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bioRxiv · 10.1101/370288

Functional phenomics: An emerging field integrating high-throughput phenotyping, physiology, and bioinformatics

York, L. M.
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Abstract

HighlightFunctional phenomics is an emerging field in plant biology that relies on high-throughput phenotyping, big data analytics, controlled manipulative experiments, and simulation modelling to increase understanding of plant physiology.\n\nAbstractThe emergence of functional phenomics signifies the rebirth of physiology as a 21st century science through the use of advanced sensing technologies and big data analytics. Functional phenomics highlights the importance of phenotyping beyond only identifying genetic regions because a significant knowledge gap remains in understanding which plant properties will influence ecosystem services beneficial to human welfare. Here, a general approach for the theory and practice of functional phenomics is outlined including exploring the phene concept as a unit of phenotype. The functional phenomics pipeline is proposed as a general method for conceptualizing, measuring, and validating utility of plant phenes. The functional phenomics pipeline begins with ideotype development. Second, a phenotyping platform is developed to maximize the throughput of phene measurements. A mapping population is screened measuring target phenes and indicators of plant performance such as yield and nutrient composition. Traditional forward genetics allows genetic mapping, while functional phenomics links phenes to plant performance. Based on these data, genotypes with contrasting phenotypes can be selected for smaller yet more intensive experiments to understand phene-environment interactions in depth. Simulation modeling can be used to understand the phenotypes and all stages of the pipeline feed back to ideotype and phenotyping platform development.

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York, L. M.. 2018-07-16. Functional phenomics: An emerging field integrating high-throughput phenotyping, physiology, and bioinformatics. https://doi.org/10.1101/370288

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