What is phenotyping in agriculture


Phenotyping, the process of measuring and analyzing observable plant characteristics, is a term used frequently in the College of Agriculture these days—and a technique that is now automated for field research at Purdue.


What are the current trends in phenotyping in agriculture?

However, currently the trend goes toward a higher diversity of phenotyped crops and research in the field. The application of plant phenotyping in the field is still under rapid development and this application has strong linkages with precision agriculture.

What are the applications of phenotyping in plant breeding?

], etc. The plant breeding process is one of the major applications of phenotyping in practice today and many developments in plant phenotyping are governed by breeding targets [ 13 R. T. Furbank and M. Tester, “Phenomics – technologies to relieve the phenotyping bottleneck,” Trends in Plant Science, vol. 16, no. 12, pp. 635–644, 2011.

What is modern plant phenotyping?

Modern plant phenotyping, often using non-invasive technologies and digital technologies, is an emerging science and provides essential information on how genetics, epigenetics, environmental pressures, and crop management (farming) can guide selection toward productive plants suitable for their environment.

What is the dictionary definition of phenotyping?

Define Phenotyping. Phenotyping synonyms, Phenotyping pronunciation, Phenotyping translation, English dictionary definition of Phenotyping. n. 1. a. The observable physical or biochemical characteristics of an organism, as determined by both genetic makeup and environmental influences. b.


What is phenotyping in plants?

Phenotyping is the foundation of any breeding selection process. However, modern plant phenotyping measures complex traits related to growth, yield, and adaptation to stress, with an improved accuracy and precision at different scales of organization, from organs to canopies (Fiorani and Schurr, 2013).

What is crop phenotyping?

Crop phenotyping aims at a quantification of quality, photosynthesis, development, architecture, growth or biomass productivity of single plants or plant stands using a broad variety of sensors and analysis procedures.

What is meant by phenotyping?

The term “phenotype” refers to the observable physical properties of an organism; these include the organism’s appearance, development, and behavior. An organism’s phenotype is determined by its genotype, which is the set of genes the organism carries, as well as by environmental influences upon these genes.

What is phenotype and genotype in agriculture?

During plant growth and development, the functional plant body (PHENOTYPE) is developed through the complex interaction between the genetic history (GENOTYPE) and the physical environment in which plants develop (ENVIRONMENT).

What is another word for phenotype?

composition, constitution, physical composition, make-up, makeup.

What is genotype in agriculture?

With regard to the comparison of plant material in a set of multi-environment yield trials, the term genotype refers to a cultivar (i.e. with material genetically homogeneous, such as pure lines or clones, or heterogeneous, such as open-pollinated populations) rather than to an individual’s genetic make-up.

What are the 3 types of phenotypes?

Polygenic inheritance can be explained by additive effects of many loci: if each “capital” allele contributes one increment to the phenotype. With one locus and additive effects we have three phenotypic classes: AA, Aa and aa.

Why are phenotypes important?

Phenotype matching is important, because it allows differential behavior toward previously unmet animals. Because phenotype matching nearly always employs information learned from relatives for discriminations, these behavioral decisions are consistent with kin selection.

How many phenotypes are there?

There are three common alleles in the ABO system. These alleles segregate and assort into six genotypes, as shown in Table 1. As Table 1 indicates, only four phenotypes result from the six possible ABO genotypes.

How does phenotype affect crops production?

By establishing the connection between genotype and phenotype, it is possible to improve agricultural production to satisfy the requirement of the growing human population. Therefore, phenotyping is as important as genotyping in establishing the relationship between genes and traits.

What is phenotypic analysis?

Thus, analysis of phenotypic change refers to a statistical approach to determine whether two or more groups have consistent or differing phenotypic change along a gradient. Generally, this is a statistical assessment of a factor or factor–covariate interaction.

What are the differences between genotypes and phenotypes?

The sum of an organism’s observable characteristics is their phenotype. A key difference between phenotype and genotype is that, whilst genotype is inherited from an organism’s parents, the phenotype is not. Whilst a phenotype is influenced the genotype, genotype does not equal phenotype.

What is phenotyping in agriculture?

Phenotyping, the process of measuring and analyzing observable plant characteristics, is a term used frequently in the College of Agriculture these days—and a technique that is now automated for field research at Purdue.

Is phenotyping a new technique?

Phenotyping is not a new technique, but measuring characteristics such as plant height, nitrogen content, and photosynthetic activity by hand is time-consuming and laborious. Automated field phenotyping using sensors, configurable harvesting equipment, and drones produces far more data in a shorter time frame, allowing researchers to more quickly close the gap between genotype and phenotype.

Why is phenotyping important?

Professor Baret defines plant phenotyping as the science of the characterization of the crops which is particularly important for decision support in agriculture and for plant breeders when selecting the best genotypes that will become the future cultivars well-adapted to different environments. As such, plant phenotyping helps to better understand …

Is plant phenotyping revolutionary?

In that sense, plant phenotyping is revolutionary and we believe that any actors in the agriculture sector can benefit from it as a wide range of data acquisition equipment and methods exist at Hiphen to adapt to your needs, budget, crops and required traits.

What is plant phenotyping?

Modern plant phenotyping, often using non-invasive technologies and digital technologies, is an emerging science and provides essential information on how genetics, epigenetics, environmental pressures, and crop management (farming) can guide selection toward productive plants suitable for their environment.

What is phenotyping in breeding?

Phenotyping is the foundation of any breeding selection process. However, modern plant phenotyping measures complex traits related to growth, yield, and adaptation to stress, with an improved accuracy and precision at different scales of organization, from organs to canopies ( Fiorani and Schurr, 2013 ).

How many countries have phenotyping?

Plant phenotyping research was published by authors working in 74 different countries. Figure 3 represents the number of papers dealing with plant phenotyping published by co-authors in the world (left) and in the EU (right). EU co-authors published 1,210 papers (41.8% of total publications considering all the co-authors) followed by USA (15.4%; N = 447), Australia (6.0%; N = 174), and India (5.6%; N = 161). More than 40% of the studies performed in the USA and Australia apply plant phenotyping in the field. In the EU, Germany published 35.8% (319) of the total publications, followed by France (23.7%; N = 211), United Kingdom (18.4%, N = 164), Italy (9.9%, N = 88), and Spain (9.5%, N = 85). The proportion of phenotyping dedicated to field phenotyping in those countries ranged from 31% (France) to 38% (Spain). ( Pallottino et al., 2018) showed how the leading countries in precision agriculture are EU, USA China and Australia. This is comparable to what was observed in this paper for plant phenotyping (Figure 3 ).

How many publications are there in plant phenotyping?

A total of 1,827 scientific publications fitted our search method based on relevance for plant phenotyping. 81.3% of the publications were research papers, 11.7% review papers, 5.9% book chapters and the remaining 1.1% were books, letters, or notes. The studies were published in 145 journals. Top journals were Frontiers in Plant Science ( N = 87; 4.8%), Journal of Experimental Botany ( N = 83; 4.5%), Plant Methods ( N = 72; 3.9%), Theoretical and Applied Genetics ( N = 70; 3.8%), and PLoS ONE ( N = 61; 3.3%). Figure 1 depicts the plant phenotyping publication numbers from 1997 to 2017. During the period 1997–2006, the total number of publications was only around 6.1%. The number of publications generally increased more steeply after 2010, but a first surge was already observed during 2008–2009, in coincidence with the 1st International plant phenotyping Conference 2008 in Canberra, Australia. In Figure 1 the number of field plant phenotyping papers with respect to other plant phenotyping papers was also reported. It is striking to observe how field plant phenotyping papers increases their importance since 2014 from a very small percentage in the early years to >30% of the total publications in 2016/2017.

Which country is the most active in phenotyping?

The same map, when standardized by dividing the plant phenotyping publications per population and multiplying the number per 10 7 (Figure 4 ), shows that Australia and Switzerland are the top world countries (left) most active in phenotyping publishing relative to their population size, EU remains at a leading position (5th) while India and USA only hold the 42nd and 68th position, respectively. In EU (right side of Figure 4) Denmark and Luxembourg are the top countries, and Germany also has a leading position (5th).

What is the most represented plant species in the EU?

We observe that Arabidopsis thaliana (blue cluster; indicating plant physiology) is the most represented plant species (8.5% of the world total plant phenotyping papers) that is under investigation (relative larger circle in EU; 10.7% of the EU plant phenotyping papers). This points toward the observation that in the EU, research studies are mainly based on a model plant based laboratory context. Root phenotyping is represented in an additional cluster (yellow). Imaging (red cluster) is very important in the EU and cross linked with many other terms. Characterization of root architecture in soil-based assays in the lab and in the field remains challenging, and any useful methodology should also be exploited in specific chain combinations. Methodologies to study root growth and architecture in 2D and 3D are a frontier in plant phenotyping ( Fiorani and Schurr, 2013 ).

How can digitization reduce the environmental impact of agriculture?

Digitization of agriculture and expansion of precision farming can reduce costs and minimize the environmental impact of agriculture ( EU, 2015 ). For example, geo-location technologies could be used by farmers to comply with the Nitrates Directive, which concerns water protection against nitrates pollution from agricultural sources ( EPRS, 2017 ). In parallel, novel agronomic strategies for canopy and soil management, alongside the development of genotypes that are more resilient to drought and heat stress, are in great demand from the Mediterranean agricultural sector ( Mhadhbi et al., 2015; Zivy et al., 2015; Ollat et al., 2016, EPRS, 2017; Haworth et al., 2018a; Novara et al., 2018; Reynolds et al., 2019 ).

Why is Mediterranean agriculture in high demand?

Moreover, solutions specifically tailored to Mediterranean agriculture (e.g., crops and environmental stresses) are in high demand, as the region is vulnerable to climate change and to desertification processes. The specific phenotyping requirements of Mediterranean crops have not yet been fully identified.

Is phenotyping heterogeneous in Europe?

Plant phenotyping remains largely heterogeneous in Europe , with a greater investment in facilities in countries such as France, Germany, or the Netherlands ( Table 1 ), followed by lower levels in Spain, Portugal, Greece, and Turkey. Developments regarding infrastructure, technology, knowledge, and training and application have been occurring at different speeds and intensities when we compare Northern and Southern EU countries. In particular, budget limitations commonly experienced by research and academic institutions in Southern European countries may preclude construction of plant-phenotyping infrastructures. Plant phenotyping in Europe is also heterogeneous in regards to the requirements of phenotyping (field vs. greenhouse crops, traits of interest) (see Table 1 ). Technological developments in precision and digital farming, alongside crop-phenotyping and phenomics, could provide valuable information regarding crop/cultivar adaptability to abiotic and biotic stress targeted toward more sustainable crop production ( Araus and Cairns, 2014; Araus et al., 2018; Reynolds et al., 2019 ). Yet, due to the high costs in the short term, establishment of farm-based phenotyping infrastructures is unachievable for many EU countries. The economic crisis, the generally small size of companies involved in this sector (i.e., breeding), lack of perception by growers/officials, and delayed public and private investments in phenotyping infrastructures have limited plant-phenotyping capabilities in Southern Europe. The lack of pilot-phenotyping infrastructures in public institutions and universities makes it more difficult to identify and meet the technological challenges associated with precision breeding and farming systems, as well as restricting public awareness about the advantages of phenotyping infrastructures. Within Mediterranean countries, France and, to a lesser extent, Italy remain as exceptions ( Table 1 ). France and Germany are pioneers in plant phenotyping, with a higher number of facilities and publication output in this domain ( Costa et al., 2019 ). In 2018, the French Phenotyping Network ( www.phenome-fppn.fr/) congregated nine phenotyping platforms, including controlled conditions (two units), semi-controlled conditions (two units), field conditions (three units), and molecular platforms (two units). This panorama contrasts with other Southern Mediterranean countries ( Table 1 ).

Why is phenotyping important?

Therefore, phenotyping technologies and protocols are important tools that are needed, e.g., to assess the structure and function of seeds, roots and root systems, storage organs above- and belowground, leaves, and entire canopies, as well as fruits, flowers, and many more.

How does a plant develop phenotypes?

A plant develops the dynamic phenotypes from the interaction of the plant with the environment. Understanding these processes that span plant’s lifetime in a permanently changing environment is essential for the advancement of basic plant science and its translation into application including breeding and crop management.

What is the Nord American Plant Phenotyping Network?

The Nord American Plant Phenotyping Network ( http://nappn.plant-phenotyping.org/) is currently an important initiative to link scientists and researchers in the rapidly evolving plant phenotyping area in northern America while the LatPP N [ 36.

What is IPPN in plant phenotyping?

On a global scale, the International Plant Phenotyping Network ( IPPN, https://www.plant-phenotyping.org/) was founded by leading research institutions to promote and educate state-of-the-art plant phenotyping in 2016.

Who is the author of the paper Genetic basis of plasticity in plants?

R. A. Laitinen and Z. Nikoloski, “Genetic basis of plasticity in plants,” Journal of Experimental Botany, vol. 70, no. 3, pp. 739–745, 2018. View at: Publisher Site | Google Scholar

What are the processes of plant life?

Plant processes such as growth, photosynthesis, and transpiration or yield formation are the basis of life on our planet, nourishing the presently 7 billion people. These processes will have to be further improved to achieve the goal of feeding the increasing population, at less footprint, on less land, and with less water, in a changing climate with increasing demand for quantity and quality of food and nonfood products from plants [ 15#N#FAO, IFAD, UNICEF, WFP, and WHO, The State of Food Security and Nutrition in the World 2018. Building climate resilience for food security and nutrition, FAO, Rome, Italy, 2018.#N#See in References#N#]. The process of intended modification of plant properties such as yield has been initiated over ten thousand years ago when people started to domesticate plants for human uses. The fact that such phenotypic selections can lead to a persistent improvement of crops, which is stable beyond generation, was the fundament of breeding from the early beginning of domestication of crops and fundamentally altered the course of human history [ 16#N#D. Zohary, M. Hopf, and E. Weiss, Domestication of Plants in the Old World, Oxford University Press, 4th edition, 2012.#N#See in References#N#]. The adaptation of plants to crop cultivation was vital to the shift from hunter-gatherer to agricultural societies, and it stimulated the development of cities and modern civilizations. Early farmers selected food plants with desirable characteristics and used these as a seed source for subsequent generations, resulting in an accumulation of characteristics over time. At that time, phenotyping was the only option to select through experience, since the basic principles of genetics have only been determined in relatively recent times. Mendel’s heritability laws discovered over a hundred years ago ultimately led to the establishment of genetics and the basis for the understanding of inheritance, which is still the basis in modern plant breeding. Measurement of diverse plant properties such as structure and function has been often performed by the collector’s eyes, manually or invasively, i.e., using destructive methods. Development of first sensors or tools to assess plant properties in response to external stimuli has been addressed by the pioneers in plant sciences in century, e.g., by Pfeffer’s development of an apparatus for plant growth measurement [ 17#N#W. Pfeffer, “Bezugsquelle und Preise einiger Apparate,” Botansche Zeitung, vol. 45, pp. 27–31, 1887. View at: Google Scholar#N#See in References#N#]. A description of historic methods for analyzing different traits has been summarized by Ruge [ 18#N#U. Ruge, “Methoden der wachstumsmessung,” in Encyclopedia of Plant Physiology, Ruhland, Ed., vol. 14, pp. 48–70, Springer, Berlin, Germany, 1961. View at: Google Scholar#N#See in References#N#].

What is plant phenotyping?

Plant phenotyping is the science of quantifying the physical and physiological traits of a plant. Plant phenotyping mainly benefits two communities: farmers and plant breeders. By better understanding the traits of the crop, a farmer can optimize crop yield by making informed crop management decisions. Similarly, understanding the crop’s behavior is crucial for plant breeders to select the best possible crop variety for a given location and environment. In the past, plant phenotyping was a manual endeavor. The process of manually observing a small set of crop samples and reporting observations periodically was slow, labor intensive and inefficient. The low throughput nature of these methods has impeded the progress in plant breeding research. However, the advent of modern data acquisition methods with various sensors, cameras and UAVs (Unmanned Aerial Vehicles) coupled with advances in machine learning techniques have resulted in the development of high-throughput plant phenotyping methods to be effectively used for precision agriculture.

Why use weak labels in plant phenotyping?

Fruit/organ counting is a well explored task by the plant phenotyping community. However, many vision-based solutions we have currently require highly accurate instance and density labels of fruits and organs in diverse set of environments. The labeling procedures are often very burdensome and error prone and, in many agricultural scenarios, it may be impossible to acquire a sufficient number of labelled samples to achieve consistent performance that are robust to image noise or other forms of covariate shift. This is why using only weak labels can be crucial for cost-effective plant phenotyping.

Is deep learning good for phenotyping?

While deep learning based plant phenotyping has shown great promise, requirement of large labeled datasets still remains to be the bottleneck. Phenotyping tasks are often specific to the environmental and genetic conditions, finding large datasets with such conditions is not always possible. This results in researchers needing to acquire their own dataset and label it, which is often a arduous and expensive affair. Moreover, small datasets often lead to models that overfit. Deep learning approaches optimized for working with limited labeled data would immensely help the plant phenotyping community, since this would encourage many more farmers, breeders, and researchers to employ reliable plant phenotyping techniques to optimize crop yield. To this end, we list out some of the recent efforts in the area of deep plant phenotyping with limited labeled data.

What is plant phenotyping?

Plant phenotypingis a rapidly emerging research area concerned with quantitative measurement of the structural and functional properties of plants.

What is phenotyping in biology?

n. 1. a. The observable physical or biochemical characteristics of an organism, as determined by both genetic makeup and environmental influences. b.

What is FDNA used for?

Through partnerships such as this, FDNA’s next-generation phenotypingtechnologies that capture, structure, and interpret complex physiological information, are used in analyzing patient clinical data and next-generation sequencing data.

What is the definition of phenotype?

(Biology) the physical and biochemical characteristics of an organism as determined by the interaction of its genetic constitution and the environment. Compare genotype. phenotypic, ˌphenoˈtypical adj.

Who partners with Focus Foundation for Recognition of Facial Phenotype of 49ers Syndrome?

FDNA Partners with The Focus Foundation for Recognition of Facial Phenotype of 49ers Syndrome

What is the physical appearance of an organism?

The physical appearance of an organism as distinguished from its genetic makeup. The phenotype of an organism depends on which genes are dominant and on the interaction between genes and environment. Compare genotype.


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