Phenomics

What is Phenomics ?

Figure1. Plant phenomics is the study of plant growth, performance and composition

• Phenomics is an area of biology concerned with the measurement of phenomes—the physical and biochemical traits of organisms—as they change in response to genetic mutation and environmental influences. It is used in functional genomics, pharmaceutical research, metabolic engineering and increasingly in phylogenetics. Plant phenomics is the study of plant growth, performance and composition.
• Forward phenomics uses phenotyping tools to 'sieve' collections of germplasm for valuable traits. The sieve or screen could be high-throughput and fully automated and low resolution, followed by higher-resolution, lower throughput measurements. Screens might include abiotic or biotic stress challenges and must be reproducible and of physiological relevance. Reverse phenomics is the detailed dissection of traits shown to be of value to reveal mechanistic understanding and allow exploitation of this mechanism in new approaches. This can involve reduction of a physiological trait to biochemical or biophysical processes and ultimately a gene or genes.

Using plant phenomics to close the 'gene to genotype' loop

• An impressive array of tools is now available for high-throughput phenotyping and the approaches described above can be used in many different ways to facilitate the process of trait identification, gene identification and genotype development necessary to produce a new crop variety. Examples of how phenomics can be used to develop a crop genotype or variety with tolerance to a particular type of drought are presented in Figure 2.
• In this scheme, phenomics features at a number of levels. ‘Forward’ phenomics can be used to identify pheno- typic, and thus genetic, variation in particular traits of interest (1 in Figure 2), for traits indicated as important and validated to be important by physiological studies (‘reverse phenomics’) of plants with differing drought tolerance (2 in Figure 2). This genetic approach can take the form of a large genotype screen using a bi-parental or multi-parent population, or by direct analysis of a ‘diversity panel’ of lines for analysis by association genetics. As discussed above, accurate, cost-effective 1 , high-throughput phenotyping is pivotal to fine mapping of traits, regardless of the genetic approach for producing allelic recombination or assessing variation by re-sequencing technologies.
• Phenomics is also essential for good quality reverse genetic studies, to test hypotheses regarding the role of particular genes in the function of a plant (4 in Figure 2), and to test the effects of altering patterns, levels or alleles of target genes on the traits of germplasm (5 in Figure 2) and the drought tolerance of the resultant crop.
  
  

Figure 2. From plant phenotyping to phenomics. Plant phenotyping can be performed at multiple organizational levels, ranging from the field and canopy, to the whole-plant, organ, tissue, and cellular level (and eventually subcellular level). Phenotypic traits of interest can be categorized as physiological, structural, or performance-related. Plant phenotyping is the quantitative or qualitative investigation of these traits at any organizational level, in a given genomic expression state and a given environment. This is shown as a single column of yellow cubes, which could be positioned anywhere in the overall cube. A phenome corresponds to all possible phenotypes under different environmental conditions of a given genotype, represented by the combination of yellow and red cubes. Genomic expression states cover the complete range of available plant genetic resources (e.g., overexpresssion lines, mutants, natural accessions, and segregating populations). Plant phenomics could be considered as the study of phenomes of multiple genomic expression states, represented by the combination of yellow, red, and blue cubes. Light-colored cubes illustrate the (in principle) infinite possibilities of environmental conditions and genomic expression states. Notably, plant phenotypes can be assessed at specific times during development, or alternatively in a dynamic manner

Plant phenotyping is a complex matter involving a plethora of systems and tools

• 'Phenomics' has been proposed as a novel discipline in biology and involves the gathering of high-dimensional phenotypic data at multiple levels of organization, to progress towards the full characterization of the complete set of phenotypes of a genome, in analogy with whole genome sequencing [1]. This ultimate aim will of course remain hypothetical; however, current and future developments in plant phenotyping and phenomics may benefit from the consideration of dimensionality, together with throughput and resolution, because our comprehension of plant process- es in general, and the genotype–phenotype relationship in particular, is far from complete (Box 1). Plant phenotypes are inherently complex because they result from the interaction of genotypes with a multitude of environmental factors. This interaction influences on the one hand the developmental program and growth of plants, which can be described by means of structural traits, and, on the other hand, plant functioning, described by means of physiological traits (Figure 1). Both the structural and physiological traits eventually determine plant performance in terms of biomass and yield. Phenotypic traits at different organizational.
  
  

Figure 2. Closing the gene to genotype loop with phenomics.

Projects List

Project Title	Species	Published years	Academic Journal	RiceWiki Project ID
A phenomics approach detected differential epigenetic growth regulation between inbreds and their hybrid in Oryza sativa	Oryza sativa	2010	Molecular Breeding	IC4R001-Phenomics-2010-X6315815
Phenomics of rice early vigour and drought response: Are sugar related and morphogenetic traits relevant?	Oryza sativa	2012	Rice	IC4R002-Phenomics-2012-24279832
A rice phenomics study—phenotype scoring and seed propagation of a T-DNA insertion-induced rice mutant population	Oryza sativa	2007	Plant Molecular Biology	IC4R003-Phenomics-2007-17701278
Integrating Image-Based Phenomics and Associatio Analysis to Dissect the Genetic Architecture of Temporal Salinity Responses in Rice	Oryza sativa	2015	Plant Physiology	IC4R004-Phenomics-2015-26111541
C4 rice: a challenge for plant phenomics	Oryza sativa	2009	Functional Plant Biology	IC4R005-Phenomics-2009-11089458
Field phenomics for response of a rice diversity panel to ten environments in Senegal and Madagascar. 1. Plant phenological traits	Oryza sativa	2015	Field Crops Research	IC4R006-Phenomics-2015-26104576
Field phenomics for response of a rice diversity panel to ten environments in Senegal and Madagascar. 2. Chilling-induced spikelet sterility	Oryza sativa	2015	Field Crops Research	IC4R007-Phenomics-2015-26104586
Integrating Image-Based Phenomics and Association Analysis to Dissect the Genetic Architecture of Temporal Salinity Responses in Rice	Oryza sativa	2015	Plant Physiology	IC4R008-Phenomics-2015-26111541
Plant phenomics and high-throughput phenotyping: accelerating rice functional genomics using multidisciplinary technologies	Oryza sativa	2013	Current Opinion in Plant Biology	IC4R009-Phenomics-2013-23578473