Once you have developed an understanding of basic single gene crosses you need to learn to extend the concepts to cover cases where there are more than two alleles of any particular gene. Of course, if you are dealing with diploid organisms then any single organism carries just two copies of the gene so what we mean is that there are more than two alleles in the population (or species). Actually, this is extremely common - the case of just two alleles is the exception. Alleles arise by the process of mutation - which is covered in detail elsewhere - and over time a population can have many alleles.
To deal with multiple alleles, no new concepts need to be developed. Instead, here are just some general points to keep in mind when applying the basic single gene cross concepts:
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The standard format is to use a single letter or word to refer to a gene. Individual alleles are then designated by a subscript or superscript. For example, A1, A2, A3, and A4 are four alleles of a single gene and B1, B2, B3, and B4 are four alleles of another gene.
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Any cross of diploids will involve a maximum of four different alleles, two from each individual. For example A1A3 x A2A4 could occur. Although there might be more alleles within the population, an individual cross can involve any number of alleles up to four, depending of course on the genotypes of the individuals. So, even if there are eight alleles in the population. a cross might involve just one: e.g. A3A3 x A3A3.
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Segregation and zygote formation are the same processes, so simply draw out a Punnett Square if you are uncertain about the genotypes that can arise in the progeny. You should be able to see that there are four possible combinations of alleles in the progeny (this does not mean that all combinations are necessarily different genotypes, just that you can arrange the parental alleles in four ways): Allele 1 from parent 1 with allele 1 from parent 2; Allele 1 from parent 1 with allele 2 from parent 2; Allele 2 from parent 1 with allele 1 from parent 2; Allele 2 from parent 1 with allele 2 from parent 2. Each of the four is one of the four squares in the Punnett Squares and each occurs with a frequency of ¼
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As a result of the previous point, from the cross A1A3 x A2A4 the four genotypes that can arise are A1A2, A1A4, A3A2 and A3A4.
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Once you know the resulting genotype frequencies you can determine the resulting phenotype frequencies based on how the alleles interact (that is, what allele is dominant to which other alleles etc.) So, figure out the cross using genotypes and then use your results to figure out the resulting phenotypes.
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You need to figure out all possible allele interactions by observation, you should never make any assumptions. What this means is that you might observe that allele A1 is dominant to allele A2 and that A2 is dominant to A3. You should not assume from this that A1 is dominant to A3, you need to observe an A1A3 heterozygote to find out how the alleles interact. (You might observe that there is incomplete dominance or even co-dominance!)
Allele Series: An allele series refers to the situation when a set of alleles forms a dominance series such that, in the case of 4 alleles (in this example) for a gene:
D1 > D2 > D3 > D4 where > means dominant to.
Where an allele in the diagram is Dominant to any other allele to the right of it in the list (so A1 is dominant to A2, A3 and A4).
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