Why is the recombination frequency you calculated likely an underestimate?

Genetics 3301

Chapter 4: Chromosome Mapping

Detecting Linkage:

Ä Inheritance of linked genes (4-2); Linkage terminology; Crossing-over during meiosis (4-3); Crossing-over during the 4-chromatid stage (4-4); Multiple crossovers (4-5).

Ä Meiotic recombination generates allelic combinations that differ from those that made either parent (4-6); the product of meiotic recombination is called a recombinant; a test cross can determine whether genes are independently assorting (which would be a 50% recombination frequency or 1:1:1:1 ratio) (4-8) or linked (which would give >50% parental phenotypes and <50% non-parental phenotypes) (4-9, 4-10); recombination frequencies can never be more than 50% since that is equal to random assortment.

Ä Recombination on the X chromosome occurs in the homogametic sex and can be detected in the heterogametic sex; X recombination occurs in female Drosophila and is detected in her sons.

Linkage Mapping:

Ä The magnitude of recombination between two linked genes is a measure of their distance apart ≠ the closer two genes are, the smaller the recombination frequency; A linkage map of genes along the chromosome can be generated by determining their recombination frequencies; a recombination frequency (RF) of 1% equals 1 genetic map unit (m.u.); to obtain a map of linked genes A, B and C you must determine the recombination frequency of A-B, B-C and A-C (4-11).

Ä A three point test cross can detect linkage and produce a map of the genes along the chromosome in one cross; double recombinant classes are the smallest and show which genes are furthest apart (4-12); double recombinants do not appear as recombinants for the genes furthest apart, which leads to an underestimate of distance between these genes compared to adding the single recombinant classes (4-12); deducing gene order by inspection (4-13).

Ä One cross over will interfere with or inhibit another crossover nearby; expected recombinants is the product of the RFs in the adjacent regions; coefficient of coincidence calculates amount of interference.

Ä Five steps for recombinant analysis in 3-point test crosses:

1)          calculate recombination frequency for each pair of genes

2)          make a linkage map

3)          determine the double crossover classes

4)          calculate the expected frequency of double crossovers assuming no interference

5)          calculate the intereference

Ä Mapping with molecular markers; RFLPs and VNTRs.

Analyzing single meioses:

Ä In some haploid organisms you can look at the products of single meioses because the meiosis products (spores) are arranged in tetrads and octads within the ascus (3-37a); Neurospora is a beneficial model system because segregate in a linear order (3-37b); one can follow chromosome segregation after the first division (M1) or second division (M2) (3-37); M2 segregation can lead to four ascus patterns because of random chromosome segregation (4-15, 4-16).

Ä RF between the centromere and a gene locus equals the number of M2 ascus patterns ˜ 2 since only half the chromatids from a meiosis are recombinant (4-15).

Statistical analysis of linkage:

Ä Determining whether two genes are linked via chi-square analysis; Null hypothesis; Assessing linkage in humans using Lod scores (4-17).

Accounting for unseen multiple crossovers:

Ä The average RF is 50% for meioses in which crossing over occurs (4-18); Mapping genes in relation to each other; classifying tetrads ≠ PD, NPD and T; RF=1/2(T)+NPD.

Key terms: Know all of these except mapping function and Poisson distribution.

Problems: 1, 2, 3, 5, 6, 7, 8, 10, 11, 13, 15, 19, 22, 28, 29, 35, 37, 42.

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Comparing recombination landscape and frequency (REC) across different taxonomic and spatial scales (boxes on the left) provides complementary data to address outstanding questions about how and why recombination varies (boxes on right).

Click on the image to see a larger version.