2018
DOI: 10.1101/267997
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Pleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discovery

Abstract: Biological organisms are complex systems that are composed of functional networks of interacting molecules and macromolecules. Complex phenotypes are the result of orchestrated, hierarchical, heterogeneous collections of expressed genomic variants. However, the effects of these variants are the result of historic selective pressure and current environmental and epigenetic signals, and, as such, their co-occurrence can be seen as genome-wide correlations in a number of different manners. Biomass recalcitrance (… Show more

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Cited by 11 publications
(28 citation statements)
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“…Networks of co-expressed genes were based on RNA-seq data for 14 tissue types from the Phytozome Populus gene atlas. Networks of associated metabolites were based on GWAS for the same population that was used here (Weighill et al, 2018). (2019)…”
Section: Categorymentioning
confidence: 99%
“…Networks of co-expressed genes were based on RNA-seq data for 14 tissue types from the Phytozome Populus gene atlas. Networks of associated metabolites were based on GWAS for the same population that was used here (Weighill et al, 2018). (2019)…”
Section: Categorymentioning
confidence: 99%
“…Partial least squares (PLS) models have been used to predict composition based on data collected from wet chemistry and other spectroscopic methods (22,24,32). One study used features in py-MBMS spectra as phenotypes to identify genes related to lignin biosynthesis in poplar using a novel multi-omic "lines of evidence" approach (33). Ions and spectral features in the context of cell wall chemistry have also been used as traits in conjunction with genetic mapping approaches and heritability studies of poplar and other hardwoods originating from various genetic backgrounds and growing conditions (1,3,34).…”
Section: Introductionmentioning
confidence: 99%
“…Given the scale of the current study, it was not possible to link individual plant genes or traits with fungal community assembly under priority effects. However, many layers of phenotypic and genotypic data have been collected for more than 1000 re-sequenced P. trichocarpa genotypes (Tuskan et al, 2006;Weighill et al, 2018). In the future, research with the P. trichocarpa foliar microbiome could leverage these rich data sets to link host traits to priority effects during microbiome assembly.…”
Section: Limitations and Future Directionsmentioning
confidence: 99%