A Multilayer Interactome Network Constructed in a Forest Poplar Population Mediates the Pleiotropic Control of Complex Traits
The effects of genes on physiological and biochemical processes are interrelated and interdependent; it is common for genes to express pleiotropic control of complex traits. However, the study of gene expression and participating pathways in vivo at the whole-genome level is challenging. Here, we de...
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Frontiers Media S.A.
2021
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oai:doaj.org-article:002f6ca2bd0b4c5cb5579ec7e20c98ab2021-11-12T06:20:18ZA Multilayer Interactome Network Constructed in a Forest Poplar Population Mediates the Pleiotropic Control of Complex Traits1664-802110.3389/fgene.2021.769688https://doaj.org/article/002f6ca2bd0b4c5cb5579ec7e20c98ab2021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fgene.2021.769688/fullhttps://doaj.org/toc/1664-8021The effects of genes on physiological and biochemical processes are interrelated and interdependent; it is common for genes to express pleiotropic control of complex traits. However, the study of gene expression and participating pathways in vivo at the whole-genome level is challenging. Here, we develop a coupled regulatory interaction differential equation to assess overall and independent genetic effects on trait growth. Based on evolutionary game theory and developmental modularity theory, we constructed multilayer, omnigenic networks of bidirectional, weighted, and positive or negative epistatic interactions using a forest poplar tree mapping population, which were organized into metagalactic, intergalactic, and local interstellar networks that describe layers of structure between modules, submodules, and individual single nucleotide polymorphisms, respectively. These multilayer interactomes enable the exploration of complex interactions between genes, and the analysis of not only differential expression of quantitative trait loci but also previously uncharacterized determinant SNPs, which are negatively regulated by other SNPs, based on the deconstruction of genetic effects to their component parts. Our research framework provides a tool to comprehend the pleiotropic control of complex traits and explores the inherent directional connections between genes in the structure of omnigenic networks.Huiying GongSheng ZhuXuli ZhuQing FangXiao-Yu ZhangRongling WuRongling WuFrontiers Media S.A.articleepistasismultilayer networkomnigenic modelpleiotropic controlsystem mappingvariable selectionGeneticsQH426-470ENFrontiers in Genetics, Vol 12 (2021) |
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epistasis multilayer network omnigenic model pleiotropic control system mapping variable selection Genetics QH426-470 |
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epistasis multilayer network omnigenic model pleiotropic control system mapping variable selection Genetics QH426-470 Huiying Gong Sheng Zhu Xuli Zhu Qing Fang Xiao-Yu Zhang Rongling Wu Rongling Wu A Multilayer Interactome Network Constructed in a Forest Poplar Population Mediates the Pleiotropic Control of Complex Traits |
| description |
The effects of genes on physiological and biochemical processes are interrelated and interdependent; it is common for genes to express pleiotropic control of complex traits. However, the study of gene expression and participating pathways in vivo at the whole-genome level is challenging. Here, we develop a coupled regulatory interaction differential equation to assess overall and independent genetic effects on trait growth. Based on evolutionary game theory and developmental modularity theory, we constructed multilayer, omnigenic networks of bidirectional, weighted, and positive or negative epistatic interactions using a forest poplar tree mapping population, which were organized into metagalactic, intergalactic, and local interstellar networks that describe layers of structure between modules, submodules, and individual single nucleotide polymorphisms, respectively. These multilayer interactomes enable the exploration of complex interactions between genes, and the analysis of not only differential expression of quantitative trait loci but also previously uncharacterized determinant SNPs, which are negatively regulated by other SNPs, based on the deconstruction of genetic effects to their component parts. Our research framework provides a tool to comprehend the pleiotropic control of complex traits and explores the inherent directional connections between genes in the structure of omnigenic networks. |
| format |
article |
| author |
Huiying Gong Sheng Zhu Xuli Zhu Qing Fang Xiao-Yu Zhang Rongling Wu Rongling Wu |
| author_facet |
Huiying Gong Sheng Zhu Xuli Zhu Qing Fang Xiao-Yu Zhang Rongling Wu Rongling Wu |
| author_sort |
Huiying Gong |
| title |
A Multilayer Interactome Network Constructed in a Forest Poplar Population Mediates the Pleiotropic Control of Complex Traits |
| title_short |
A Multilayer Interactome Network Constructed in a Forest Poplar Population Mediates the Pleiotropic Control of Complex Traits |
| title_full |
A Multilayer Interactome Network Constructed in a Forest Poplar Population Mediates the Pleiotropic Control of Complex Traits |
| title_fullStr |
A Multilayer Interactome Network Constructed in a Forest Poplar Population Mediates the Pleiotropic Control of Complex Traits |
| title_full_unstemmed |
A Multilayer Interactome Network Constructed in a Forest Poplar Population Mediates the Pleiotropic Control of Complex Traits |
| title_sort |
multilayer interactome network constructed in a forest poplar population mediates the pleiotropic control of complex traits |
| publisher |
Frontiers Media S.A. |
| publishDate |
2021 |
| url |
https://doaj.org/article/002f6ca2bd0b4c5cb5579ec7e20c98ab |
| work_keys_str_mv |
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