8. Linkage

Linkage and Chromosome Mapping [Eukaryotes]

Linkage: Genes show linkage if on same chromosome

-tendency for genes [actually their alleles] or segments of DNA closely positioned along a chromosome to segregate together at meiosis, and therefore be inherited together Linkage groups can be established.

-Groups of linked genes that tend to segregate together

-Number of linkage groups corresponds to haploid number of chromosomes

if the individual is heteromorphic chromosomes then it displays a haploid number +1???

Independent Assortment

No linkage: Independent assortment of two pairs of chromosomes, each containing one heterozygous gene pair

Large number of meiotic events produce:

Four genetically different gametes in equal proportions

Each containing a different combination of alleles

all four gametes are equally likely (from the diagram on slide 4)

Complete linkage

Complete linkage produces parental or noncrossover gametes in equal proportions. No crossing over occurs between the genes. Only two genetically different gametes are produced.

functionally crossing over cannot occur between them because the genes are so close together

Complete linkage→ paraental/non-cross over gametes

Complete linkage produces parental or noncrossover gametes in equal proportions.

No crossing over occurs between the genes. Only two genetically different gametes are produced.

Improbable for two randomly selected genes linked on same chromosomes

Have seen with Wheat Grain Hardness Locus [3 genes] -genes for Puroindoline A, Puroindoline B and Grain Softness Protein 1, parental linkage never broken in experimental crosses [Why? Sample size!]

Complete linkage is a sample size problem

rare that you see complete linkage

never had an experimental result showing

only a few thousand bp of DNA between these genes. Theoretically it can happen that crossing over occurs in this region but it would be so rare

if close together they essentially act like one big gene and are inherited together

Partial linkage

Crossover between two linked genes occurs sometimes

-involves two nonsister chromatids

-generates recombinant or crossover gametes: two new allele combinations

-proportion of non-recombinant/parental gametes and recombinant gametes determined by frequency of crossing over.

-this in turn is a function of how far apart the two genes are on the chromosome

if two genes are fairly far apart crossing over between them is more common

Partial linkage with two genes on a single pair of homologs

Partial Linkage: Two genes on a single pair of homologs, crossover sometimes occurs between genes

Ratio of “noncrossover” [parental/non-recombinant] gametes to “crossover” [recombinant] gametes determined by frequency of crossing over between the two genes

Crossing over sometimes occurs between the two genes

the only crossing over events that break linkage are the ones that occur between genes

how likely it is a function of how far apart they are?

Undetected Linkage

Two linked genes with loci far apart on the chromosome

If 50% recombination occurs (two parental types and two recombinant gametes) Transmission indistinguishable from independently assorting genes.

Crossing over “always” occurs between the two loci. The four allele combinations are equally likely and mimic the outcomes for independent assortmen

Undetected linkage: Two genes on a single pair of homologs; exchange occurs between two nonsister chromatids all the time

always have the nco and crossover gametes

genetic outcomes are the same, from phenotypic perspective despite different arrangements of the genes

Linkage/ recombination mapping

Linked genes exist in a linear order along the chromosome.

Relative distance between two loci influence amount of recombination and crossing over.

Two loci farther apart along chromosome—random crossover more likely

Single crossover (SCO) between two nonsister chromatids alters linkage between two genes if crossover occurs between those two genes.

Alfred Sturtevant: First chromosomal map

Alfred Sturtevant: First chromosomal map

• Realized recombination could be used to map [ I prefer order] sequence of linked genes

• Variations in strength of linkage used to determine sequences [order] in linear dimension of chromosome

• Recombination frequencies between linked genes are additive.

• Frequency of exchange estimate of relative distance between two genes along chromosome

take this with a grain of salt, we will see what he means by that

better approximation, it is not exact

one map unit

One map unit (mu) -% recombination between two genes on chromosome -sometimes called a cM [centimorgan] Two linked genes > 50 map units apart -crossover is theoretically expected to occur between them in 100% of tetrads -behave like independently assorting genes.

Two point mapping

-determination of the “map distance” between two linked genes/loci -parents are selected and mated: F1 flies are heterozygous for the two genes/loci understudy

-next, test cross equivalent performed: ONE SEX heterozygous F1 flies, other sex either homozygous recessive flies or hemizygous recessive male in the case of X-linked traits. Why? Recombination/crossing over can occur at different rates in the two sexes

-for Drosophila melanogaster, the F1 flies used in this cross will ALWAYS be female.

-WHY? Crossing over effectively doe NOT occur during gamete production in male fruit flies -last cross allows for the detection of the novel allele combinations generated by crossing over during gamete formation [meiosis] in the heterozygous F1 flies.

-new non-parental phenotypes will be detected.

males have lower recombination rates for some reason...we don't know why

using this to detect the occurance of recombination

Two point mapping criteria

One parent must be heterozygous for both genes under consideration.

Cross must be constructed to determine genotype of all gametes.

A sufficient number of offspring must be produced for representative sample crossover.

For drosophila this is always the female

Key thing to note female that is homozygous for two traits and male is hemizygous for wild (FIrst cross)

For the second cross: female heterozygous

male hemizygous (for the mutants)

one of the main reasons why particularly when you have two genes that are far apart. has to do witht the phenomenon on the next slide

we didn't know whether the yellow and m were on the same side of w or opposite sides, so he ddid not appreciate this

As the Distance between two genes increases, mapping estimates become

As the Distance between Two Genes Increases, Mapping Estimates Become LESS accurate

Why? Multiple cross over events between genes

Expected frequency of multiple exchanges between two genes predicted from distance between them

Genes farther apart have greater probability that undetected crossovers will occur. [See next slide]

Degree of inaccuracy increases as distance between them increases

Most accurate maps are constructed from closely linked genes.

Farther apart genes are on chromosomes from diagram

The farther apart they are the more likely for a double crossing over event to happen

As the map distance increases between you have increased likelihood of crossing over events that you cannot detect

Not much deviation from what we detect and the actual map distance

the further apart the map units are the farther it strays from the theoretical

SCO and mutliple crossovers

• Single crossovers are used to determine distance between two linked genes.

• Multiple crossovers between chromatids of tetrad facilitate production of more extensive chromosome maps.

• Double crossovers (DCOs)

• Result from double exchanges of genetic material

• Used to determine order of three genes on chromosome

• To study double exchanges require

• Three pairs of genes, each heterozygous for two alleles

• Process called “three point mapping”

**(ab+/a+b) is the proper way to show genotype when they are linked

Three point mapping

-determination of the “map distances” between three linked genes/loci as well as the order of the loci in the linkage group [or on the chromosome]

-parents are selected and mated: F1 flies are heterozygous for the three genes/loci understudy -next, test cross equivalent performed: ONE SEX heterozygous F1 flies other sex either homozygous recessive flies or hemizygous recessive male in the case of X-linked traits.

- last cross allows for the detection of the novel allele combinations generated by crossing over during gamete formation [meiosis] in the heterozygous F1 flies.

-new non-parental phenotypes will be detected.

for drosophila it is always the female that is heterozygous

Three-point mapping criteria

One parent must be heterozygous for all three genes under consideration. Cross must be constructed to determine genotype of all gametes. A sufficient number of offspring must be produced for representative sample crossover.

Noncrossover phenotypes

• Occur in greatest proportion of offspring • Double-crossover phenotypes • Occur in smallest proportion Single-crossover phenotypes will be intermediate In number.

Non-crossover, Single-crossover and Double-crossover Phenotypes are represented by “Reciprocal Classes”.

- Pairs of phenotypes complement each other (one is wild type and the other is mutant for all three genes).

will represent the phenotypes that show up in the highest number

reciprocal classes where all the wild type is expressed and all the mutants are also expressed

you have a pair of phenotypes and if the mutant is present in one it is absent in the other, and if one as the wild it is absent in the other

non-cross over is the ones that are the most abundant (SCO+DCO)/ total X100

Determining gene order from three-point cross

: • Determine distribution of alleles on each homolog of heterozygous parent. • Determine the rearrangement that produces observed double-crossover phenotypes. [The allele pair for the locus in the “middle” is “swapped” to generate the “double-crossover” reciprocal class.

Distance between two genes in three-point cross is equal to percentage of all detectable exchanges occurring between them. • Includes all single and double crossovers

Three steps of doing a reciprocal cross

Group the phenotypes into “reciprocal classes”. [ii] What was the original arrangement of alleles in the heterozygous females used in this cross? [iii] Construct a map showing the map distances between the loci for a, b, and c. Show how you calculated these map distances