Metabotyping as a Stopover in Genome-to-Phenome Mapping

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

doi:10.1038/s41598-019-38483-0

Metabotyping as a Stopover in Genome-to-Phenome Mapping

Journal Article · Tue Feb 12 00:00:00 EST 2019 · Scientific Reports

DOI:https://doi.org/10.1038/s41598-019-38483-0· OSTI ID:1502135

Handakumbura, Pubudu P. ^[1]; ^[1]; Rivas-Ubach, Albert ^[1]; Fortin, Dan ^[1]; ^[2]; Jansson, Christer ^[1]

Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

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 singlenucleotide 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 enviorment. 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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231; AC05-76RL01830

OSTI ID:: 1502135

Alternate ID(s):: OSTI ID: 1546645

Report Number(s):: PNNL-SA--135368

Journal Information:: Scientific Reports, Journal Name: Scientific Reports Journal Issue: 1 Vol. 9; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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