To reach this conclusion, one has to do a dihybrid cross. This means that two genes responsible for different traits need to be analyzed at the same time.

1) Starting with a parental generation of a cross between two pure lines (homozygous for both genes) with different traits, a plant with yellow and round seeds (YYRR) and another with green and wrinkled seeds (yyrr). The F1 will be phenotypically homogeneous (yellow and round), and genotypically heterozygous (YyRr).

2) If the individuals from the F1 are crossed with one another, we have to do a Punnett Square to determine the phenotypic ratio of the F2.

If the genes assort independently, the F1 individuals will produce their different gametes with the same probability. Each possible gamete will appear in a 1/4 proportion: YR, Yr, yR, yr.
The 9:3:3:1 ratio is a result of analyzing the possible phenotypes that result from the dihybrid cross.

See the attached image for an illustration of the crosses in each generation and the Punnett Square.

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Explanation:

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