Mendel drew several important conclusions from the results of his monohybrid crosses. First, he reasoned that, although the F₁ plants display the phenotype of only one parent, they must inherit genetic factors from both parents because they transmit both phenotypes to the F₂ generation. The presence of both round and wrinkled seeds in the F₂ plants could be explained only if the F₁ plants possessed both round and wrinkled genetic factors that they had inherited from the P generation. He concluded that each plant must therefore possess two genetic factors encoding a characteristic.

The genetic factors (now called alleles) that Mendel discovered are, by convention, designated with letters: the allele for round seeds is usually represented by R and the allele for wrinkled seeds by r. The plants in the P generation of Mendel’s cross possessed two identical alleles: RR in the round-seeded parent and rr in the wrinkled-seeded parent (Figure 3.4a).

The second conclusion that Mendel drew from his monohybrid crosses was that the two alleles in each plant separate when gametes are formed, and one allele goes into each gamete. When two gametes (one from each parent) fuse to produce a zygote, the allele from the male parent unites with the allele from the female parent to produce the genotype of the offspring. Thus, Mendel’s F₁ plants inherited an R allele from the round-seeded plant and an r allele from the wrinkled-seeded plant (Figure 3.4b). However, only the trait encoded by the round allele (R) was observed in the F₁: all the F₁ progeny had round seeds. Those traits that appeared unchanged in the F₁ heterozygous offspring Mendel called dominant, and those traits that disappeared in the F₁ heterozygous offspring he called recessive. Alleles for dominant traits in plants are often symbolized with uppercase letters (e.g., R), while alleles for recessive traits are often symbolized with lowercase letters (e.g., r). When dominant and recessive alleles are present together, the recessive allele is masked, or suppressed. The concept of dominance was the third important conclusion that Mendel derived from his monohybrid crosses.

Mendel’s fourth conclusion was that the two alleles of an individual plant separate with equal probability into the gametes. When plants of the F₁ (with genotype Rr) produced gametes, half of the gametes received the R allele for round seeds and half received the r allele for wrinkled seeds. The gametes then paired randomly to produce the following genotypes in equal proportions among the F₂: RR, Rr, rR, rr (Figure 3.4c). Because round (R) is dominant over wrinkled (r), there were three round seeds (RR, Rr, rR) for every one wrinkled seed (rr) in the F₂. This 3:1 ratio of round to wrinkled progeny that Mendel observed in the F₂ could be obtained only if the two alleles of a genotype separated into the gametes with equal probability.

The conclusions that Mendel developed about inheritance from his monohybrid crosses have been further developed and formalized into the principle of segregation and the concept of dominance. The principle of segregation (Mendel’s first law) states that each individual diploid organism possesses two alleles for any particular characteristic, one inherited from the maternal parent and one from the paternal parent. These two alleles segregate (separate) when gametes are formed, and one allele goes into each gamete. Furthermore, the two alleles segregate into gametes in equal proportions. The concept of dominance states that when two different alleles are present in a genotype, only the trait encoded by one of them—the “dominant” allele—is observed in the phenotype.

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Mendel confirmed these principles by allowing his F₂ plants to self-fertilize and produce an F₃ generation. He found that the plants grown from the wrinkled seeds—those displaying the recessive trait (rr)—produced an F₃ in which all plants produced wrinkled seeds. Because his wrinkled-seeded plants were homozygous for wrinkled alleles (rr), only wrinkled alleles could be passed on to their progeny (Figure 3.4d).

The plants grown from round seeds—the dominant trait—fell into two types (see Figure 3.4c). With self-fertilization, about ⅔ of these plants produced both round and wrinkled seeds in the F₃ generation. These plants were heterozygous (Rr), so they produced ¼ RR (round), ½ Rr (round), and ¼ rr (wrinkled) seeds, giving a 3:1 ratio of round to wrinkled among their progeny in the F₃. About ⅓ of the F₂ plants grown from round seeds were of the second type; they produced only the round-seeded trait in the F₃. These plants were homozygous for the round allele (RR) and could thus produce only round-seeded offspring in the F₃ generation. Mendel planted the seeds obtained in the F₃ and carried these plants through three more rounds of self-fertilization. In each generation, ⅔ of the round-seeded plants produced round and wrinkled offspring, whereas ⅓ produced only round offspring. These results are entirely consistent with the principle of segregation.

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