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Dihybrid cross

More complicated crosses can be made by looking at two or more genes. The Punnett square only works, however, if the genes are independent of each other, which means that having a particular allele of gene X does not imply having a particular allele of gene Y.

The following example illustrates a dihybrid cross between two heterozygous pea plants. R represents the dominant allele for shape (round), while r represents the recessive allele (wrinkled). Y represents the dominant allele for color (yellow), while y represents the recessive allele (green). If each plant has the genotype Rr Yy, and since the alleles for shape and color genes are independent, then they can produce four types of gametes with all possible combinations: RY, Ry, rY and ry.


RY Ry rY ry
RY RRYY RRYy RrYY RrYy
Ry RRYy RRyy RrYy Rryy
rY RrYY RrYy rrYY rrYy
ry RrYy Rryy rrYy rryy

Since dominant traits mask recessive traits, there are nine combinations that have the phenotype round yellow, three that are round green, three that are wrinkled yellow and one that is wrinkled green. The ratio 9:3:3:1 is typical for a dihybrid cross.


Tree method

Another way to solve dihybrid and multihybrid crosses is to use the tree method


This method is particularly advantageous when crossing homozygous organisms.

Situations where Punnett squares do not apply

The phenotypic ratios of 3:1 and 9:3:3:1 are theoretical predictions based on the assumptions of segregation and independent assortment of alleles (see Mendelian inheritance). Deviations from expected ratios can occur if any of the following conditions exists:

  • the alleles in question are on the same chromosome and linked
  • one parent lacks a copy of the gene, e.g. human males have only one X chromosome, from their mother, so only the maternal alleles have an effect on the organism (see sex linkage)
  • the survival rate of different genotypes is not the same, e.g. one combination of alleles may be incompatible with life so that the affected offspring expires in utero
  • alleles may show incomplete dominance or co-dominance (see dominance relationship)
  • there are genetic interactions (epistasis) between alleles of different genes
  • the trait is inherited on genetic material from only one parent, e.g. mitochondrial DNA is only inherited from the mother (see maternal effect)
  • the alleles are imprinted

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