Mendel began his studies with crosses between true-breeding strains that differed in a single contrasting characteristic. Crossing peas is not as easy as it may sound. Pea flowers include both female and male reproductive organs enclosed together within petals (Fig. 16.4). Because of this arrangement, pea plants usually fertilize themselves (self-fertilize). Performing crosses between different plants is a tedious and painstaking process. First, the flower of the designated female parent must be opened at an early stage and the immature anthers (male reproductive organs) clipped off and discarded, so the plant cannot self-fertilize. Then mature pollen from the designated male parent must be collected and deposited on the stigma (female reproductive organ) of the female parent, from where it travels to the reproductive cells in the ovule at the base of the flower. And finally, a cloth bag must be tied around the female flower to prevent stray pollen from entering. No wonder Mendel complained that his eyes hurt!

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For each of the seven pairs of contrasting traits, true-breeding strains differing in the trait were crossed. Fig. 16.5 illustrates a typical result, in this case for a cross between a plant producing yellow seeds and a plant producing green seeds. In these kinds of crosses, the parental generation is referred to as the P₁ generation, and the first offspring, or filial, generation is referred to as the F₁ generation. In the cross of P₁ yellow × P₁ green, Mendel observed that all the F₁ progeny had yellow seeds. This result was shown to be independent of the seed color, yellow or green, of the pollen donor because both of the crosses shown below yielded progeny plants with yellow seeds:

Crosses like these, in which the expressions of the trait in the female and male parents are interchanged, are known as reciprocal crosses. Mendel showed that reciprocal crosses yielded the same result for each of his seven pairs of contrasting traits.

Moreover, for each pair of contrasting traits, only one of the traits appeared in the F₁ generation. For simple crosses involving two parents that are true breeding for different traits, the trait that appears in the F₁ generation is said to be dominant, and the contrasting trait that does not appear is said to be recessive. For each pair of traits illustrated in Fig. 16.3, the dominant trait is shown on the left, and the recessive on the right. Thus, yellow seed is dominant to green seed, round seed is dominant to wrinkled seed, and so forth.

Mendel explained these findings by supposing that there is a hereditary factor for yellow seeds and a different hereditary factor for green seeds, likewise a hereditary factor for round seeds and a different one for wrinkled seeds, and so on. We now know that the hereditary factors that result in contrasting traits are different forms of a gene that affect the trait. The different forms of a gene are called alleles. The alleles of a gene are variations of the DNA sequence of a gene that occupies a particular region along a chromosome. The particular combination of alleles present in an individual constitutes its genotype, and the expression of the trait in the individual constitutes its phenotype. As noted, Mendel found that, for each of his traits, one phenotype was dominant and the other phenotype was recessive.

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In the cross between true-breeding plants that produce yellow seeds and true-breeding plants that produce green seeds, the genotype of each F₁ seed includes an allele for yellow from the yellow parent and an allele for green from the green parent. The phenotype of each F₁ seed is nevertheless yellow, because yellow is dominant to green.

The molecular basis of dominance in this case is the fact that, in diploid organisms, only one copy of a gene is needed to carry out its normal function. The yellow color in pea seeds results from an enzyme that breaks down green chlorophyll, allowing yellow pigments to show through. Green seeds result from a mutation in this gene that inactivates the enzyme, and so the green chlorophyll is retained. In an F₁ hybrid, such as that in Fig. 16.5, which receives a nonmutant gene from one parent and a mutant gene from the other, the seeds are yellow because one copy of the nonmutant gene produces enough of the enzyme to break down the chlorophyll to yield a yellow seed.