title: Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing.
abstract: As a consequence of their remarkable adaptability, fast growth, and superior wood properties, eucalypt tree plantations have emerged as key renewable feedstocks (over 20 million ha globally) for the production of pulp, paper, bioenergy, and other lignocellulosic products. However, most biomass properties such as growth, wood density, and wood chemistry are complex traits that are hard to improve in long-lived perennials. Systems genetics, a process of harnessing multiple levels of component trait information (e.g., transcript, protein, and metabolite variation) in populations that vary in complex traits, has proven effective for dissecting the genetics and biology of such traits. We have applied a network-based data integration (NBDI) method for a systems-level analysis of genes, processes and pathways underlying biomass and bioenergy-related traits using a segregating Eucalyptus hybrid population. We show that the integrative approach can link biologically meaningful sets of genes to complex traits and at the same time reveal the molecular basis of trait variation. Gene sets identified for related woody biomass traits were found to share regulatory loci, cluster in network neighborhoods, and exhibit enrichment for molecular functions such as xylan metabolism and cell wall development. These findings offer a framework for identifying the molecular underpinnings of complex biomass and bioprocessing-related traits. A more thorough understanding of the molecular basis of plant biomass traits should provide additional opportunities for the establishment of a sustainable bio-based economy.
authors.affiliation: Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa; mamon@psb.ugent.be eshchar.mizrachi@fabi.up.ac.za kathleen.marchal@intec.ugent.be zander.myburg@fabi.up.ac.za.|Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa.
authors.forename: Eshchar
authors.initials: E
authors.lastname: Mizrachi
authors.affiliation: Department of Information Technology, Ghent University, iMinds, 9052 Gent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.
authors.forename: Lieven
authors.identifier: 0000-0003-1909-8119
authors.initials: L
authors.lastname: Verbeke
authors.affiliation: Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa.|Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa.
authors.forename: Nanette
authors.initials: N
authors.lastname: Christie
authors.affiliation: Department of Information Technology, Ghent University, iMinds, 9052 Gent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.
authors.forename: Ana C
authors.initials: AC
authors.lastname: Fierro
authors.affiliation: Department of Wood Science, University of British Columbia, Vancouver, BC, Canada V6T 1Z4.
authors.forename: Shawn D
authors.initials: SD
authors.lastname: Mansfield
authors.affiliation: Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401.
authors.forename: Mark F
authors.initials: MF
authors.lastname: Davis
authors.affiliation: Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401.
authors.forename: Erica
authors.initials: E
authors.lastname: Gjersing
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831.
authors.forename: Gerald A
authors.initials: GA
authors.lastname: Tuskan
authors.affiliation: Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium; mamon@psb.ugent.be eshchar.mizrachi@fabi.up.ac.za kathleen.marchal@intec.ugent.be zander.myburg@fabi.up.ac.za.|Department of Plant Systems Biology, VIB, 9052 Gent, Belgium.
authors.forename: Marc
authors.initials: M
authors.lastname: Van Montagu
authors.affiliation: Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa.|Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.|Department of Plant Systems Biology, VIB, 9052 Gent, Belgium.
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.affiliation: Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa; mamon@psb.ugent.be eshchar.mizrachi@fabi.up.ac.za kathleen.marchal@intec.ugent.be zander.myburg@fabi.up.ac.za.|Department of Information Technology, Ghent University, iMinds, 9052 Gent, Belgium.|Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.
authors.forename: Kathleen
authors.initials: K
authors.lastname: Marchal
authors.affiliation: Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0028, South Africa; mamon@psb.ugent.be eshchar.mizrachi@fabi.up.ac.za kathleen.marchal@intec.ugent.be zander.myburg@fabi.up.ac.za.|Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa.
authors.forename: Alexander A
authors.initials: AA
authors.lastname: Myburg
mesh_terms: D018533:Biomass; D002244:Carbon / Q000378:metabolism; D002473:Cell Wall / Q000378:metabolism; D002874:Chromosome Mapping; D003433:Crosses, Genetic; D005052:Eucalyptus / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D006824:Hybridization, Genetic; D008031:Lignin / Q000378:metabolism*; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D008957:Models, Genetic; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D040641:Quantitative Trait Loci; D014934:Wood / Q000378:metabolism
chemical_list: D010940:Plant Proteins; C036909:lignocellulose; D002244:Carbon; D008031:Lignin
keywords: bioenergy; cell wall; lignocellulosic biomass; network-based data integration; systems genetics