Variants of a gene are called alleles, which can be either dominant or recessive. An organism's genotype (its genetic makeup) determines its phenotype (its expressed traits).
Through his experimentation with cross-breeding different varieties of pea plants, Gregor Mendel concluded that there were two variants for pea color and that the yellow one masked the green one. Today, scientists understand that diploid organisms carry two copies of each gene. The copies of the genes may be different. A version of a gene is known as an allele. When one allele masks the expression of another, it is said to be a dominant allele. The allele whose expression is masked by another allele is a recessive allele. When an individual has two identical alleles for a gene, it is said to be homozygous. If an individual carries two identical dominant alleles for a gene, it is called homozygous dominant, while individuals with two recessive alleles are called homozygous recessive. When an individual has two different alleles for a gene, it is said to be heterozygous. A heterozygous individual will have a phenotype of the dominant allele but may pass the recessive allele to offspring.
The observable characteristics (in Mendel's case, the color of the pea) of an organism that result from genetic and environmental influences is the organism's phenotype. The genetic makeup of the organism is its genotype, while its expressed traits make up its phenotype. Mendel's law of independent assortment is the principle that states that alleles of different genes are sorted into gametes independently of one another. However, some genes lie very close to each other on their chromosomes. These genes that are frequently inherited together are called linked genes.
The tool geneticists use to predict the possible genotypic outcomes of a cross between two individuals is called a Punnett square (named after its creator, Reginald C. Punnett, a British geneticist). The alleles of one parent are listed individually across the top, while the alleles of the other parent are listed individually down the left side. The square is then filled in with the corresponding alleles. By convention, the dominant allele is written using an uppercase letter, and the recessive allele is written using the same letter in lowercase.
The Punnett square for Mendel's pea plants uses the letter Y to represent the color of the peas, because the dominant color is yellow.
Punnett Square Showing Parent Pea Pod Color Inheritance
A Punnett square can then be used to predict the offspring of the self-pollination of the first generation (F1). When the first generation of pea plants self-pollinates, a Punnett square can then be used to determine the chances of the offspring having yellow peas or green peas. The resulting offspring have a 3:1 chance of having yellow peas as opposed to green peas.
Punnett Square showing F1 Generation Pea Pod Color Inheritance
Importantly, a Punnett square doesn't show how many offspring will have each genotype. Rather, it shows the chances each offspring has of having each genotype. In other words, self-pollinating a plant with genotype Yy four times does not guarantee two offspring with Yy genotype, one with YY, and one with yy. Each event has the same chance as the others of producing each genotype. Thus, the pollination of a plant with genotype Yy with another plant with genotype Yy gives a 25 percent chance of an offspring with genotype YY, a 50 percent chance of an offspring with genotype Yy, and a 25 percent chance of an offspring with genotype yy. Because both genotypes YY and Yy have plants with yellow peas, this cross results in a 75 percent chance of an offspring with a phenotype of yellow peas and a 25 percent chance of an offspring with green peas.