The term gene was a word that Mendel never knew. It was not coined until 1909, when the Danish geneticist Wilhelm Johannsen first used it. The definition of a gene varies with the context of its use, and so its definition will change as we explore different aspects of heredity. For our present use in the context of genetic crosses, we will define a gene as an inherited factor that determines a characteristic.
Genes frequently come in different versions called alleles. In Mendel’s crosses, seed shape was determined by a gene that exists as two different alleles: one allele codes for round seeds and the other codes for wrinkled seeds. All alleles for any particular gene will be found at a specific place on a chromosome called the locus for that gene. (The plural of locus is loci; it’s bad form in genetics — and incorrect — to speak of locuses.) Thus, there is a specific place — a locus — on a chromosome in pea plants where the shape of seeds is determined.
This locus might be occupied by an allele for round seeds or one for wrinkled seeds. We will use the term allele when referring to a specific version of a gene; we will use the term gene to refer more generally to any allele at a locus.
The genotype is the set of alleles that an individual organism possesses. A diploid organism that possesses two identical alleles is homozygous for that locus. One that possesses two different alleles is heterozygous for the locus. Another important term is phenotype, which is the manifestation or appearance of a characteristic. A phenotype can refer to any type of characteristic: physical, physiological, biochemical, or behavioral. Thus, the condition of having round seeds is a phenotype, a body weight of 50 kg is a phenotype, and having sickle-cell anemia is a phenotype.
Here, the term characteristic or character refers to a general feature such as eye color; the term trait or phenotype refers to specific manifestations of that feature, such as blue or brown eyes.
A given phenotype arises from a genotype that develops within a particular environment.
The genotype determines the potential for development; it sets certain limits, or boundaries, on that development. How the phenotype develops within those limits is determined by the effects of other genes and environmental factors, and the balance between these influences varies from character to character.
For some characters, the differences between phenotypes are determined largely by differences in genotype; in other words, the genetic limits for that phenotype are narrow. Seed shape in Mendel’s peas is a good example of a characteristic for which the genetic limits are narrow and the phenotypic differences are largely genetic. For other characters, environmental differences are more important; in this case, the limits imposed by the genotype are broad.
The height that an oak tree reaches at maturity is a phenotype that is strongly influenced by environmental factors, such as the availability of water, sunlight, and nutrients. Nevertheless, the tree’s genotype still imposes some limits on its height: an oak tree will never grow to be 300 m tall no matter how much sunlight, water, and fertilizer are provided. Thus, even the height of an oak tree is determined to some degree by genes. For many characteristics, both genes and environment are important in determining phenotypic differences.
An obvious but important concept is that only the genotype is inherited. Although the phenotype is determined, at least to some extent, by genotype, organisms do not transmit their phenotypes to the next generation. The distinction between genotype and phenotype is one of the most important principles of modern genetics. The next section describes Mendel’s careful observation of phenotypes through several generations of breeding experiments. These experiments allowed him to deduce not only the genotypes of the individual plants, but also the rules governing their inheritance.