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I have a question about the recombination frequency I hope you have time to answer.

Background: If we look at homozygous individual A/A B/B which has been formed from the gametes AB and AB, this individual will in turn have the gametes AB, AB, AB, AB. These are the same as the gametes that were used to form the individual.

My question: Is the recombination frequency 0? Or should we consider the A's and B's as different, i.e like A$_1$, A$_2$, B$_1$, B$_2$. Then we get the possible gametes A$_1$B$_1$ (parental), A$_1$B$_2$ (recombinant),A$_2$B$_2$ (par), A$_2$B$_1$ (recomb). We then get that the recombination frequency is 50 percent (which it should be according to the source given at the bottom). Which interpretation is correct?

Definitions used in my question:

"Meiotic recombination is any meiotic process that generates a haploid product with new combinations of the alleles carried by the haploid genotypes that united to form the meiocyte." (Griffiths et. al, Introduction to Genetic Analysis, tenth edition, International Edition, p. 95)

Recombinants: "Recombinants are meiotic output different from meiotic input." (same book).

Recombination fraction: "Recombination fraction (also called recombination frequency) between two loci is defined as the ratio of the number of recombined gametes to the total number of gametes produced." (Shizhong Xu, Principles of Statistical Genomics, Springer, Chapter 2, page 11, 2013).

Furthermore: "When genes are unlinked, they have a recombination frequency of 0.5, which means 50 percent of offspring are recombinants and the other 50 percent are parental types." (Source: Boundless. “Genetic Linkage and Distances.” Boundless Biology. Boundless, 21 Jul. 2015. Retrieved 11 Sep. 2015 from https://www.boundless.com/biology/textbooks/boundless-biology-textbook/modern-understandings-of-inheritance-13/chromosomal-theory-and-genetic-linkage-97/genetic-linkage-and-distances-427-11654/)

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Welcome to Biology.SE

Your question stems from the confusion between measuring a recombination rate and the actual recombination rate.

In the A/A, B/B individuals you describe, recombinations still occur. Those recombination just don't affect linkage disequilibrium between the Aa and the Bb loci as there is no variance at those loci in the individuals you considered. There is therefore, no way to tell whether or a recombination event occurred in a specific case. You need genetic variance at both loci in order to have a linkage disequilibrium which can be affected by recombination. But it is not because you can't measure the recombination rate that recombinations does not occur.

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