Making sense of genotype-phenotype distinctions

Since the terms genotype, phenotype, and gene were coined by Johannsen (1911), four conceptually distinct meanings of genotype have emerged:

a) The whole of the genome and other hereditary materials that are perpetuated over generations (e.g., mitochondria DNA)—or, at least, those parts that vary within the species and thus define the individual organism in contrast to others in the same species.
b) The specific form of genes—alleles—at single locus or a small set of loci on the genome or other hereditary materials.
c) The class of individuals who share the genome and any other hereditary materials. This sense of genotype applies when the term is used as a synonym for variety or line in agricultural or laboratory breeding, in which a group of individuals are related by genealogy from a common ancestor or set of ancestors. Such relatedness by descent can take three forms: pure (inbred or cloned) lines; offspring of a given pair of parents or ancestors; or an open pollinated plant variety in which hereditary materials vary within replicable bounds among individuals in the class.
d) The class of individuals who share alleles at a locus or small set of loci. Other parts of their genome and other hereditary materials may vary among the individuals.
The corresponding senses of phenotype are, for some defined or implied conditions:
a) The whole set of traits exhibited by an individual organism.
b) The trait associated with the alleles.
c) The distribution of traits exhibited across the class of individuals who share the genome and any other hereditary materials.
d) The distribution of traits exhibited across the class of individuals who share alleles at a locus or small set of loci.
None of these genotype-phenotype distinctions maps well to the original distinction of Johannsen. To make sense of the differences and shifts in meaning it is necessary to examine the control of biological materials and conditions involved in establishing what counts as reliable knowledge about heredity and variation for the given scientists or writers.
to be continued (comments welcome)

Reference:

Johannsen, W. (1911). “The Genotype Conception of Heredity”. The American Naturalist 45 (531): 129–59. doi:10.1086/279202. JSTOR 2455747.

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