Phenotype versus genotype

Since its first mention by Danish botanist Wilhelm Johannsen over 100 years ago, the term ‘phenotype’ has been used to describe a wide range of characteristics in plants, microbes, fungi and animals.

In short, the functional body (phenotype) of an organism, e.g. a plant, is formed during plant growth and development from the dynamic interaction between the genetic background (genotype) and the physical world in which the plant develops (environment). These interactions determine plant performance and productivity measured as accumulated biomass and commercial yield and resource use efficiency.

Plant phenotyping as a scientific tool

The term ‘phenotyping’ was beginning to be used in the 1960s indicating a quantitative analysis of characteristics of an organism or traits to the description of the variability of proteins and metabolic pathways that determine the character of living plants. Within the last decades, phenotyping has developed as an essential tool for the characterisation of an enormous amount of processes, functions, and structures of plants mostly by non-destructive optical analyses of plant traits based on images. As such, plant phenotyping started to become a toolbox applicable for plant scientists to understand plant-environment interaction as well as to plant breeders to select desirable genotypes for their specific field of interest such as for instance drought tolerance, pathogen resistance or increased yield.

Why do we need plant phenotyping?

Today, the yield of key crops typically increases by about 1% per year , which is below the required rate of 1.5-2.2% improvement to meet increased global demand (FAO). In the past decades, genetic improvement has been a major source of yield increase, together with improved cropping systems. Designing high yielding varieties adapted to contrasting environmental conditions including those associated with climate change and new agricultural management systems is an urgent priority. However, creating new varieties in plant breeding is a long-term process, as developing and bringing new varieties to the markets may take up 15 years or even more.

While genotyping is now very rapid and relatively cheap due to “industrialized sequencing pipelines”, plant phenotyping, i.e., the quantitative analysis of crop performance, remains a bottleneck. Substantial and concerted action for accelerating development and increasing availability of phenotyping infrastructures is required to substantially accelerate plant breeding. This is addressed by the establishment of an integrated plant phenotyping infrastructure.

EMPHASIS plays a key role by integrating the European plant phenotyping infrastructure and ensuring an effective utilisation of synergies.