Genetic recombination

Genetic recombination rearranges inherited genetic material into new combinations. In the meiosis example considered here, chromosomal crossover exchanges segments between nonsister chromatids of homologous chromosomes. A transmitted chromatid can consequently contain DNA from both parental homologues. This produces new haplotypes without requiring a new mutation at either scored genetic locus. See Meiosis.

For phase-known genotype $AB/ab$, a single chromosomal crossover between the selected genetic loci can yield $Ab$ and $aB$ on the participating chromatids; the other two chromatids can remain $AB$ and $ab$. Thus an exchange in the four-chromatid bundle does not mean every resulting gamete is recombinant. Only a chromosomal crossover encountered along the transmitted chromatid within the selected interval affects its two-locus score.

Follow parental origin along the transmitted chromatid from the first genetic locus to the second. Each exchange switches that origin. An odd number of such chromosomal crossovers changes the endpoint combination; an even number restores parental phase. Two exchanges can therefore leave the scored haplotype as $AB$ even though an internal segment came from the other parental homologous chromosome. Recombinant status is relative to the chosen genetic loci, not a complete record of exchanges along the chromosome.

This integer parity distinction connects the physical process of genetic recombination to the observed recombination fraction. It also explains why a long genetic map interval can accumulate many exchanges while its endpoint recombination fraction approaches $1/2$ in the Haldane mapping function model.

A recombination regulator with anti-crossover effects in characterized plant contexts; effects on fertility and crossover number differ among genes, species and hybrid backgrounds.

A recombination regulator with anti-crossover effects in characterized plant contexts; effects on fertility and crossover number differ among genes, species and hybrid backgrounds.

A recombination regulator with anti-crossover effects in characterized plant contexts; effects on fertility and crossover number differ among genes, species and hybrid backgrounds.

Nonreciprocal transfer of sequence information during repair or recombination. Transmission need not be symmetric between alleles.

A bias in transmission or repair favouring G/C over A/T at suitable heterozygous sites. It can produce substitution patterns resembling selection without a corresponding organism-level fitness advantage.

An inherited variant that changes the rate or pattern of genetic recombination. Its spread requires a reproductive advantage to its own lineage, directly or through associations with other variants, rather than a benefit only to a distant future species.

A reduction in reproductive performance caused by breaking favorable inherited associations through genetic recombination. Its possibility prevents treating exchange as universally advantageous.

The proposal that genetic recombination can accelerate adaptation by combining beneficial alleles that arise in different lineages. Recombination also produces other combinations, so the benefit depends on the inherited associations and ensuing natural selection.

Exchange or repair using corresponding DNA sequences as templates. It can restore a broken molecule and can yield crossover or noncrossover products; sequence repair and reshuffling of inherited alleles are compatible outcomes.

Recombination between related chromosomes derived from different ancestral genomes, distinguished from recombination between true homologues.

The rate of recombination events under the stated scale, for example per genomic interval per generation. It should not be silently equated with a two-marker recombination fraction, which can hide multiple exchanges.

A chromosomal crossover is a reciprocal exchange of segments between nonsister chromatids of homologous chromosomes during meiosis. It can change the haplotypes inherited at selected genetic loci; whether it does so depends on the transmitted chromatid and interval.

A meiotic crossover from an alternative pathway that is substantially less subject to interference.

A meiotic crossover from the interference-sensitive pathway associated with ZMM proteins and HEI10.

A pro-crossover E3 ubiquitin ligase whose dosage can influence crossover number.

Mechanisms promoting at least one crossover per homolog pair to support balanced segregation.

Crossover interference means that an exchange affects the occurrence of other nearby chromosomal crossovers. The Haldane mapping function assumes this dependence is absent. See Meiosis.

Under an infinite sites mutation model, two variable sites on one unrecombined rooted tree have nested or disjoint derived-allele clades. At most three of the four biallelic haplotypes can then occur. Observation of all four haplotypes proves that the single-tree, single-mutation-per-site model cannot hold: some ancestral genetic recombination is necessary if recurrent mutation is excluded. The test gives no proof of absence of recombination when only three haplotypes occur.

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A recombination hotspot is a short region with an elevated local rate of genetic recombination. Repeated ancestral breakpoints there can separate neighboring haplotype blocks of strong linkage disequilibrium.

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The recombination fraction is the probability that a transmitted gamete carries a recombinant haplotype between two specified genetic loci, relative to the parent's known haplotype phase. Write it as $r$ here; the symbol $\theta$ is also common in genetic linkage analysis. In the ordinary symmetric two-locus model, $0\le r\le 1/2$, with $r=0$ for complete genetic linkage and $r=1/2$ for independent assortment.

For phase-known genotype $AB/ab$, fair Mendelian segregation and equal reciprocal gamete probabilities giveFor example, 1,000 independent informative transmissions with observed counts $400,400,100,100$ in this order have empirical recombination fraction $(100+100)/1000=0.2$. Those illustrative counts match the expected values in the toy model, but actual counts fluctuate. The genetic linkage diagram shows both the parental and recombinant classes, so their separate probabilities are not confused with the total $r$.

The recombination fraction measures the probability of an odd number of origin switches along the transmitted chromatid. It is neither the expected value of the exchange count nor the probability of at least one exchange: even positive counts can be invisible at the two endpoints. Converting an observed recombination fraction to a genetic map distance therefore needs an explicit model such as the Haldane mapping function. The distinction between transmitted-chromatid counts and four-chromatid exchange counts is discussed in Weeks, Tang and Kwon (2009), Casares' map function: No need for a 'corrected' Haldane's map function, Genetica 135, 305–307.