Let’s take a moment to consider in more detail exactly what an allele is and how it determines a phenotype. Although Mendel had no information about the physical nature of the genetic factors in his crosses, modern geneticists have now determined the molecular basis of these factors and how they encode a trait such as wrinkled seeds.

Alleles, such as the R and r alleles that encode round and wrinkled peas, usually represent specific DNA sequences. The locus that determines whether a pea is round or wrinkled is a sequence of DNA on pea chromosome 5 that encodes a protein called starch-branching enzyme isoform 1 (SBEI). The R allele, which produces round seeds in pea plants, encodes a normal, functional form of SBEI. This enzyme converts a linear form of starch into a highly branched form. The r allele, which encodes wrinkled seeds, is a different DNA sequence that contains a mutation or error; it encodes an inactive form of the enzyme that does not produce the branched form of starch and leads to the accumulation of sucrose within the rr pea. Because the rr pea contains a large amount of sucrose, the developing seed absorbs water and swells. Later, as the pea matures, it loses water. Because rr peas have absorbed more water and expanded more during development, they lose more water during maturation and afterward appear shriveled or wrinkled. The r allele for wrinkled seeds is recessive because the presence of a single R allele in the heterozygote encodes enough SBEI enzyme to produce branched starch and round seeds.

Research has revealed that the r allele contains an extra 800 base pairs of DNA that disrupt the normal coding sequence of the gene. The extra DNA appears to have come from a transposable element, a type of DNA sequence that has the ability to move from one location in the genome to another, which we will discuss further in Chapter 13.