Metabotyping as a Stopover in Genome-to-Phenome Mapping
Abstract
Predicting phenotypic expression from genomic and environmental information is arguably the greatest challenge in today's biology. Being able to survey genomic content, e.g., as single-nucleotide polymorphism data, within a diverse population and predict the phenotypes of external traits, represents the holy grail across genome-informed disciplines, from personal medicine and nutrition to plant breeding. In the present study, we propose a two-step procedure in bridging the genome to phenome gap where external phenotypes are viewed as emergent properties of internal phenotypes, such as molecular profiles, in interaction with the environment. Using biomass accumulation and shoot-root allometry as external traits in diverse genotypes of the model grass Brachypodium distachyon, we established correlative models between genotypes and metabolite profiles (metabotypes) as internal phenotypes, and between metabotypes and external phenotypes under two contrasting watering regimes. Our results demonstrate the potential for employing metabotypes as an integrator in predicting external phenotypes from genomic information.
- Authors:
-
[1];
[2];
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1502135
- Alternate Identifier(s):
- OSTI ID: 1546645
- Report Number(s):
- PNNL-SA-135368
Journal ID: ISSN 2045-2322
- Grant/Contract Number:
- AC05-76RL01830; AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Scientific Reports
- Additional Journal Information:
- Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 2045-2322
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Handakumbura, Pubudu P., Stanfill, Bryan, Rivas-Ubach, Albert, Fortin, Dan, Vogel, John P., and Jansson, Christer. Metabotyping as a Stopover in Genome-to-Phenome Mapping. United States: N. p., 2019.
Web. doi:10.1038/s41598-019-38483-0.
Handakumbura, Pubudu P., Stanfill, Bryan, Rivas-Ubach, Albert, Fortin, Dan, Vogel, John P., & Jansson, Christer. Metabotyping as a Stopover in Genome-to-Phenome Mapping. United States. https://doi.org/10.1038/s41598-019-38483-0
Handakumbura, Pubudu P., Stanfill, Bryan, Rivas-Ubach, Albert, Fortin, Dan, Vogel, John P., and Jansson, Christer. Tue .
"Metabotyping as a Stopover in Genome-to-Phenome Mapping". United States. https://doi.org/10.1038/s41598-019-38483-0. https://www.osti.gov/servlets/purl/1502135.
@article{osti_1502135,
title = {Metabotyping as a Stopover in Genome-to-Phenome Mapping},
author = {Handakumbura, Pubudu P. and Stanfill, Bryan and Rivas-Ubach, Albert and Fortin, Dan and Vogel, John P. and Jansson, Christer},
abstractNote = {Predicting phenotypic expression from genomic and environmental information is arguably the greatest challenge in today's biology. Being able to survey genomic content, e.g., as single-nucleotide polymorphism data, within a diverse population and predict the phenotypes of external traits, represents the holy grail across genome-informed disciplines, from personal medicine and nutrition to plant breeding. In the present study, we propose a two-step procedure in bridging the genome to phenome gap where external phenotypes are viewed as emergent properties of internal phenotypes, such as molecular profiles, in interaction with the environment. Using biomass accumulation and shoot-root allometry as external traits in diverse genotypes of the model grass Brachypodium distachyon, we established correlative models between genotypes and metabolite profiles (metabotypes) as internal phenotypes, and between metabotypes and external phenotypes under two contrasting watering regimes. Our results demonstrate the potential for employing metabotypes as an integrator in predicting external phenotypes from genomic information.},
doi = {10.1038/s41598-019-38483-0},
journal = {Scientific Reports},
number = 1,
volume = 9,
place = {United States},
year = {Tue Feb 12 00:00:00 EST 2019},
month = {Tue Feb 12 00:00:00 EST 2019}
}
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Cited by: 17 works
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Figures / Tables:
Figure 1: Genotype-phenotype predictions. The figure illustrates the relationships between plant genotype (G), plant epigenotype (Eg), internal phenotype (Pi; e.g., biochemical, physiological or cellular properties), external phenotype (Pe; e.g., morphological or phenological properties), and the surrounding environment (E). Bridging the genotype-to-external phenotype gap is indicated by predicting external phenotype directlymore »
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Comparative study of biomass determinants of 12 poplar (Populus) genotypes in a high-density short-rotation culture
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Ecological metabolomics
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dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering
journal, July 2015
- Galili, Tal
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How can we make plants grow faster? A source–sink perspective on growth rate
journal, October 2015
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A Model to Describe the Partitioning of Photosynthate during Vegetative Plant Growth
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Untargeted Metabolic Quantitative Trait Loci Analyses Reveal a Relationship between Primary Metabolism and Potato Tuber Quality
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Variation in Adult Plant Phenotypes and Partitioning among Seed and Stem-Borne Roots across Brachypodium distachyon Accessions to Exploit in Breeding Cereals for Well-Watered and Drought Environments
journal, May 2015
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Exploiting the Brachypodium Tool Box in cereal and grass research
journal, May 2011
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Similar local, but different systemic, metabolomic responses of closely related pine subspecies to folivory by caterpillars of the processionary moth
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Resource Limitation in Plants-An Economic Analogy
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Phytosequestration: Carbon Biosequestration by Plants and the Prospects of Genetic Engineering
journal, October 2010
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- BioScience, Vol. 60, Issue 9
The effects of domestication on the scaling of below- vs. aboveground biomass in four selected wheat (Triticum; Poaceae) genotypes
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Works referencing / citing this record:
The metabolome as a link in the genotype-phenotype map for peroxide resistance in the fruit fly, Drosophila melanogaster
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Genetic Variation for Seed Metabolite Levels in Brachypodium distachyon
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