A time-dependent genome-wide SNP-SNP interaction analysis of chicken body weight

Fang-Ge Li,Hui Li

doi:10.1186/s12864-019-6132-0

Abstract

BackgroundThe 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.ResultsWe 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.ConclusionsWith 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.

Highlights

The important property of the quantitative traits of model organisms is time-dependent
Carlborg et al revealed that an apparently major locus for chicken growth belonged to a genetic network of four interacting loci, which indicates that epistatic interactions between genes were important for quantitative traits in chicken [9]
Single nucleotide polymorphism (SNP) genotyping and phenotypic values After quality control, the following was included in this study: a total of 48,152 SNPs on 28 autosomes, the Z chromosome, linkage groups, and 672 SNPs not assigned to any chromosomes in chickens (Table 1)

Summary

Introduction

The important property of the quantitative traits of model organisms is time-dependent. Our study aims to provide insights into the mechanistic basis of epistatic interactions affecting the phenotypes of model organisms. Epistatic interactions (non-linear interactions between segregating loci) are gaining attention in contemporary biology, yet their role in the genetic architecture of quantitative traits is still obscure and controversial. Studies on fruit fly (Drosophila melanogaster), yeast (Saccharomyces cerevisiae), mouse (Mus musculus), thale cress (Arabidopsis thaliana), maize (Zea mays), and human (Homo sapiens) demonstrate that epistasis is pervasive and is an important factor in determining the variation of quantitative phenotypes [1,2,3,4]. Our previous studies detected epistatic interactions and demonstrated that they could affect the variation in chicken phenotypes [10,11,12].

Methods

Results

Discussion

Conclusion