Phenomics is the systematic study of traits that make up a

phenotype In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology or physical form and structure, its developmental processes, its biochemical and physiological prop ...

, and was coined by UC Berkeley and LBNL scientist Steven A. Garan. As such, it is a transdisciplinary area of research that involves

biology Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that process hereditar ...

data science Data science is an interdisciplinary field that uses scientific methods, processes, algorithms and systems to extract or extrapolate knowledge and insights from noisy, structured and unstructured data, and apply knowledge from data across a bro ...

engineering Engineering is the use of scientific method, scientific principles to design and build machines, structures, and other items, including bridges, tunnels, roads, vehicles, and buildings. The discipline of engineering encompasses a broad rang ...

and other fields. Phenomics is concerned with the measurement of the

where a

phenome A phenome, similar to phenotype, is the set of all traits expressed by a cell, tissue, organ, organism, or species. Just as the genome and proteome signify all of an organism's genes and proteins, the phenome represents the sum of its phenotyp ...

is a set of traits (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. The relationship between phenotype and genotype enables researchers to understand and study

pleiotropy Pleiotropy (from Greek , 'more', and , 'way') occurs when one gene influences two or more seemingly unrelated phenotypic traits. Such a gene that exhibits multiple phenotypic expression is called a pleiotropic gene. Mutation in a pleiotropic ge ...

. Phenomics concepts are used in

functional genomics Functional genomics is a field of molecular biology that attempts to describe gene (and protein) functions and interactions. Functional genomics make use of the vast data generated by genomic and transcriptomic projects (such as genome sequencin ...

, pharmaceutical research,

metabolic engineering Metabolic engineering is the practice of optimizing genetic and regulatory processes within cells to increase the cell's production of a certain substance. These processes are chemical networks that use a series of biochemical reactions and enz ...

agricultural research Agricultural science (or agriscience for short) is a broad multidisciplinary field of biology that encompasses the parts of exact, natural, economic and social sciences that are used in the practice and understanding of agriculture. Profession ...

, and increasingly in

phylogenetics In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups ...

. Technical challenges involve improving, both qualitatively and quantitatively, the capacity to measure phenomes.

Applications

Plant sciences

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 University of Arizona The University of Arizona (Arizona, U of A, UArizona, or UA) is a Public university, public Land-grant university, land-grant research university in Tucson, Arizona. Founded in 1885 by the 13th Arizona Territorial Legislature, it was the first ...

's Field ScannerThe TerraRef Gantry System of the University of Arizona on the fields of the Maricopa Research Center
/ref> in Maricopa, Arizona is a platform developed to measure field phenotypes, and the Maize Genomes to Fields Initiative is an example of a large-scale, distributed field phenomics project across many environments and years. Controlled environment systems include the Enviratron at

Iowa State University Iowa State University of Science and Technology (Iowa State University, Iowa State, or ISU) is a public land-grant research university in Ames, Iowa. Founded in 1858 as the Iowa Agricultural College and Model Farm, Iowa State became one of the ...

, the Plant Cultivation Hall under construction at IPK, and platforms at the Donald Danforth Plant Science Center, the

University of Nebraska-Lincoln A university () is an educational institution, institution of higher education, higher (or Tertiary education, tertiary) education and research which awards academic degrees in several Discipline (academia), academic disciplines. ''University'' ...

, and elsewhere.

Pharmaceutical sciences

Phenomics profiling of cells is emerging as a powerful technology to study cellular responses to genetic or chemical perturbations. High content-microscopy, in combination with fluorescent probes, can be used for capturing rich phenotypic information. Phenomics analysis of cells is used, among others, for the study of functional genomics, disease phenotyping, compound target identification, mechanism of action (MoA) prediction and toxicity studies.

Standards, methods, tools, and instrumentation

A Minimal Information About a Plant Phenotyping Experiment (MIAPPE) standard is available and in use among many researchers collecting and organizing plant phenomics data. A diverse set of computer vision methods exist to analyze 2D and 3D imaging data of plants. These methods are available to the community in various implementations, ranging from end-user ready cyber-platforms in the cloud such as DIRTDigital Imaging of Root Traits (DIRT)
/ref> and PlantItPlantIt: free image-based plant phenotyping automation in the cloud
/ref>to programming frameworks for software developers such as PlantCV.PlantCV
/ref> 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.

Research coordination and communities

The International Plant Phenotyping Network (IPPN)IPPN - International Plant Phenotyping Network
/ref> 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),NAPPN - North American Plant Phenotyping Network
/ref> and others. The European research infrastructure for plant phenotyping, EMPHASIS,EMPHASIS
/ref> 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.

Applications

Plant sciences

Pharmaceutical sciences

Standards, methods, tools, and instrumentation

Research coordination and communities

See also

References

Further reading