc2020-11-25T03:33:34ZengBMCBMC Genomics1471-21642019-10-012011910.1186/s12864-019-6132-0A time-dependent genome-wide SNP-SNP interaction analysis of chicken body weightFang-Ge Li0Hui Li1College of Science, Northeast Agricultural UniversityKey Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural AffairsAbstract Background The important property of the quantitative traits of model organisms is time-dependent. However, the methodology for investigating the genetic interaction network over time is still lacking. Our study aims to provide insights into the mechanistic basis of epistatic interactions affecting the phenotypes of model organisms. Results We performed an exhaustive genome-wide search for significant SNP-SNP interactions associated with male birds’ body weight (BW) (n = 475) at multiple time points (day of hatch (BW0) and 1, 3, 5, and 7 weeks (BW1, BW3, BW5, and BW7)). Statistical analysis detected 67, four, and two significant SNP pairs associated with BW0, BW1, and BW3, respectively, with a significance threshold at 8.67 × 10− 12 (Bonferroni-adjusted: 1%). Meanwhile, no significant SNP pairs associated with BW5 and BW7 were found. The SNP-SNP interaction networks of BW0, BW1, and BW3 were built and annotated. Conclusions With strong annotated information and a strict significant threshold, SNP-SNP interactions underpinned the gene-gene interactions that might occur between chromosomes or within the same chromosome. Comparing and combing the networks, the results indicated that the genetic network for chicken body weight was dynamic and time-dependent.http://link.springer.com/article/10.1186/s12864-019-6132-0 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Fang-Ge Li Hui Li |
spellingShingle |
Fang-Ge Li Hui Li A time-dependent genome-wide SNP-SNP interaction analysis of chicken body weight BMC Genomics |
author_facet |
Fang-Ge Li Hui Li |
author_sort |
Fang-Ge Li |
title |
A time-dependent genome-wide SNP-SNP interaction analysis of chicken body weight |
title_short |
A time-dependent genome-wide SNP-SNP interaction analysis of chicken body weight |
title_full |
A time-dependent genome-wide SNP-SNP interaction analysis of chicken body weight |
title_fullStr |
A time-dependent genome-wide SNP-SNP interaction analysis of chicken body weight |
title_full_unstemmed |
A time-dependent genome-wide SNP-SNP interaction analysis of chicken body weight |
title_sort |
time-dependent genome-wide snp-snp interaction analysis of chicken body weight |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2019-10-01 |
description |
Abstract Background The important property of the quantitative traits of model organisms is time-dependent. However, the methodology for investigating the genetic interaction network over time is still lacking. Our study aims to provide insights into the mechanistic basis of epistatic interactions affecting the phenotypes of model organisms. Results We performed an exhaustive genome-wide search for significant SNP-SNP interactions associated with male birds’ body weight (BW) (n = 475) at multiple time points (day of hatch (BW0) and 1, 3, 5, and 7 weeks (BW1, BW3, BW5, and BW7)). Statistical analysis detected 67, four, and two significant SNP pairs associated with BW0, BW1, and BW3, respectively, with a significance threshold at 8.67 × 10− 12 (Bonferroni-adjusted: 1%). Meanwhile, no significant SNP pairs associated with BW5 and BW7 were found. The SNP-SNP interaction networks of BW0, BW1, and BW3 were built and annotated. Conclusions With strong annotated information and a strict significant threshold, SNP-SNP interactions underpinned the gene-gene interactions that might occur between chromosomes or within the same chromosome. Comparing and combing the networks, the results indicated that the genetic network for chicken body weight was dynamic and time-dependent. |
url |
http://link.springer.com/article/10.1186/s12864-019-6132-0 |
work_keys_str_mv |
AT fanggeli atimedependentgenomewidesnpsnpinteractionanalysisofchickenbodyweight AT huili atimedependentgenomewidesnpsnpinteractionanalysisofchickenbodyweight AT fanggeli timedependentgenomewidesnpsnpinteractionanalysisofchickenbodyweight AT huili timedependentgenomewidesnpsnpinteractionanalysisofchickenbodyweight |
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