Why might a Punnett square not be useful for crosses with more than 1 gene?
Punnet Square is a graphical representation to study the inheritance pattern of phenotypes and genotypes with the helps of the alleles of genes. When more than two traits are being observed, a Punnett square becomes unwieldy and other tools are used to predict the outcomes of such crosses. Because, when more than one gene is present on the chromosome, the genes might have linked. If the genes are linked, then the expected genotypic and phenotypic ratio and real ratio is not comparable to actual number of progeny. The recombination of genes is depends on the distance between the genes. If the genes are too nearer, then the recombination is less whereas if the distance between the genes is more the recombination frequency is more. It means that the distnce between the genes is directly proportional to the recombination frequency.
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