9.6 Experimental Determination of Recombination Frequency

Let us now consider a complete experiment in which our objective is to measure recombination frequency (Figure 9.6.1). We need at least two alleles for each of two genes, and we must know which combinations of alleles were present in the parental gametes. The simplest way to do this is to start with pure-breeding lines that have contrasting alleles at two loci. For example, we could cross short-tailed (aa), brown mice (BB) with long-tailed (AA), white mice (bb). Thus, (aaBB) are short-tailed and brown, while (AAbb) are long-tailed and white (Figure 9.6.1 P cross). Based on the genotypes of the parents, we know that the parental gametes will be aB or Ab (but not ab or AB), and all the progeny will be dihybrids, AaBb. We do not know at this point whether the two loci are on different chromosomes, or whether they are on the same chromosome, and if so, how close together they are.

A cross showing brown and yellow mice used to measure recombination frequency between two loci.
Figure 9.6.1 An Experiment to Measure Recombination Frequency Between Two Loci. The loci affect coat color (B/b) and tail length (A/a).

The recombination events that may be detected will occur during meiosis in the dihybrid individual. If the loci are completely or partially linked, then prior to meiosis, alleles aB will be located on one chromosome, and alleles Ab will be on the other chromosome. These are the parental gametes based on our knowledge of the genotypes of the gametes that produced the dihybrid. Thus, recombinant gametes produced by the dihybrid will have the genotypes ab or AB.

Now that we have identified the parental and recombinant gametes, how do we determine the genotype of the gametes produced by the dihybrid individual? The most practical method is to use a test cross (Figure 9.6.1 F1 to tester), in other words, to mate AaBb to an individual that has only recessive alleles at both loci (aabb). This will give a different phenotype in the second generation for each of the four possible combinations of alleles in the gametes of the dihybrid (Figure 9.6.2).

Diagram of a Punnett Square showing an example of a test cross where homozygous recessive tester can only produce one gamete type so only one is listed.
Figure 9.6.2 Punnett Square of Example Test Cross. Homozygous recessive tester can only produce one gamete type so only one is listed. Phenotypes are listed below. Using the phenotypes and what we know of the parents, we can identify which phenotypes came from recombinant or parental gametes.

We can then infer unambiguously the genotype of the gametes produced by the dihybrid individual, and therefore calculate the recombination frequency between these two loci. For example, if only two phenotypic classes were observed in the F2 (i.e. short tails and brown fur (aaBb), and white fur with long tails (Aabb)) we would know that the only gametes produced following meiosis of the dihybrid individual were of the parental type: aB and Ab, and the recombination frequency would therefore be 0%. Alternatively, we may observe multiple classes of phenotypes in the F2 in ratios such as shown in Table 9.6.1.

Table 9.6.1 Example of quantitative data observed in a genetic mapping experiment involving two loci – data correspond to the F2 generation in the cross shown in Figure 9.5.2.
Tail Phenotype Fur Phenotype Number of Progeny Gamete from Dihybrid Genotype of F2 from Test Cross (P)arental or (R)ecombinant
Short Brown 48 aB aaBb P
Long White 42 Ab Aabb P
Short White 13 ab aabb R
Long Brown 17 AB AaBb R

Given the data in Table 9.6.1, the calculation of recombination frequency is straightforward:

RF  =  # recombinant offspring/Total offspring

            RF        =          ___13+17___

                                    48+42+13+17

                        =          0.25

Because the recombination frequency is below 0.30, we can say that the tail length gene and the fur colour gene are partially linked.

Note: The use of linkage and recombination frequency, will be extended to Genetic Mapping in Chapter 11.

Media Attributions

References

Canham, L. (2017). Figure 9. Punnett Square of example test cross…[digital image]. In Locke, J., Harrington, M., Canham, L. and Min Ku Kang (Eds.), Open Genetics Lectures, Fall 2017 (Chapter 18, p. 7). Dataverse/ BCcampus. http://solr.bccampus.ca:8001/bcc/file/7a7b00f9-fb56-4c49-81a9-cfa3ad80e6d8/1/OpenGeneticsLectures_Fall2017.pdf

Deyholos, M. (2017). Figure 8. An experiment to measure recombination frequency…[digital image]. In Locke, J., Harrington, M., Canham, L. and Min Ku Kang (Eds.), Open Genetics Lectures, Fall 2017 (Chapter 18, p. 7). Dataverse/ BCcampus. http://solr.bccampus.ca:8001/bcc/file/7a7b00f9-fb56-4c49-81a9-cfa3ad80e6d8/1/OpenGeneticsLectures_Fall2017.pdf

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Open Genetics by Natasha Ramroop Singh, Thompson Rivers University is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, except where otherwise noted.

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