Gene coexpression networks reveal key drivers of phenotypic divergence in porcine muscle.
Gene coexpression networks reveal key drivers of phenotypic divergence in porcine muscle.
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基因共表达网络揭示了猪肌肉表型差异的关键驱动因素
DOI：
10.1186/s12864-015-1238-5
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发表时间：
2015-02-05
期刊：
影响因子：
4.4
通讯作者：
Liu QX
中科院分区：
文献类型：
--
作者：
Zhao X;Liu ZY;Liu QX
背景野生猪的驯化导致了肥胖和瘦的表型品种，进化基因组研究试图确定这种表型多样性背后的调控机制。然而，揭示肌肉表型变异的基础上差异表达基因的分子机制已被证明是困难的。为了表征调节肌肉表型变异的机制，人工选择下，我们的目的是提供一个综合的基因组组织加权基因共表达网络analysis.ResultsOur分析的基础上，20个公开的下一代测序数据集的瘦和肥胖的猪肌肉产生的10个发展阶段。利用37头家猪和11头野猪的基因组重测序数据对构建的共表达模块进行了进化分析。我们的研究结果表明，肌肉发育的调控可能比以前认识到的更为复杂，并且受到肌肉、神经和免疫相关基因的协调作用。确定了调节肌肉表型分化的品种特异性模块，并确定了数百个在肌肉发育中起主要作用的枢纽基因负责品种之间的关键功能差异。我们的进化分析表明，在肌肉表型divergence.ConclusionsMuscle表型分歧的积极选择下的编码序列的变化的作用是minor的分歧被发现由人工选择下的共表达网络模块的分歧，而不是由基因的编码序列的变化。我们的研究结果提出了多条证据，表明模块和肌肉表型之间的联系，并提供了肌肉发育和表型变异的基因组组织的分子基础的见解。
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.
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