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Some definitions from Genetics
Here are some definitions to start with:
Allele
A snippet of DNA at a specified locus on a chromosome. Usually, the snippet of DNA equals one gene, but not always (people are now talking about alleles in junk DNA, where there are no genes that normally express themselves). Diploid organisms have paired homologous chromosomes; therefore each chromosome of the pair has a version of each allele. These versions may be identical, or different. When identical, the individual is homozygous, otherwise the individual is heterozygous.
Alleles may often be dominant or recessive, which refers to whether or not they express their traits in the phenotype. A dominant allele will always express itself in the phenotype, whereas a recessive allele will only express if no dominant allele is present (two recessive alleles present instead). However, many alleles are neither dominant or recessive. They can be incompletely dominant (traits of both alleles are blended, also known as blended inheritance), such as when crossing Antirrhinums — flowers with incompletely dominant red and white alleles for petal color — the resulting offspring have pink petals. Or they may be co-dominant, such as A and B human blood types, each of which is expressed, resulting in an AB blood type.
Note that it is not necessary that all genes will only have two possible alleles. For example, in human blood types there are 3 possible alleles: A, B, and i. Type A produces antigen A, type B produces antigen B, and type i does not produce any antigen at all, leading to condition O. This is why they are known as ABO blood types. While multiple alleles of a gene may exist in the wild (in a given population), any particular individual can only have 2 alleles since there are only 2 homologous chromosomes for a diploid organism. The alleles in any individual determine his phenotype, given the caveats that alleles can be dominant, co-dominant, incompletely dominant, or recessive. Also, not all traits are controlled by a specific gene. Some traits can be controlled by more than a single gene (therefore by more than 2 alleles). Such traits are called polygenic.
Relationship
of alleles to phenotype in human blood groups |
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Allele
1 |
Allele
2 |
Genotype |
Phenotype |
A |
A |
AA |
A |
A |
B |
AB |
AB |
A |
i |
Ai |
A |
B |
A |
BA |
AB |
B |
B |
BB |
B |
B |
i |
Bi |
B |
i |
A |
iA |
A |
i |
B |
iB |
B |
i |
i |
ii |
O |
Note that there are 9 possible permutations of alleles, which lead to 6 possible genotypes (Ai = iA, Bi = iB, AB = BA) and 4 possible phenotypes (AA = A, BB = B).
Single Nucleotide Polymorphism
A Single Nucleotide Polymorphism, or SNP, is the variation of a single nucleotide pair (A-T replaced with C-G, or vice versa) within a defined DNA snippet. This DNA snippet might be a gene (both in coding and non-coding regions of the gene), or a non-gene (intergenic) part of the chromosome. As such, an SNP creates alleles. Most SNPs only have two versions of the allele, one with A-G and the other with C-T at the specified location.
Even SNPs within the coding region of a gene don't necessarily create differences in the amino acids coded, because of the degeneracy of the genetic code. An SNP in which the amino acid is not changed is called synonymous, while an SNP in which the amino acid is changed as a result of the SNP is called non-synonymous. SNPs not in protein-coding regions may still have consequences for gene splicing, transcription factor binding, or the sequence of non-coding RNA.
SNPs are important in the study of population genetics. The minor allele frequency is the ratio of chromosomes in the population carrying the less common variant to those with the more common variant. Therefore, by definition it is always less than one (though some people now express them as a percentage instead). Since populations differ, the minor allele frequency can only be stated for a defined population.