Phenomics

Phenomics is the systematic study of phenotypes.[1] As such, it is a transdisciplinary area of research that involves biology, data sciences, engineering and other fields. Phenomics is concerned with the measurement of phenomes where a phenome is the set of phenotypes (physical and biochemical traits) that can be produced by a given organism over the course of development and in response to genetic mutation and environmental influences.[2] Phenomics concepts are used in functional genomics, pharmaceutical research, metabolic engineering, agricultural research, and increasingly in phylogenetics.[3]

One major area of effort involves improving, both qualitatively and quantitatively, the capacity to measure phenomes.

Applications

In plant sciences, phenomics research occurs in both field and controlled environments. Field phenomics encompasses the measurement of phenotypes that occur in both cultivated and natural conditions, whereas controlled environment phenomics research involves the use of glass houses, growth chambers, and other systems where growth conditions can be manipulated. The TERRA-REF Gantry in Maricopa, Arizona is a platform developed to measure field phenotypes, and the Maize Genomes to Fields Initiative[4] is an example of a large-scale, distributed field phenomics project across many environments and years. Controlled environment systems include the Enviratron[5] at Iowa State University, the Plant Cultivation Hall under construction at IPK, and platforms at the Donald Danforth Plant Science Center, the University of Nebraska-Lincoln, and elsewhere.

Standards, methods, tools, and instrumentation

A Minimal Information About a Plant Phenotyping Experiment (MIAPPE) standard[6] is available and in use among many researchers collecting and organizing plant phenomics data. Emerging analysis methods exist, including a diverse set of software packages in computer vision available via PlantCV. Many research groups are focused on developing systems using the Breeding API, a Standardized RESTful Web Service API Specification for communicating Plant Breeding Data.

The Australian Plant Phenomics Facility (APPF), an initiative of the Australian government, has developed a number of new instruments for comprehensive and fast measurements of phenotypes in both the lab and the field. The NAPPN maintains a list of plant phenomics facilities in North America.[7]

Research coordination and communities

The International Plant Phenotyping Network (IPPN) is an organization that seeks to enable exchange of knowledge, information, and expertise across many disciplines involved in plant phenomics by providing a network linking members, platform operators, users, research groups, developers, and policy makers. Regional partners include, the European Plant Phenotyping Network (EPPN), the North American Plant Phenotyping Network (NAPPN), and others.

The European research infrastructure for plant phenotyping, EMPHASIS,[8] enables researchers to use facilities, services and resources for multi-scale plant phenotyping across Europe. EMPHASIS aims to promote future food security and agricultural business in a changing climate by enabling scientists to better understand plant performance and translate this knowledge into application.[8]

See also

References
  1. Bilder, R.M.; Sabb, F.W.; Cannon, TD; London, ED; Jentsch, JD; Parker, DS; Poldrack, RA; Evans, C; Freimer, NB (2009). "Phenomics: The systematic study of phenotypes on a genome-wide scale". Neuroscience. 164 (1): 30–42. doi:10.1016/j.neuroscience.2009.01.027. PMC 2760679. PMID 19344640.
  2. Houle, David; Govindaraju, Diddahally R.; Omholt, Stig (2010). "Phenomics: the next challenge". Nature Reviews Genetics. 11 (12): 855–866. doi:10.1038/nrg2897. PMID 21085204.
  3. O'Leary, M. A.; Bloch, J. I.; Flynn, J. J.; Gaudin, T. J.; Giallombardo, A.; Giannini, N. P.; Goldberg, S. L.; Kraatz, B. P.; Luo, Z.-X.; Meng, J.; Ni, X.; Novacek, M. J.; Perini, F. A.; Randall, Z.; Rougier, G. W.; Sargis, E. J.; Silcox, M. T.; Simmons, N. B.; Spaulding, M.; Velazco, P. M.; Weksler, M.; Wible, J. R.; Cirranello, A. L. (2013). "The placental mammal ancestor and the post-K-Pg radiation of placentals". Science. 332: 662–667.
  4. AlKhalifah, Naser; Campbell, Darwin A.; Falcon, Celeste M.; Gardiner, Jack M.; Miller, Nathan D.; Romay, Maria Cinta; Walls, Ramona; Walton, Renee; Yeh, Cheng-Ting; Bohn, Martin; Bubert, Jessica; Buckler, Edward S.; Ciampitti, Ignacio; Flint-Garcia, Sherry; Gore, Michael A.; Graham, Christopher; Hirsch, Candice; Holland, James B.; Hooker, David; Kaeppler, Shawn; Knoll, Joseph; Lauter, Nick; Lee, Elizabeth C.; Lorenz, Aaron; Lynch, Jonathan P.; Moose, Stephen P.; Murray, Seth C.; Nelson, Rebecca; Rocheford, Torbert; Rodriguez, Oscar; Schnable, James C.; Scully, Brian; Smith, Margaret; Springer, Nathan; Thomison, Peter; Tuinstra, Mitchell; Wisser, Randall J.; Xu, Wenwei; Ertl, David; Schnable, Patrick S.; De Leon, Natalia; Spalding, Edgar P.; Edwards, Jode; Lawrence-Dill, Carolyn J. (9 July 2018). "Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets". BMC Research Notes. 11 (1): 452. doi:10.1186/s13104-018-3508-1.
  5. Bao, Yin; Zarecor, Scott; Shah, Dylan; Tuel, Taylor; Campbell, Darwin A.; Chapman, Antony V. E.; Imberti, David; Kiekhaefer, Daniel; Imberti, Henry; Lübberstedt, Thomas; Yin, Yanhai; Nettleton, Dan; Lawrence-Dill, Carolyn J.; Whitham, Steven A.; Tang, Lie; Howell, Stephen H. (23 October 2019). "Assessing plant performance in the Enviratron". Plant Methods. 15 (1): 117. doi:10.1186/s13007-019-0504-y.
  6. Papoutsoglou, Evangelia A.; Faria, Daniel; Arend, Daniel; Arnaud, Elizabeth; Athanasiadis, Ioannis N.; Chaves, Inês; Coppens, Frederik; Cornut, Guillaume; Costa, Bruno V.; Ćwiek‐Kupczyńska, Hanna; Droesbeke, Bert; Finkers, Richard; Gruden, Kristina; Junker, Astrid; King, Graham J.; Krajewski, Paweł; Lange, Matthias; Laporte, Marie-Angélique; Michotey, Célia; Oppermann, Markus; Ostler, Richard; Poorter, Hendrik; Ramı́rez‐Gonzalez, Ricardo; Ramšak, Živa; Reif, Jochen C.; Rocca‐Serra, Philippe; Sansone, Susanna-Assunta; Scholz, Uwe; Tardieu, François; Uauy, Cristobal; Usadel, Björn; Visser, Richard G. F.; Weise, Stephan; Kersey, Paul J.; Miguel, Célia M.; Adam‐Blondon, Anne-Françoise; Pommier, Cyril (2020). "Enabling reusability of plant phenomic datasets with MIAPPE 1.1". New Phytologist. 227 (1): 260–273. doi:10.1111/nph.16544.
  7. list of plant phenomics facilities in North America
  8. EMPHASIS

Further reading
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