Metabotyping as a Stopover in Genome-to-Phenome Mapping View Full Text


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Article Info

DATE

2019-12

AUTHORS

Pubudu P. Handakumbura, Bryan Stanfill, Albert Rivas-Ubach, Dan Fortin, John P. Vogel, Christer Jansson

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. More... »

PAGES

1858

References to SciGraph publications

  • 2009-12. Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon in BMC PLANT BIOLOGY
  • 2011-12. Exploring molecular backgrounds of quality traits in rice by predictive models based on high-coverage metabolomics in BMC SYSTEMS BIOLOGY
  • 2005-02. The isolation and antioxidative effects of vitexin fromAcer palmatum in ARCHIVES OF PHARMACAL RESEARCH
  • 2010-12. Phenomics: the next challenge in NATURE REVIEWS GENETICS
  • 2015-07. Expression of barley SUSIBA2 transcription factor yields high-starch low-methane rice in NATURE
  • 2016-12. Genotypic variation in biomass allocation in response to field drought has a greater affect on yield than gas exchange or phenology in BMC PLANT BIOLOGY
  • 2017-06. Allometry varies among related families of Norway spruce in ANNALS OF FOREST SCIENCE
  • 2005. Mutation: Sugar Signaling Mutants in Arabidopsis in PROGRESS IN BOTANY
  • 2017-12. Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure in NATURE COMMUNICATIONS
  • 2002-01. Metabolomics – the link between genotypes and phenotypes in PLANT MOLECULAR BIOLOGY
  • 2014-12. Metabolome-based genome-wide association study of maize kernel leads to novel biochemical insights in NATURE COMMUNICATIONS
  • 2007-09. Proposed minimum reporting standards for chemical analysis in METABOLOMICS
  • 2010-12. MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data in BMC BIOINFORMATICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41598-019-38483-0

    DOI

    http://dx.doi.org/10.1038/s41598-019-38483-0

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1112072002

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30755686


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