1/ Definition

You probably already crossed the word “trait” in scientific presentation or in papers, but you are still confused about what is exactly a phenotyping trait? At Hiphen, we always use the term "trait" to define all the different measurements that we can make for your plant phenotyping projects.

Generally speaking, a phenotyping trait, also called phene, is a quantitative or qualitative characteristic of an individual resulting from the expression of its genome in a given environment. This term is not restricted to plants and a trait can be determined at the scale of an organ, a plant or a canopy. The collection of traits, or phene, constitute the phenotype of the individual. In consequence, Plant phenotyping is the science of measuring traits to determine plant or canopy phenotype.

At Hiphen, we are specialist of non-destructive traits assessments thanks to our in-house technology to collect and analyze images from drones or phenomobiles. It allows to calculate traits multiple times during the season as opposed to destructive assessments. Monitoring the phenotyping allows to explain the quantitative and qualitative performance of your field. However, the term “trait” covers a lot of different reality: let’s take a deep dive!

 

2/ Categories of traits

The measurement of traits with high-throughput plant phenotyping produces variables: a discrete or continuous quantity that quantifies the traits that can then be used to compare different individuals. Traits availability and the precision of the associated variables depend both on sensors’ technological development and interpretation methods maturity.

However, a phenotyping trait can be from a very different nature. At Hiphen, we define categories of traits:

  • State traits which are measured at a specific time and are intrinsic properties of the crop/plant/organ. It models the plant structure and composition at a specific time.
  • Dynamic traits which are based on repeated estimates of state traits over a specific period but do not need additional inputs except a time scale. It often models the raw plant performance over a period of time.
  • Agroclimatic / Functional traits describe the quality of the plant processes, for instance its efficiency to use water. It represents a “net” performance of the plant, opposed to dynamic traits, and allow to understand the main driver of the yield or specific plant behavior. It is also expected to be more heritable characteristic of the plant. It often requires a combination of dynamic and environmental traits with.

 

traits diagram

 

For instance, we present in the diagram how at Hiphen we will evaluate the photosynthetic efficiency of your crop. After your UAV flights, we will be able to interpret your raw data into state traits/variables (step 1) (remember, it can be biophysical, biochemical, or sanitary!). By repeating your flights during the growing season at key phenological stages we will be able to integrate over time the state traits/ variables and transform them into dynamic traits (step 2) such as vigor or senescence (stay green). We can transform these dynamic traits into true agronomical traits (step 3) by combining them with environment information using agronomic modeling. Meanwhile, you just have to relax, sit back and enjoy clean, qualitative information from your trial on our data platform: Cloverfield.

By the way, here is an example of the distribution of a trait (green fraction or Fcover here) in Cloverfield:

field map with colored boxes

Feel free to contact us should you have any question about a specific phenotyping trait at www.hiphen-plant.com/contact/. We look forward to hearing from you!

Speak soon,

Your Hiphen team.

 

Phenotyping Traits Appendix

States traits

The states traits can be measured directly on the canopy and take exactly one value at a precise time. They can be categorized into three groups:

  • Biophysical traits describe the structural and morphological characteristics of canopies, plants, or organs. The aerial parts of the plant that are more easily accessible are often described: at the canopy level focus is generally on Green Fraction, Green Area index, Leaf orientation, plant height, lodging, plant density, ear density.
  • Biochemical traits provide information on the plant biochemistry. For instance, the chlorophyll content of a leaf or a canopy is an important biochemical trait that determines the photosynthetic potential.
  • Sanitary traits provide information on the plant health. For example, the detection of disease symptoms, the determination of contaminated parts of the plant are sanitary traits that are often derived from visual scoring of the symptoms severity made by human experts.

 

Example of state traits/variables:

Trait Mechanistic AI
Machine Learning​ Deep Learning​
Green Cover Fraction ✓​ ✓​ ✓​
Leaf Area Index ✓​ ✓​ ✓​
Height ✓​ ✓​
Lodging Score ✓​ ✓​
Leaf Chlorophyl Content ✓​ ✓​ ✓​
Canopy Chlorophyll Content ✓​ ✓​ ✓​
Plants Density ✓​ ✓​
Crop Cover Fraction ✓​
Senescence Fraction  ✓​
Head Density ✓​
Disease Fraction ✓​

 

Dynamic traits

Dynamic traits are based on repeated observations of state traits. Popular dynamic traits among breeders are the early vigor or the stay green. The early vigor is the plant or canopy growth speed, while the stay green is the plant or senescent canopy rate. Specific characteristics of the plant architecture plasticity are evaluated dynamically, such as the leaf rolling. Phenological traits are also dynamic traits that are measured by detecting qualitative changes in plant morphology. In wheat, tillering, stem elongation and heading or flowering are evaluated by monitoring biophysical traits such as plant height or wheat head density.

 

Functional traits

Several definitions of functional traits exist in the literature due to the concept being explored in the context of plant phenotyping and ecology. C.M Caruso in the International Journal of Plant Science vol. 181 proposes that “functional traits are generally considered aspects of plant phenotypes that influence growth, survival, and reproduction by mediating interactions with the biotic and abiotic environment”. We propose to define functional traits as traits describing canopy, plants, or organ reactions to the environment. Since they account explicitly for the environmental 17 conditions on some processes, they are expected to be less sensitive to some environmental factors. They will therefore be more heritable than most of the other traits. Efficiency traits are commonly used functional traits that evaluates the efficiency with which elements are used by the plant to grow. They include the radiation (RUE), water (WUE) and nitrogen (NUE) use efficiencies.

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