Often there is more than one variant of a gene in a given population; these variants are called alleles. Punnett squares are a simple visual aid to help you calculate the proportion of offspring from a cross with a specific combination of alleles. Drawing up a Punnett square for a self-fertilized plant is especially easy because you already know what must be on both the top and the side of the square, so the rest just involves filling in the square itself.
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Draw a square on your paper and divide it into four equal squares by drawing two more lines. Your square now has two rows by two columns.
Write one of the two alleles the plant possess at the top of each column. For every given gene in its genome, the plant will have two alleles, one of which is inherited from the paternal line and the other inherited from the maternal line. These alleles may be identical, in which case the plant is homozygous for that gene, or they may be different, in which case the plant is heterozygous for that gene. If the plant inherited two alleles of a given gene, and one of these is represented by an upper-case "R" for a dominant trait while the other is represented by a lower-case "r" for a recessive trait, for example, you would write "R" above one column and "r" above the other.
Write the same two alleles next to each row in the square.
Fill in each of the four boxes in the square by writing the allele for that row together with the allele for that column. For example, if you have a self-fertilized plant with alleles R and r, one box would end up with RR, another with rr, and two more with Rr. Once all four boxes are full, you have completed your Punnett square. The results indicate the expected ratios of allelic combinations in the offspring.
Note that the only real difference between a Punnett square for a self-fertilized plant and a Punnett square for a normal cross is that the genotype or combination of alleles for both parents is the same because the same plant serves as both "mother" and "father."