Gene coexpression networks reveal key drivers of phenotypic divergence in porcine muscle.

Xiao Zhao,Qing-Xin Liu,Zhao-Yang Liu

doi:10.1186/s12864-015-1238-5

Abstract

BackgroundDomestication of the wild pig has led to obese and lean phenotype breeds, and evolutionary genome research has sought to identify the regulatory mechanisms underlying this phenotypic diversity. However, revealing the molecular mechanisms underlying muscle phenotype variation based on differentially expressed genes has proved to be difficult. To characterize the mechanisms regulating muscle phenotype variation under artificial selection, we aimed to provide an integrated view of genome organization by weighted gene coexpression network analysis.ResultsOur analysis was based on 20 publicly available next-generation sequencing datasets of lean and obese pig muscle generated from 10 developmental stages. The evolution of the constructed coexpression modules was examined using the genome resequencing data of 37 domestic pigs and 11 wild boars. Our results showed the regulation of muscle development might be more complex than had been previously acknowledged, and is regulated by the coordinated action of muscle, nerve and immunity related genes. Breed-specific modules that regulated muscle phenotype divergence were identified, and hundreds of hub genes with major roles in muscle development were determined to be responsible for key functional distinctions between breeds. Our evolutionary analysis showed that the role of changes in the coding sequence under positive selection in muscle phenotype divergence was minor.ConclusionsMuscle phenotype divergence was found to be regulated by the divergence of coexpression network modules under artificial selection, and not by changes in the coding sequence of genes. Our results present multiple lines of evidence suggesting links between modules and muscle phenotypes, and provide insights into the molecular bases of genome organization in muscle development and phenotype variation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1238-5) contains supplementary material, which is available to authorized users.

Highlights

Domestication of the wild pig has led to obese and lean phenotype breeds, and evolutionary genome research has sought to identify the regulatory mechanisms underlying this phenotypic diversity
HOXB7, HEY2 and PBX2 encode proteins that directly regulate muscle development [28,29,30], and ELOF1 encodes a conserved transcription elongation factor, which might regulate the basic transcription process of muscle genes [27]. These results suggested that the conserved coexpression network modules contained genes that were associated with the regulation of basic muscle development; implying that the key processes that regulate muscle development are similar in the two breeds
We identified significant differences in coexpression networks modules between the Lde and LT breeds, which may be responsible for divergence of the muscle phenotypes

Summary

Introduction

Domestication of the wild pig has led to obese and lean phenotype breeds, and evolutionary genome research has sought to identify the regulatory mechanisms underlying this phenotypic diversity. To characterize the mechanisms regulating muscle phenotype variation under artificial selection, we aimed to provide an integrated view of genome organization by weighted gene coexpression network analysis. More than 730 pig breeds or lines have undergone natural and artificial selection in different environments, especially catering to the distinct needs of humans, which has provided the large diversity of morphological and physiological characteristics that currently exist worldwide [5,9,10]. The identification of gene expression regulatory networks in pig breeds with distinct muscle phenotypes is necessary to understand how muscle has been modified during pig domestication

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