Genetics - Chapter 5 - Linkage & Chromosome Mapping in Eukaryotes

Linkage (generally)

Genes near each other on a chromosome tend to be inherited together

Chromosomes mimic the movement of the alleles of genes

(since the genes are moving with them during cell division and replication)

Dihybrid cross: different perspective

In a dihybrid cross, there are four phenotypic groups; offspring have either the

• parental phenotype

• Recominant phenotype

Parental phenotype

Two of the phenotypic classes have the same phenotypes as the parents (one like one parent and other like the second parent)

Recominant phenotype

• The remaining two phenotypes share only one trait in common with each parent

• New combinations

Parental vs recombinant phenotype example

share all vs share one

Review: test cross

The testcross is a cross to an individual that carries only recessive alleles for the trait

• to determine whether an individual that is displaying the dominant phenotype is homozygous or heterozygous for that trait

• phenotypes in the offspring are determined by the alleles found in the hybrid

Cross the hybrid (mono-, di-, tri-hybrid) to fully homozygous recessive

• expect 1:1 for mono

• expect 1:1:1:1 for di

• expect 1:1:1:1:1:1:1:1 for tri

Testcross (unlinked genes)

Important: 50% are parental and 50% are recombinant (relative to the P generation) in dihybrid

• Why 50%

  • BECAUSE in independent assortment, half of the gametes are parental and half are recombinant

    • The recombinants occur by the random alignment on the meiotic metaphase plane

    • Each combination is equally likely

“funny observation”

1. Morgan crossed wild-type flies x purple-eyed, vestigial winged flies, F1 was wild type, F2 was 1195 purple-eyed, vestigial winged, 151 vestigial winged, 154 purple eyed, 1339 wild-type

2. He tried again and crossed purple eyed x vestigial, F1 was wild type, F2 was 157 purple, vestigial, 965 vestigial, 1067 purple eyes, 146 wild type

3. This showed chiasmata, interpreted as sites where chromosomes exchange

4. Morgan determined that these genes are linked, do not assort independently

Map unit

One map unit is defined as 1% recombinant offspring

(# recombinants / total # of offspring) x 100

Example: 151+154 = 303, 303/2335 = 12.9% recombinant so about 13 mu apart

Linkage mapping

Determines the relative position of genes by following phenotypes

Based on recombination that occurs during meiosis

• Independent assortment - 50% of the offspring have parental phenotypes, 50% have recombinant phenotypes

• Linkage - parental phenotypes are more than 50% and recombinant phenotypes are less than 50%

What are the unit of transmission in meiosis?

CHROMOSOMES (not genes)

Linked genes

cannot undergo independent assortment

Recombination (crossing over)

is required in meiosis and results in the formation of recombinant chromosomes

The frequency of crossing over between any two genes on a single chromosome

is proportional to distance between those genes

Linkage concept

Alleles of genes that are close together on a chromosome tend to be inherited together during meiosis

Loci that are near each other are less likely to be separated by recombination during chromosomal cross-over in meiosis. it is probabilistic

Locus

the location of a certain gene on a chromosome; loci is the plural of locus

Linkage vs independent assortment

Independent: equal proportions of each type (alignment in meiosis I)

Linkage: different proportions (crossing over in meiosis I)

Crossing over in meiosis generates new chromosomes and affects linkage of genes

If segments of two nonsister chromatids are exchanged..

• between the genes we are following → it leads to a recombination

• between genes we are not following → leads to no recombinants

How to do a mapping problem (generally)

1. Cross true-breeding parents for 3 genes with contrasting traits

2. Test-cross the F1 hybrids (to fully recessive individuals)

3. Put F2 offspring into “parental” or “recombinant” classes

4. Determine the frequency of recombinants

5. Convert 1% recombinant to 1 mu

Poisson distribution

The occurence of crossovers in a specific chromosomal region

Describes the distribution of ‘successes’ in samples when the average probability of successes is low

• When the probability is low, usually there will be no crossover in a region

Why is there a limit in mapping to 50 mu?

Because the maximum observable recombination frequency between any two genes is 50%

Aside: as more complicated crossing over patterns appear, it can sometimes be hard to detect recombinants AND as genes get farther apart, it increases the probability of undetected crossovers

Interference

• Inhibition of further crossover events, usually by another crossover event nearby

• Reduces expected number of multiple crossovers, generally seen when looking for recombinants of the middle gene of three when mapping

• The amount of interference can be calculated: I = 1 - C

• C is the coefficient of coincidence, C = observed DCO/expected DCO

Complete interference

No double crossovers occur

Positive interference

Fewer double crossover events than expected occur, I is a positive number

Negative interference

More double crossover events than expected, I is a negative number (theoretical, cases are usually not seen)

Two genes that are 60 mu apart are expected to show __ recombination

50%

Genes farther apart are more likely to cross over than genes close together

Meiotic Mapping

Strategy 1: determine the gene in the middle first, and then map from that gene to both of the adjacent genes

Strategy 2: map distances between all three genes (A → B, B → C, A→C) and there is only one way to assemble this information

Meiotic Mapping again

1. Organize progeny classes into four pairs with complementary phenotypes

2. Note the differences in frequency

   1. One pair will be the most frequent

      1. This pair describes the parental class

      2. They have the phenotypes of the individuals in the parental class

      3. They arise from gametes that do NOT crossover between the genes in question

   2. All of the other pairs show recombination; this recombination changes the alleles of one of the genes from the parental configuration of alleles for the other two genes

      1. Of these 3 pairs, two represent single-crossover classes (SCO) and the least frequent represents the double-crossover class (DCO)

   3. The allele that changes position in the DCO class corresponds to the gene that is in the middle

      1. Make a map of the order of these genes (this is important for strat 1)

Notes:

• The gene whose alleles change places in the least frequent class (in pink) when compared with the parental class (in blue) identifies the gene that is in the middle

• To determine the distance from C to A, add up the recombinants (A is with c and a is with C): 2+3+50+45 = 100 100/1000=0.10

• To determine the distance from C to B, add up the recombinants (B is with c and b is with C): 2+3+75+70 = 150 150/1000=0.15

• Calculate interference. Expected DCO is 0.10×0.15×1000 = 15 Observed DCO is 2+3 = 5 I = 1 – (5/15) = 0.66

• In strategy 2, you don’t know the middle gene. Calculate the distance from A to B (A – b; a – B) 50+45+75+70 = 240 240/1000=0.24

Parental vs recombinant

Mendelian genetic diseases

autosomal dominant

autosomal recessive

X-linked dominant or recessive

Can be rare, highly penetrant (typically due to alleles of a single gene and good phenotype to genotype correspondence), and little to no environmental component

Non-mendelian, complex traits (common) genetic diseases

Due to the combination of multiple genes and environmental influences

Can be common, variable, polygenic (with modest effects from multiple genes), heterogeneous with variable expressivity (different genetic factors, phenotypic expression is variable), environmental component

Mitochondrial (matrilineal) genetic diseases

This is non-nuclear inheritance; aka, extranuclear inheritance

Human genetic markers

Blood groups, serum protein electrophoretic variants, RFLPs (restriction site variation), microsatelites (size variation), SNPs (single nucleotide polymorphisms)

GWAS (Genome-wide association studies)

DNA sequence variation is “co-dominant” when the alleles differ. They may or may not directly affect a phenotype.

Ex. microsatelites and SNPs

SNPs

• Found throughout genome

• Used by geneticists to identify and locate related genes

• Used to screen for diseases

In GWAS, mapping is to SNPs

Independent: each of the SNP alleles is equally likely to be found in both groups

Linkage: the SNP alleles show skewed distribution: one allele is more common in affected people

NOTE: look for threshold, chromosomes that go above should be looked into