A guide on how to identify an allele
Alleles are different varieties of a single gene. For example, we often talk about a mutant allele and a wildtype allele for some gene. Discus like most all animals are diploid meaning they have 2 alleles for each gene. One allele came from the mother and the other allele came from the father. When it comes time to reproduce, discus make sperm and eggs through meiosis that each only have 1 allele (haploid) chosen at random from the 2 they carry. Fertilization brings two alleles back together to make a diploid fish.
An essential step in understanding Discus genetics is connecting the observed segregation of traits in a cross to specific alleles of different genes. This can be confusing so I’ve assembled the following guide to help you know what to look for. To use this guide, you should first identify phenotypes that are segregating in a cross. Segregating means that some progeny have the trait and some don’t. You should then try to match the pattern of segregation to the following examples while keeping in mind the possible sources of confusion.
A gene is a chunk of DNA on a chromosome which typically encodes a protein. Alleles are different varieties of a particular gene. The wildtype allele by definition encodes a protein with normal function. A mutant allele may encode a protein with no function, it might encode a protein with a new function, or it might encode a protein with normal function but turned on in different cells than normal.
Recessive alleles. Recessive alleles are only seen phenotypically when homozygous. They are denoted with lowercase italics. For example, if a is a recessive allele and + is the wildtype allele then the possible combinations of alleles in an individual are
genotype: phenotype
+/+: wildtype
a/+: wildtype
a/a: mutant
The possible crosses are as follows with results shown genotype (phenotype)
a/+ x +/+: 50% a/+ (wildtype), 50% +/+ (wildtype)
a/+ x a/+ = 25% a/a (mutant), 50% a/+ (wildtype), 25% +/+ (wildtype)
a/a x a/+ = 50% a/a (mutant), 50% a/+ (wildtype)
a/a a/a = 100% a/a (mutant)
If a trait disappears in one generation and reappears in the next generation, then it is most likely recessive (the other option is that epistasis as explained below is hiding a dominant phenotype).
Dominant alleles. Dominant alleles have the same phenotype when heterozygous or homozygous. They are denoted with uppercase italics. For example, if B is a dominant allele and + is the wildtype allele then the possible combinations of alleles in an individual are:
genotype: phenotype
+/+: wiltype
B/+: mutant
B/B: mutant
The possible crosses are as follows with results shown genotype (phenotype)
B/+ x +/+: 50% B/+ (mutant), 50% +/+ (wildtype)
B/+ x B/+ = 25% B/B (mutant), 50% B/+ (mutant), 25% +/+ (wildtype)
B/B x B/+ = 50% B/B (mutant), 50% B/+ (mutant)
B/B B/B = 100% B/B (mutant)
Dominant alleles cannot hide except through epistasis.
Semidominant alleles. Semidominant alleles have one phenotype when heterozygous and a different (often more pronounced) phenotype when homozygous. They are denoted with uppercase italics. For example, if C is a semidominant allele and + is the wildtype allele then the possible combinations of alleles in an individual are:
genotype: phenotype
+/+: wiltype
C/+: mutant phenotype 1
C/C: mutant phenotype 2
The possible crosses are as follows with results shown genotype (phenotype)
C/+ x +/+: 50% C/+ (phenotype 1), 50% +/+ (wildtype)
C/+ x C/+ = 25% C/C (phenotype 2), 50% C/+ (phenotype 1), 25% +/+ (wildtype)
C/C x C/+ = 50% C/C (phenotype 2), 50% C/+ (phenotype 1)
C/C x C/C = 100% C/C (phenotype 2)
Possible sources of confusion.
Some traits will not follow the above rules. Common reasons are as follows:
Small sample size. When you flip a fair coin there is a 50% chance it will be heads and 50% chance it will be tails. But this does not guarantee that your results will always be 50:50. If you flip a coin twice, there is a 50% chance you’ll get one head and one tail and a 50% chance you’ll get the same thing twice. The more you flip it, the more likely that the results will be near 50%. The same math holds for alleles and is called a binomial distribution. There are binomial calculators online that will tell you the chances of getting observed vs. predicted that might help you decide if your numbers match the predictions closely enough to fit the above predictions are not (http://stattrek.com/online-calculator/binomial.aspx). For the a/+ x a/+ cross, if you look at 40 progeny, the chances of seeing N a/a individuals is:
N p
5 2.7%
6 5.3%
7 8.6%
8 11.8%
9 14%
10 14%
11 13%
12 11%
13 7.6%
14 5%
15 2.8%
Incomplete penetrance. Incomplete penetrance means that not all of the animals that should have a phenotype based on their genotype, do have a phenotype. Incomplete penetrance causes there to be more phenotypically wildtype progeny than reflected in the numbers above. Whether or not an incompletely penetrant allele shows a phenotype can be based on what other genes (modifiers) are present in the genome, on the environment, or on chance. If your trait consistently follows one of the above patterns but just with lower number of mutants, then it might be due to an incompletely penetrant allele.
Epistasis. Epistasis means that the phenotype of one genetic locus (gene) hides the effect of another genetic locus (gene). For example albino mutants cannot make the black pigment melanin and are recessive. In Pigeon blood mutants which is dominant, the melanin producing cells called melanocytes are scattered rather than localized in stress bars. Imagine the following cross:
Pb/+; alb/+ x +/+; alb/+ (one parent is phenotypically Pigeon blood and neither are albino). The progeny are:
12.5%: Pb/+; +/+ (Pigeon blood)
12.5%: +/+; +/+ (wildtype)
25%: Pb/+; alb/+ (Pigeon blood)
25%: +/+; alb/+ (wildtype)
12.5%: Pb/+; alb/alb (albino)
12.5%: +/+; alb/alb (albino)
If you sum up the phenotypes you get 37.5% Pigeon blood, 25% albino, and 37.5% wildtype. If you were just focused on Pigeon blood then these numbers would be confusing. To understand the numbers you must understand that albino is epistatic to Pigeon blood (the double mutant has the same phenotype as albino). In this case a recessive allele of one gene is hiding the phenotype of a dominant allele of another gene.
Multiple genes with the same phenotype. It is possible for two different genetic loci (genes) to have the same phenotype when mutated. For example, it seems that there are two different albino mutations in Discus. They are both all white when homozygous but one of them has red retinas (rabbit eyes, true albino) and the other has maroon retinas (grape eye, lutino). If alleles for both genes were present in a cross, then the ratio of the offspring would appear weird if you didn’t consider this possibility. To determine if two alleles are for the same gene or for different genes you can do a complementation test. For recessive alleles, you determine if having 1 copy of 1 allele and 1 copy of the other allele gives the same phenotype as having 2 copies of either allele. If it does then it is the same gene, if not (it complements) then they are different genes.
Lethality. It is possible that an allele might give one phenotype when heterozygous and result in lethality in homozygotes. This appears to be the case for snakeskin.
Polygenic. Some traits are controlled by more than one genetic locus in such a way that it is difficult to establish any kind of pattern between genotype and phenotype by only looking at one gene.
Sex linked. In mammals and birds sex is determined by sex chromosomes. In mammals, XX is female and XY is male. In birds, WW is male and WZ is female. The Y and Z chromosomes typically lose genes over the course of evolution until they only have the sex determination gene on them. This means that male mammals have only one copy of X-linked genes so dominant and recessive no longer apply. For example, color blindness is recessive in females but males with one bad copy are color blind. However, many fish species do not use sex chromosomes for determining sex, and sex determination systems evolve quite quickly. As far as I know, it is unknown how sex is determined in Discus.
Note: You should not think that dominant genes are "stronger" and recessive genes are "weaker". Dominant and recessive implies nothing except whether the heterozygotes have one phenotype or the other. Likewise you should not say that an allele is more dominant or more recessive. This is like saying an animal is more dead than another. Dominant and recessive can't be modified by a superlative.
Re: A guide on how to identify an allele
Re: A guide on how to identify an allele
Quote:
Originally Posted by
warlock4169
:confused:
yea thats some intense biology... havent brushed up on that since 10th grade.
Re: A guide on how to identify an allele
I hate biology -.-' Nice write up tho, i only understand part of it hehe.
Re: A guide on how to identify an allele
i was high school biology teacher.. it was a fun topic in my class..
but for discus not so much..
i just buy them for their Phenotype.. not Genotype..
Re: A guide on how to identify an allele
Quote:
Originally Posted by
SeaDragon
Ahh good ole bio, this info is great food for thought. Discus are certainly way better then learning it with fruit flies! Now if only we could get them to tell us which individuals carry the albino genes!
Sent from the bottom of my aquarium using Tapatalk
Stay on the bottom of your tank, you are too critical :D
Good article for everybody wants to know how compicated genetics can be.
