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Title: Pleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discovery

Biological organisms are complex systems that are composed of functional networks of interacting molecules and macro-molecules. 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 (i.e., the resistance of plants to degradation or deconstruction, which ultimately enables access to a plant's sugars) is a complex polygenic phenotype of high importance to biofuels initiatives. This study makes use of data derived from the re-sequenced genomes from over 800 different Populus trichocarpa genotypes in combination with metabolomic and pyMBMS data across this population, as well as co-expression and co-methylation networks in order to better understand the molecular interactions involved in recalcitrance, and identify target genes involved in lignin biosynthesis/degradation. A Lines Of Evidence (LOE) scoring system is developed to integrate the information in the different layers and quantify the number of lines of evidence linking genes to target functions. This new scoring system was applied to quantify the lines of evidence linking genes to lignin-related genes and phenotypes acrossmore » the network layers, and allowed for the generation of new hypotheses surrounding potential new candidate genes involved in lignin biosynthesis in P. trichocarpa, including various AGAMOUS-LIKE genes. Lastly, the resulting Genome Wide Association Study networks, integrated with Single Nucleotide Polymorphism (SNP) correlation, co-methylation, and co-expression networks through the LOE scores are proving to be a powerful approach to determine the pleiotropic and epistatic relationships underlying cellular functions and, as such, the molecular basis for complex phenotypes, such as recalcitrance.« less
Authors:
 [1] ;  [1] ;  [2] ;  [3] ;  [2] ;  [4] ;  [5] ;  [6] ;  [7] ;  [8] ;  [2] ;  [9] ;  [2] ;  [2] ;  [1]
  1. Univ. of Tennessee, Knoxville, TN (United States). Bredesen Center for Interdisciplinary Research and Graduate Education; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division; Univ. of Tennessee, Knoxville, TN (United States). Inst. of Agriculture, Dept. of Plant Sciences
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
  5. HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
  6. West Virginia Univ., Morgantown, WV (United States). Dept. of Biology
  7. National Renewable Energy Lab. (NREL), Golden, CO (United States)
  8. Univ. of Tennessee, Knoxville, TN (United States). Inst. of Agriculture, Dept. of Plant Sciences
  9. West Virginia Univ., Morgantown, WV (United States)
Publication Date:
Report Number(s):
NREL/JA-5100-71744
Journal ID: ISSN 2296-598X
Grant/Contract Number:
AC36-08GO28308; AC05-00OR22725; AC02-05CH11231
Type:
Published Article
Journal Name:
Frontiers in Energy Research
Additional Journal Information:
Journal Volume: 6; Journal ID: ISSN 2296-598X
Publisher:
Frontiers Research Foundation
Research Org:
National Renewable Energy Lab. (NREL), Golden, CO (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; multi-omic data layering; LOE scores; lines of evidence; GWAS; SNP correlation; association networks
OSTI Identifier:
1436886
Alternate Identifier(s):
OSTI ID: 1454749; OSTI ID: 1471945

Weighill, Deborah, Jones, Piet, Shah, Manesh, Ranjan, Priya, Muchero, Wellington, Schmutz, Jeremy, Sreedasyam, Avinash, Macaya-Sanz, David, Sykes, Robert, Zhao, Nan, Martin, Madhavi Z., DiFazio, Stephen, Tschaplinski, Timothy J., Tuskan, Gerald, and Jacobson, Daniel. Pleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discovery. United States: N. p., Web. doi:10.3389/fenrg.2018.00030.
Weighill, Deborah, Jones, Piet, Shah, Manesh, Ranjan, Priya, Muchero, Wellington, Schmutz, Jeremy, Sreedasyam, Avinash, Macaya-Sanz, David, Sykes, Robert, Zhao, Nan, Martin, Madhavi Z., DiFazio, Stephen, Tschaplinski, Timothy J., Tuskan, Gerald, & Jacobson, Daniel. Pleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discovery. United States. doi:10.3389/fenrg.2018.00030.
Weighill, Deborah, Jones, Piet, Shah, Manesh, Ranjan, Priya, Muchero, Wellington, Schmutz, Jeremy, Sreedasyam, Avinash, Macaya-Sanz, David, Sykes, Robert, Zhao, Nan, Martin, Madhavi Z., DiFazio, Stephen, Tschaplinski, Timothy J., Tuskan, Gerald, and Jacobson, Daniel. 2018. "Pleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discovery". United States. doi:10.3389/fenrg.2018.00030.
@article{osti_1436886,
title = {Pleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discovery},
author = {Weighill, Deborah and Jones, Piet and Shah, Manesh and Ranjan, Priya and Muchero, Wellington and Schmutz, Jeremy and Sreedasyam, Avinash and Macaya-Sanz, David and Sykes, Robert and Zhao, Nan and Martin, Madhavi Z. and DiFazio, Stephen and Tschaplinski, Timothy J. and Tuskan, Gerald and Jacobson, Daniel},
abstractNote = {Biological organisms are complex systems that are composed of functional networks of interacting molecules and macro-molecules. 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 (i.e., the resistance of plants to degradation or deconstruction, which ultimately enables access to a plant's sugars) is a complex polygenic phenotype of high importance to biofuels initiatives. This study makes use of data derived from the re-sequenced genomes from over 800 different Populus trichocarpa genotypes in combination with metabolomic and pyMBMS data across this population, as well as co-expression and co-methylation networks in order to better understand the molecular interactions involved in recalcitrance, and identify target genes involved in lignin biosynthesis/degradation. A Lines Of Evidence (LOE) scoring system is developed to integrate the information in the different layers and quantify the number of lines of evidence linking genes to target functions. This new scoring system was applied to quantify the lines of evidence linking genes to lignin-related genes and phenotypes across the network layers, and allowed for the generation of new hypotheses surrounding potential new candidate genes involved in lignin biosynthesis in P. trichocarpa, including various AGAMOUS-LIKE genes. Lastly, the resulting Genome Wide Association Study networks, integrated with Single Nucleotide Polymorphism (SNP) correlation, co-methylation, and co-expression networks through the LOE scores are proving to be a powerful approach to determine the pleiotropic and epistatic relationships underlying cellular functions and, as such, the molecular basis for complex phenotypes, such as recalcitrance.},
doi = {10.3389/fenrg.2018.00030},
journal = {Frontiers in Energy Research},
number = ,
volume = 6,
place = {United States},
year = {2018},
month = {5}
}

Works referenced in this record:

The MYB46 Transcription Factor Is a Direct Target of SND1 and Regulates Secondary Wall Biosynthesis in Arabidopsis
journal, September 2007
  • Zhong, R.; Richardson, E. A.; Ye, Z.-H.
  • The Plant Cell Online, Vol. 19, Issue 9, p. 2776-2792
  • DOI: 10.1105/tpc.107.053678

A 34K SNP genotyping array for Populus trichocarpa : Design, application to the study of natural populations and transferability to other Populus species
journal, January 2013
  • Geraldes, A.; DiFazio, S. P.; Slavov, G. T.
  • Molecular Ecology Resources, Vol. 13, Issue 2, p. 306-323
  • DOI: 10.1111/1755-0998.12056

The Path Forward for Biofuels and Biomaterials
journal, January 2006
  • Ragauskas, Arthur J.; Williams, Charlotte K.; Davison, Brian H.
  • Science, Vol. 311, Issue 5760, p. 484-489
  • DOI: 10.1126/science.1114736

Lignin Biosynthesis and Structure
journal, May 2010
  • Vanholme, R.; Demedts, B.; Morreel, K.
  • Plant Physiology, Vol. 153, Issue 3, p. 895-905
  • DOI: 10.1104/pp.110.155119

Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa
journal, August 2012

The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)
journal, September 2006