Each of the traits that Mendel observed in his pea plants came in one of two varieties; modern science calls any gene that gives rise to more than one version of the same trait an allele. So, for example, the tall gene and the short gene are different alleles (variations) of the height gene.

 

    Every somatic cell contains two complete sets of chromosomes, one from each parent. Now you can understand why homologous chromosomes are similar, but not identical: although they contain the same genes, they may not contain the same alleles for these genes.

 

 

    Going back to Mendel’s plants, we can now say that all of his true-breeding plants contained two of the same alleles for each of the observed genes. Tall plants in this P generation had two alleles for tallness (TT), and short P generation plants had two alleles for shortness (tt). Anytime an organism’s two alleles for a specific trait are identical, that the individual is said to be homozygous (“homo” means same) for that trait.

 

    On the other hand, crossing the tall and short plants to produce F₁ hybrids created a generation of plants with one tall allele and one short allele (Tt). An organism with two opposing alleles for a single gene is said to be heterozygous for that trait.

 

    Genotype and Phenotype

 

    Although the P generation of pure-breeding tall plants looked the same as their hybrid F₁ offspring, the P and F₁ generations did not have identical genetic makeups. The genetic makeup of a certain trait (e.g., TT, Tt, or tt) is called its genotype, while the physical expression of these traits (e.g., short or tall) is called a phenotype.

 

    For any given trait, an organism’s genotype will indicate alleles from both parents, while the phenotype only indicates the allelic form that is physically expressed in that individual. This distinction between genetic makeup and physical appearance explains the apparent “disappearance” of the recessive alleles in the F₁ generation. Mendel’s results for the F₂ generation can also be reinterpreted in light of these new distinctions. Mendel’s results showed that 75 percent of the F₂ offspring exhibited the dominant phenotype, a ratio of 3:1 dominant to recessive. But from a genetic perspective, the breakdown would actually be around 25 percent homozygous dominant (TT), 50 percent heterozygous with a dominant phenotype (Tt), and 25 percent homozygous recessive (tt)—a ratio of 1:2:1.

 

 

    The Punnett square is a convenient graphical method for representing the genotypes of the parental gametes and all the possible offspring they produce. The Punnett square below shows the mating of two F₁ hybrids (Aa genotype). We call this mating a monohybrid cross, because it involves only one gene. According to the law of segregation, two possible gametes are formed: A and a. The paternal gametes are listed as columns across the top of the square, and maternal gametes are listed as rows down the left side of the square. Combining the gametes in the intersecting boxes provides the genotypes of all possible offspring.