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Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing

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Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
IBCN, bioenergy, cell wall, lignocellulosic biomass, network-based data integration, systems genetics, CELLULOSE MICROFIBRIL ORIENTATION, LOCUS QTL ANALYSIS, POPULUS-TRICHOCARPA, EUCALYPTUS-GRANDIS, NATURAL-POPULATIONS, COMPLEX TRAITS, WOOD FORMATION, BIOSYNTHESIS, GENOME, ARABIDOPSIS

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Citation

Please use this url to cite or link to this publication:

Chicago
Mizrachi, Eshchar, Lieven Verbeke, Nanette Christie, Ana Carolina Elisa Fierro Gutierrez, Shawn D Mansfield, Mark F Davis, Erica Gjersing, et al. 2017. “Network-based Integration of Systems Genetics Data Reveals Pathways Associated with Lignocellulosic Biomass Accumulation and Processing.” Proceedings of the National Academy of Sciences of the United States of America 114 (5): 1195–1200.
APA
Mizrachi, E., Verbeke, L., Christie, N., Fierro Gutierrez, A. C. E., Mansfield, S. D., Davis, M. F., Gjersing, E., et al. (2017). Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(5), 1195–1200.
Vancouver
1.
Mizrachi E, Verbeke L, Christie N, Fierro Gutierrez ACE, Mansfield SD, Davis MF, et al. Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2017;114(5):1195–200.
MLA
Mizrachi, Eshchar, Lieven Verbeke, Nanette Christie, et al. “Network-based Integration of Systems Genetics Data Reveals Pathways Associated with Lignocellulosic Biomass Accumulation and Processing.” PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 114.5 (2017): 1195–1200. Print.
@article{8510463,
  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.},
  author       = {Mizrachi, Eshchar and Verbeke, Lieven and Christie, Nanette and Fierro Gutierrez, Ana Carolina Elisa and Mansfield, Shawn D and Davis, Mark F and Gjersing, Erica and Tuskan, Gerald A and Van Montagu, Marc and Van de Peer, Yves and Marchal, Kathleen and Myburg, Alexander A},
  issn         = {0027-8424},
  journal      = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA},
  keyword      = {IBCN,bioenergy,cell wall,lignocellulosic biomass,network-based data integration,systems genetics,CELLULOSE MICROFIBRIL ORIENTATION,LOCUS QTL ANALYSIS,POPULUS-TRICHOCARPA,EUCALYPTUS-GRANDIS,NATURAL-POPULATIONS,COMPLEX TRAITS,WOOD FORMATION,BIOSYNTHESIS,GENOME,ARABIDOPSIS},
  language     = {eng},
  number       = {5},
  pages        = {1195--1200},
  title        = {Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing},
  url          = {http://dx.doi.org/10.1073/pnas.1620119114},
  volume       = {114},
  year         = {2017},
}

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