Part 1: Phenotype Vocabulary in MAB

Phenotyping is central to all plant breeding activities. Phenotyping is the measuring of traits or characteristics that an organism has, for example, its yield, color, shape, height, and so on. This section specifically addresses those aspects of phenotyping which are especially relevant to Marker Assisted Breeding (MAB; you may also see this described using the term, MAS, which stands for Marker Assisted Selection.), in particular to Quantitative Trait Loci (QTL), which are discussed in a later chapter.  Phenotyping’s sister term is genotyping, which is assessing the genetic or DNA information of the organism. Together, phenotyping and genotyping are the cores of Marker Assisted Breeding.

Standardizing the names you assign to the traits you are measuring is very important. For researchers to be able to share discoveries and information, they must be confident that everyone understands the same thing by a particular trait name. Otherwise it is impossible to compare experiments done by different people, or for another researcher to understand your results. For example, the term “kernel size” could refer to either length and/or width, weight, or just a visual score on a numerical scale. Similarly, while some refer to "kernels" (Illustration 1), others may use the word "grain" or "seed" or even "caryopsis" to denote exactly the same thing.

An ontology is a structured controlled vocabulary, where term definitions are agreed upon and used consistently by a community.  For example, the grain yield of a wheat crop is commonly expressed as kilograms per hectare of mature grain at 14% moisture content; and grain size as the weight of 1,000 dehusked grains. A number of publicly available ontologies have been developed, where you can browse the terms used for a large number of traits, letting you name each trait in the same way as other colleagues within the plant research community.

For examples, see the Integrated Breeding Platform (see each crop) or Gramene.