Difficulty: Intermediate | Prerequisites: Part 1 of these notes (Ch. 15, Sections 15.1 and 15.2), understanding of meiosis (especially crossing over in prophase I)
Mendel's law of independent assortment works perfectly when genes are on different chromosomes. But genes on the same chromosome tend to travel together during meiosis, which is called linkage. Crossing over during prophase I can break that linkage, producing recombinant offspring. The frequency with which this happens tells you how far apart the genes sit on the chromosome, which is the basis of genetic mapping. This section is where you move from abstract ratios to physical distances along a chromosome.
Genes on the same chromosome are inherited together more often than not, violating independent assortment. Crossing over during meiosis I occasionally separates linked alleles, and the frequency of these recombinant offspring is proportional to the physical distance between the genes. This relationship lets geneticists build linkage maps of chromosomes.
Linked genes
Two or more genes on the same chromosome that tend to be inherited together. These deviate from Mendel's law of independent assortment.
Think of it as genes that are physical neighbours on a chromosome, so they usually travel as a package into the same gamete.
Genetic recombination
The production of offspring with combinations of traits that differ from those found in either parent of the P generation.
Parental types (parental phenotypes)
Offspring whose phenotype matches one of the P generation parents. In a testcross of linked genes, these are the majority class.
Recombinant types (recombinants)
Offspring with new combinations of traits not seen in either P generation parent. These arise from crossing over between linked genes.
Recombination frequency
The percentage of recombinant offspring among total offspring. For unlinked genes (on different chromosomes), recombination frequency is 50%. For linked genes, it is less than 50%, and the closer the genes, the lower the frequency.
In simple terms, this is the number that tells you how tightly linked two genes are.
Crossing over
The exchange of segments between non-sister chromatids of homologous chromosomes during prophase I of meiosis. This is the physical mechanism that produces recombinant chromosomes from linked genes.
Genetic map
An ordered list of genetic loci along a particular chromosome, constructed from recombination data.
Linkage map
A genetic map based on recombination frequencies. Distances are expressed in map units (centimorgans).
Map unit (centimorgan, cM)
The unit of distance on a linkage map. One map unit equals a 1% recombination frequency between two genes.
Think of it as: 17% recombination frequency = 17 map units apart.
Cytogenetic map
A map that locates genes with respect to physical chromosomal features (such as banding patterns), as opposed to recombination frequencies. The gene order matches a linkage map, but the spacing differs.
Morgan studied body colour (gray vs black) and wing size (normal vs vestigial) in Drosophila. Both are autosomal, with mutant alleles recessive to wild type.
He crossed wild-type flies (b+ b+ vg+ vg+) with double-mutant flies (b b vg vg) to produce F1 dihybrids (b+ b vg+ vg), then performed a testcross of the F1 female with a homozygous recessive male.
If the genes assorted independently, he expected a 1:1:1:1 ratio of four phenotype classes.
Instead, the results were heavily skewed toward parental phenotypes (965 wild type, 944 black-vestigial) with far fewer recombinants (206 gray-vestigial, 185 black-normal).
Conclusion: the genes for body colour and wing size are on the same chromosome (linked). The small number of recombinants comes from crossing over.
Key distinction: linked vs sex-linked
Linked genes: two or more genes on the same chromosome (any chromosome) that tend to be inherited together.
Sex-linked gene: a single gene located on a sex chromosome. These are different concepts.
Three processes generate genetic variation in sexually reproducing organisms:
Independent assortment of chromosomes at metaphase I
Crossing over during prophase I
Random fertilisation (any sperm can fertilise any egg)
For genes on different chromosomes, independent assortment produces 50% parental types and 50% recombinant types in a testcross.
A 50% recombination frequency is the hallmark of unlinked genes.
For linked genes, more than 50% of offspring have parental phenotypes.
Crossing over between the two gene loci during prophase I produces recombinant chromosomes.
The recombination frequency is always less than 50% for linked genes and reflects the distance between them.
Morgan's data worked out
Recombination frequency = (206 + 185) / (965 + 944 + 206 + 185) x 100 = 391 / 2,300 x 100 = 17%
This means the b and vg loci are 17 map units apart on the same chromosome.
Alfred H. Sturtevant, working in Morgan's lab, hypothesised that recombination frequency reflects physical distance between genes.
His reasoning: the farther apart two genes are, the more points exist between them where a crossover can occur, so the higher the recombination frequency.
One map unit (1 cM) = 1% recombination frequency.
Linkage map example (Drosophila chromosome 2)
Body colour (b) to cinnabar eye colour (cn): 9% recombination
Cinnabar (cn) to vestigial wing (vg): 9.5% recombination
Body colour (b) to vestigial wing (vg): 17% recombination
The only consistent order is b -- cn -- vg, with cn roughly midway between b and vg.
Limits of linkage mapping
The maximum observed recombination frequency between any two genes is 50%, even for genes far apart on the same chromosome. At that point they behave as if unlinked.
Genes very far apart on one chromosome are mapped by summing recombination frequencies from intervening, closer gene pairs.
Sturtevant found that Drosophila genes fell into four linkage groups, matching the four chromosome pairs.
Linkage maps give approximate, not exact, physical distances. Crossing-over frequency is not uniform along a chromosome, so map units do not correspond perfectly to base pairs.
Cytogenetic maps locate genes by chromosomal features (banding). Gene order matches the linkage map, but spacing differs.
Students often think linked genes can never be separated. They can, by crossing over. Linkage reduces recombination frequency below 50%, but does not eliminate it.
Students sometimes believe a 50% recombination frequency proves the genes are on different chromosomes. It does not prove this. Genes very far apart on the same chromosome can also show 50% recombination. The correct statement is that they are genetically unlinked, which may or may not mean physically separate chromosomes.
Students often forget that map units are not proportional to base pairs across different regions of a chromosome, because crossing-over frequency varies along the chromosome's length.
Students sometimes confuse recombination frequency with the percentage of offspring that are recombinant in a specific cross. Recombination frequency is a property of the two loci, not of a single cross.
⚠️ Calculating recombination frequency from testcross data is a core exam skill. Know the formula: (number of recombinants / total offspring) x 100.
⚠️ Be able to determine gene order from three-gene recombination data (the gene in the middle has the smallest recombination frequencies with the other two).
⚠️ Know that 50% recombination = genetically unlinked. This is the maximum observable frequency.
⚠️ Understand the difference between a linkage map and a cytogenetic map.
True or False: Two genes with a recombination frequency of 50% must be on different chromosomes. (False. They could be far apart on the same chromosome.)
Fill in the blank: One map unit equals a ____% recombination frequency. (1%)
True or False: Linked genes always produce 100% parental-type offspring. (False. Crossing over produces some recombinant offspring.)
Fill in the blank: In Morgan's testcross, the recombination frequency between b and vg was approximately ____%. (17%)
Q: In a testcross of a dihybrid female (AaBb, with A and B linked in cis) to a homozygous recessive male, you observe 420 AB, 410 ab, 82 Ab, and 88 aB offspring. What is the recombination frequency, and how far apart are the genes?
A: Recombinants = 82 + 88 = 170. Total = 420 + 410 + 82 + 88 = 1,000. Recombination frequency = 170/1,000 x 100 = 17%. The genes are 17 map units (cM) apart.
Q: Three genes on the same chromosome show these recombination frequencies: A-B = 12%, B-C = 7%, A-C = 5%. What is the order of the genes?
A: A-C (5%) + C-B (7%) = 12%, which matches A-B (12%). The order is A -- C -- B.
Q: Why does recombination frequency have an observed maximum of 50%?
A: Even for very distant loci on the same chromosome, multiple crossovers between them randomise which allele combination ends up in each gamete. The net result approaches a 50/50 split of parental and recombinant types, the same ratio as independent assortment.
Q: Explain why map units do not correspond perfectly to physical distances in base pairs.
A: Crossing-over frequency is not uniform along a chromosome. Some regions (e.g. near centromeres) have lower crossover rates, so a given number of base pairs in those regions corresponds to fewer map units than the same number of base pairs in a region with frequent crossing over.
This material builds directly on meiosis (Ch. 13), specifically the behaviour of homologous chromosomes during prophase I. It connects to Part 1 of these notes (sex-linked inheritance) because Morgan's same Drosophila work revealed both sex linkage and autosomal linkage. Genetic mapping is also the conceptual ancestor of modern genome sequencing and physical mapping.
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