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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 biomassmore » and bioprocessing-related traits. Furthermore, 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.« less

Authors:
 [1]; ORCiD logo [2];  [1];  [2];  [3];  [4];  [4];  [5];  [6];  [7];  [8];  [1]
  1. Univ. of Pretoria, Pretoria (South Africa)
  2. Ghent Univ., Gent (Belgium)
  3. Univ. of British Columbia, Vancouver, BC (Canada)
  4. National Renewable Energy Lab. (NREL), Golden, CO (United States)
  5. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  6. Ghent Univ., Gent (Belgium); VIB, Gent (Belgium)
  7. Univ. of Pretoria, Pretoria (South Africa); Ghent Univ., Gent (Belgium); VIB, Gent (Belgium)
  8. Univ. of Pretoria, Pretoria (South Africa); Ghent Univ., Gent (Belgium)
Publication Date:
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)
OSTI Identifier:
1343087
Alternate Identifier(s):
OSTI ID: 1394604
Report Number(s):
NREL/JA-2700-67898
Journal ID: ISSN 0027-8424
Grant/Contract Number:  
AC36-08GO28308; AC05-00OR22725
Resource Type:
Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 114; Journal Issue: 5; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; systems genetics; lignocellulosic biomass; cell wall; bioenergy; network-based data integration

Citation Formats

Mizrachi, Eshchar, Verbeke, Lieven, Christie, Nanette, Fierro, Ana C., Mansfield, Shawn D., Davis, Mark F., Gjersing, Erica, Tuskan, Gerald A., Van Montagu, Marc, Van de Peer, Yves, Marchal, Kathleen, and Myburg, Alexander A. Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing. United States: N. p., 2017. Web. doi:10.1073/pnas.1620119114.
Mizrachi, Eshchar, Verbeke, Lieven, Christie, Nanette, Fierro, Ana C., Mansfield, Shawn D., Davis, Mark F., Gjersing, Erica, Tuskan, Gerald A., Van Montagu, Marc, Van de Peer, Yves, Marchal, Kathleen, & Myburg, Alexander A. Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing. United States. doi:10.1073/pnas.1620119114.
Mizrachi, Eshchar, Verbeke, Lieven, Christie, Nanette, Fierro, Ana C., Mansfield, Shawn D., Davis, Mark F., Gjersing, Erica, Tuskan, Gerald A., Van Montagu, Marc, Van de Peer, Yves, Marchal, Kathleen, and Myburg, Alexander A. Tue . "Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing". United States. doi:10.1073/pnas.1620119114. https://www.osti.gov/servlets/purl/1343087.
@article{osti_1343087,
title = {Network-based integration of systems genetics data reveals pathways associated with lignocellulosic biomass accumulation and processing},
author = {Mizrachi, Eshchar and Verbeke, Lieven and Christie, Nanette and Fierro, Ana C. 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.},
abstractNote = {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. Furthermore, 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.},
doi = {10.1073/pnas.1620119114},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 5,
volume = 114,
place = {United States},
year = {2017},
month = {1}
}

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