AVIAN GENETICS

When two or more genes reside on the same chromosome, whether sex chromosome or autosome, they are considered linked. Linked genes do not independently assort during gamete formation. However, linked genes do not always stay together because homologous non-sister chromatids may exchange segments of varying length with each other. This chromatid exchange, referred to as crossover, occurs during prophase I of meiosis when homologous chromosomes synapse. In the Figure below, the sex-linked genes for Opaline (op) and Cinnamon (cin) are used to demonstrate crossover. In this case, the male is heterozygous for both traits. You will also notice that the mutations are arranged such that they do not both occur on the same chromosome. This arrangement ([+,op][cin,+]) is referred to as repulsion. If both dominant (or wild-type) alleles are on one chromosome and both recessive (or mutants) are on the other the linkage relationship ([+,+][op,cin]) is referred to as coupling.

The Bird Tracker program will compute crossover for sex-linked genes only. The Dark Factor gene and Blue gene within Budgerigars are linked autosomal genes. Since the Bird Tracker program will treat these genes as independently assorting genes the user should realize that the displayed percentages are not accurate when working predictions with these genes. The Bird Tracker program allows the user to control the location of the sex-linked mutations by selecting the Decouple button in the Sex-Linked Mutations selection box on the Add Genetic Traits Screen. This function is important since the arrangement of sex-linked genes in the heterozygous state will effect your offspring results.

From the above example, the male can provide four different types of gametes to the fertilization process ([op,+] [op,cin] [+,+] and [+,cin]). These four gametes are expected to be equally frequent as products of a single meiosis. However, unless a single crossover (or its functional equivalent from odd numbers of multiple crossovers) always occurs between the two marker loci, the [op,+] and [+,cin] non-recombinant gametes (in a very large population of gametes) will be more frequent than the recombinant gametes. The closer two loci are, the less likely a crossover event occurs between them, and the greater the disparity between these two classes of gametes. If coupling were applied to the above example the type of gametes produced would be the same. The only difference between the two situations is the statistical outcome.

Crossover rate can be effected by sex, age, temperature, proximity of allele to the centromere, inversion and many other factors. The highest probability of crossover that could be seen between any two genes for any species is no more than 50%. If crossover was to occur at its maximum frequency (~50%) then the alleles would appear to be independently assorting.

With sex-linked traits, crossover only occurs in males because only males have a homologous set of sex chromosomes. For linked mutations occurring on the avian autosomes, crossover will be observed and it will be at the same frequency for both sexes. Currently, the dark factor locus and the blue locus within Budgerigars have been determined to reside on the same autosomal chromosome thus making them linked genes. This situation also requires a different designation system for gene relationships other than coupling and repulsion since the dark factor gene (D) is a partial dominant mutation and the blue gene (b) is a recessive mutation. Type 1 is specified for two dominant (or recessive) alleles linked together. Type 2 is specified for dominant with recessive linkage. The chromosome layout for each type is presented below.

The physical point at which chromosomes exchange during crossover is referred to as a chiasma (plural chiasmata). Each type of chromosome within a species has a characteristic (or average) number of chiasmata. The frequency with which a chiasma occurs between any two genes also has a characteristic or average probability. The further apart two genes are located on the chromosome, the greater the opportunity for a chiasma to occur between them. The probability of chiasma occurring between two linked genes is calculated as follows:

The chromosomes that are not involved in the crossover are referred to as non-crossover or parental types. Those involved with the crossover are referred to as recombinant or crossover types.

Next, I will discuss application of crossover to the Punnett square. When applying sex-linked genes to the Punnett square, the crossover gametes produced by the male should be included. Again, the female cannot produce any crossover gametes for sex-linked genes. I will use the example above with a Normal Male heterozygous for Opaline and Lutino in repulsion phase (X^{+, op}X^{ino, +}) crossed to a Normal Female (X^+,+Y). See Figure 18.

In the above case, I applied a 30% crossover rate for the two loci. This crossover frequency is correct for the Lutino and Opaline loci in Budgerigars but has not yet been proven and formally documented for other species.

The crossover frequency for any two genes is determined from breeding results. In the above example, since cinnamon opaline female offspring can only be produced if crossover occurs you would record the number of this type offspring produced, divide this number by the total number of offspring then multiply this number by 4 to determine the crossover rate. For example, if you have a pair of birds, as shown in the breeding cross above, and breed them over a long period of time and let's say they produced 200 chicks 15 of which were cinnamon opaline females then the crossover frequency is:

Let us assume we have a male heterozygous for four sex-linked traits. This would then present three various regions for crossover to be observed. See Figure 19. 

The possible Parental and Single Crossover gametes produced by the example in Figure 19 would be:

The maximum frequency of recombinant gametes for any two loci is 50% because this would represent 100% single chiasma frequency. Crossover rate is directly related to the distance between the two linked genes. Gene distances are expressed as map units. One map unit is equivalent to 1% recombinant progeny. If the a-b distance is 50 map units, b-c is 30 map units and c-d is 40 map units, the distance a-d would be 120 map units. But in a cross involving segregation of only the two most distant markers (a-d), the number of recombinant progeny would not be expected to exceed 50% because of multiple crossover, some of which produce the equivalent of non-crossover.

When discussing more than two genes on a chromosome that experience crossover then you must also factor in two strand double crossover and multiple even-numbered crossovers. The figure below shows the sequence of events involved in double crossover using a male heterozygous for three sex-linked traits.

The double crossover frequency is the product of each single crossover. Thus, if the crossover frequency between genes a and b is 10% and between b and c is 20% then the double crossover rate is expected to be 2% (i.e., 10% x 20% = 2%) if there is no interference. Interference is a phenomenon in which a given crossover tends to inhibit the formation of a nearby crossover. The gametes produced by this male will be as follows:

Note that in the above example, the rate of double crossover (2%) has been subtracted from the total crossover frequency for a-b (10% - 2% = 8%) and b-c (20% - 2% = 18%) to derive the single crossover rates. Additionally, the following can be stated:

Double crossover has been studied in fruit flies and from these studies, it has been determined that double crossover usually does not occur between fruit fly genes less than 5 map units apart (1 map unit = 1% crossover rate). In the above example, the distance between genes a and c is 30 map units (i.e., 30% total crossover rate including single and double crossovers = 30 map units).