Questions: Genetic Recombination and Linkage Analysis

Question 1

Two genes on the same chromosome show 50% recombination frequency when tested in a two-point cross. What does this tell you about their relationship?

• A. They are on different chromosomes and assort independently
• B. They are very far apart on the same chromosome — far enough that multiple crossovers randomize allele combinations
• C. They are exactly 50 centimorgans apart and always produce equal parental and recombinant classes
• D. One gene is suppressing recombination near the other

Answer: (B)

50% recombination is the maximum observable frequency — it looks identical to independent assortment regardless of whether genes are on different chromosomes or very far apart on the same chromosome. Two distant linked genes experience so many crossovers between them that parental and recombinant classes become equally frequent. You cannot distinguish 'different chromosomes' from 'very far apart same chromosome' using recombination frequency alone — other evidence (e.g., physical mapping) is required.

Question 2

In a three-point cross (gene order unknown), the parental classes are ABC and abc. The double crossover classes observed are ABc and abC. Which gene is in the middle?

• A. Gene A, because it appears in the double crossover class
• B. Gene B, because it is flanked by A and C
• C. Gene C, because its allele flips in the double crossover relative to the parentals
• D. Cannot be determined without knowing the single-crossover classes

Answer: (C)

The double crossover class reveals the middle gene: it is the one whose allele has switched position relative to the parental combination while the flanking genes retain their original pairings. In the parentals (ABC / abc), gene C is in the original uppercase-uppercase or lowercase-lowercase combination with A and B. In the double crossovers (ABc and abC), C has flipped relative to the other two, meaning C must be in the middle — both single crossovers flank it, so two crossovers together flip only C.

Question 3

Two genes that are 40 centimorgans apart will produce 40% recombinant offspring in a test cross.

• T. True
• F. False

Answer: False

This is approximately but not exactly true — and for large map distances it becomes significantly wrong. Map distances are additive (you can add adjacent segment distances), but recombination frequencies are not, because double crossovers between distant markers go undetected and restore parental combinations. The Haldane mapping function corrects for this, showing that recombination frequency saturates below 50% for large map distances. Only for short distances (< ~15 cM) is recombination frequency approximately equal to map distance.

Question 4

Positive interference (coefficient of coincidence < 1) means that a crossover at one site reduces the probability of a second crossover occurring nearby.

• T. True
• F. False

Answer: True

Interference = 1 − COC, where COC = observed double crossovers / expected double crossovers. Positive interference (most common in eukaryotes) means fewer double crossovers are seen than expected by chance — a crossover physically inhibits nearby crossovers. COC < 1 means fewer observed doubles than expected, so interference is positive. This is thought to result from structural constraints in the synaptonemal complex that prevent crossover machinery from acting at closely spaced sites.

Question 5

Why do two-point crosses systematically underestimate the true map distance between genes that are far apart on the same chromosome?

Model answer: Double crossovers between distant genes restore the parental allele combination, making them invisible as recombinants. Every undetected double crossover counts as 'no recombination' when in fact two events occurred, so the measured recombination frequency is lower than the true genetic distance.

Map distance in centimorgans represents the total crossover activity, including double crossovers. But in a two-point cross, double crossovers between the two markers produce offspring that look like parentals — both crossovers cancel each other out from the observer's perspective. Three-point crosses solve this by having a middle marker that 'catches' each crossover event separately, allowing double crossovers to be detected and properly credited to the distance calculation.