Chapter 5: Genetic linkage and chromosome chromosome mapping. mapping. Overview Introduction Linkage and recombination of genes in a chromosome Principles of genetic mapping Building linkage maps Chromosome and chromatid interference Genetic mapping in human and animal pedigrees Mapping by tetrad analysis Special features of recombination Overview Introduction Linkage and recombination of genes in a chromosome Principles of genetic mapping Building linkage maps Chromosome and chromatid interference Genetic mapping in human and animal pedigrees Mapping by tetrad analysis Special features of recombination Introduction Genes located on the same chromosome might be expected to be in COMPLETE might be expected to be in COMPLETE linkage. As a result of crossing-over however As a result of crossing over, however, recombinant progeny with genotypes not observed in the parents are not observed in the parents are observed.
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Genetic linkage and chromosome mapping. · Chapter 5: Genetic linkage and chromosome mapping. Overview Introduction Linkaggge and recombination of genes in a chromosome Principles
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Chapter 5:
Genetic linkage and chromosomechromosomemapping.mapping.
OverviewIntroductionLinkage and recombination of genes in a g gchromosomePrinciples of genetic mappingBuilding linkage mapsChromosome and chromatid interferenceGenetic mapping in human and animal pedigreesMapping by tetrad analysisSpecial features of recombination
OverviewIntroductionLinkage and recombination of genes in a g gchromosomePrinciples of genetic mappingBuilding linkage mapsChromosome and chromatid interferenceGenetic mapping in human and animal pedigreesMapping by tetrad analysisSpecial features of recombination
IntroductionGenes located on the same chromosome might be expected to be in COMPLETE might be expected to be in COMPLETE linkage.As a result of crossing-over however As a result of crossing over, however, recombinant progeny with genotypes not observed in the parents are not observed in the parents are observed.
IntroductionThe probability of recombination increases with genetic distance. Thus increases with genetic distance. Thus recombination rate can be used as a unit of distance between loci and used unit of distance between loci and used to build maps.Linkage analysis is very important in Linkage analysis is very important in genetics. It is often the first step towards isolating genes underlying towards isolating genes underlying defined phenotypes including inherited diseasesdiseases.
OverviewIntroductionLinkage and recombination of genes in a g gchromosomePrinciples of genetic mappingBuilding linkage mapsChromosome and chromatid interferenceGenetic mapping in human and animal pedigreesMapping by tetrad analysisSpecial features of recombination
Linkage and recombination of ggenes in a chromosome
Mendel’s second law: parental versus recombinant gametesSyntenic loci may be linked, i.e. F1’s produce more parental than recombinant gametesThe recombination rate is the same whether the mutant alleles are in cis or trans in the F1 parentparentThe chi-squared test for linkageE h i f li k d h h t i ti Each pair of linked genes has a characteristic frequency of recombinationRecombination in females versus malesRecombination in females versus males
Mendel’s second law: parental pversus recombinant gametes
Mendel’s second law: parental pversus recombinant gametes
Linkage and recombination of ggenes in a chromosome
Mendel’s second law: parental versus recombinant gametesSyntenic loci may be linked, i.e. F1’s produce more parental than recombinant gametesThe recombination rate is the same whether the mutant alleles are in cis or trans in the F1 parentparentThe chi-squared test for linkageE h i f li k d h h t i ti Each pair of linked genes has a characteristic frequency of recombinationRecombination in females versus malesRecombination in females versus males
Syntenic loci may be linked Syntenic loci may be linked
66.5% parentals
33.5% recombinants
Linkage and recombination of ggenes in a chromosome
Mendel’s second law: parental versus recombinant gametesSyntenic loci may be linked, i.e. F1’s produce more parental than recombinant gametesThe recombination rate is the same whether the mutant alleles are in cis or trans in the F1 parentparentThe chi-squared test for linkageE h i f li k d h h t i ti Each pair of linked genes has a characteristic frequency of recombinationRecombination in females versus malesRecombination in females versus males
Coupling versus repulsion of of p g psyntenic alleles
Repulsion Coupling
Coupling versus repulsion of of p g psyntenic alleles
62.3% parentals6 3% pa e ta s
37.7% recombinants
Linkage and recombination of ggenes in a chromosome
Mendel’s second law: parental versus recombinant gametesSyntenic loci may be linked, i.e. F1’s produce more parental than recombinant gametesThe recombination rate is the same whether the mutant alleles are in cis or trans in the F1 parentparentThe chi-squared test for linkageE h i f li k d h h t i ti Each pair of linked genes has a characteristic frequency of recombinationRecombination in females versus malesRecombination in females versus males
The chi-squared test for linkageLinkage and recombination of ggenes in a chromosome
Mendel’s second law: parental versus recombinant gametesSyntenic loci may be linked, i.e. F1’s produce more parental than recombinant gametesThe recombination rate is the same whether the mutant alleles are in cis or trans in the F1 parentparentThe chi-squared test for linkageE h i f li k d h h t i ti Each pair of linked genes has a characteristic frequency of recombinationRecombination in females versus malesRecombination in females versus males
Each pair of linked genes has a p gcharacteristic frequency of rec.
98 6% parentals98.6% parentals
1.4% recombinants
Linkage and recombination of ggenes in a chromosome
Mendel’s second law: parental versus recombinant gametesSyntenic loci may be linked, i.e. F1’s produce more parental than recombinant gametesThe recombination rate is the same whether the mutant alleles are in cis or trans in the F1 parentparentThe chi-squared test for linkageE h i f li k d h h t i ti Each pair of linked genes has a characteristic frequency of recombinationRecombination in females versus malesRecombination in females versus males
Recombination in females versus males
DrosophilaOther organisms (including Other organisms (including mammals)
OverviewIntroductionLinkage and recombination of genes in a g gchromosomePrinciples of genetic mappingBuilding linkage mapsChromosome and chromatid interferenceGenetic mapping in human and animal pedigreesMapping by tetrad analysisSpecial features of recombination
Genetic mapping
Hypothesis (Sturtevant & Morgan)Test 1: recombination between genes Test 1: recombination between genes results from a physical exchange bet een ch omosomes (Ste n 1936)between chromosomes (Stern, 1936)Test 2: Crossing-over takes place at the 4-strand stage of meiosisFrequency of recombination versus Frequency of recombination versus map distance: Haldane’s mapping functionfunction
Hypothesis (Sturtevant & yp (Morgan)
Recombination is due to an exchange of segments between homologous segments between homologous chromosomes in the process called crossing-over , manifested physically as crossing over , manifested physically as a chiasmaThe likelihood of a crossing-over The likelihood of a crossing over between two loci depends on their distance on the chromosome thus distance on the chromosome, thus explaining variable recombination rates => should allow “mapping”=> should allow mapping
Hypothesis (Sturtevant & Morgan)Test 1: recombination between genes Test 1: recombination between genes results from a physical exchange bet een ch omosomes (Ste n 1936)between chromosomes (Stern, 1936)Test 2: Crossing-over takes place at the 4-strand stage of meiosisFrequency of recombination versus Frequency of recombination versus map distance: Haldane’s mapping functionfunction
Recombination results from a physical Recombination results from a physical exchange between homologues Genetic mapping
Hypothesis (Sturtevant & Morgan)Test 1: recombination between genes Test 1: recombination between genes results from a physical exchange bet een ch omosomes (Ste n 1936)between chromosomes (Stern, 1936)Test 2: Crossing-over takes place at the 4-strand stage of meiosisFrequency of recombination versus Frequency of recombination versus map distance: Haldane’s mapping functionfunction
Crossing-over takes place at 4-g pstrand stage of meiosis
Crossing-over takes place at 4-g pstrand stage of meiosis
Genetic mapping
Hypothesis (Sturtevant & Morgan)Test 1: recombination between genes Test 1: recombination between genes results from a physical exchange bet een ch omosomes (Ste n 1936)between chromosomes (Stern, 1936)Test 2: Crossing-over takes place at the 4-strand stage of meiosisFrequency of recombination versus Frequency of recombination versus map distance: Haldane’s mapping functionfunction
Frequency of recombination q y(FR) versus map distance (MD)
FR (%): proportion of recombinant gametes (two proportion of recombinant gametes (two loci) Non-additive (see hereafter)Non-additive (see hereafter)
MD (centiMorgan = cM):½ average number of crossing-overs (m) / meiotic cell (between two loci)additive
Difference: multiple cross-overs p
Frequency of recombination q yversus map distance
Frequency of recombination q yversus map distance
Nota bene Haldane’s mapping function
Haldane’s mapping function0 crossing-over:
P0=e-m
R 0%Rec = 0%1 crossing-over:
P1= m1e-m/1!/Rec = 50%
2 crossing-over:P2
...!2
2!1
1021
+++=−−
−mm
m emxemxxemP2 = Rec = ?%
3 crossing-over:g……
1 crossing-overg=> 50% recombinant gametes
Haldane’s mapping function0 crossing-over:
P0=e-m
R 0%Rec = 0%1 crossing-over:
P1= m1e-m/1!/Rec = 50%
2 crossing-over:P2 2 m/2!
...!2
2!1
1021
+++=−−
−mm
m emxemxxemP2 = m2e-m/2!Rec = ?%
3 crossing-over:g……
2 crossing-overg=> 50% rec. gam. !!
Haldane’s mapping function0 crossing-over:
P0=e-m
R 0%Rec = 0%1 crossing-over:
P1= m1e-m/1!/Rec = 50%
2 crossing-over:P2 2 m/2!
...!2
2!1
1021
+++=−−
−mm
m emxemxxemP2 = m2e-m/2!Rec = 50%
3 crossing-over:g…Rec = 50%
Haldane’s mapping function
( ) ( )MDmFR 211 11 −−( ) ( )MDm eeFR 221
21 11 −=−=
Haldane’s mapping function
=Haldane’s MF
Haldane’s mapping function
Non-syntenic loci are characterized by a RF of 50%a RF of 50%Syntenic loci are characterized by a RF ≤ 50%RF ≤ 50%
OverviewIntroductionLinkage and recombination of genes in a g gchromosomePrinciples of genetic mappingBuilding linkage mapsChromosome and chromatid interferenceGenetic mapping in human and animal pedigreesMapping by tetrad analysisSpecial features of recombination
Building linkage mapsg g pMultiple two-point crosses
Building linkage mapsg g pThree-point crosses
Parental (most frequent) genotypes
Building linkage mapsg g pThree-point crosses
Double recombinant (DR) (rarest) genotypes
Building linkage mapsg g pThree-point crosses
Identification of parental genotypes + double-recombinants unambiguously double recombinants unambiguously determines locus order => Lz-Su-Gl
Building linkage mapsg g pThree-point crosses
Lz_Su_GlLzxSu GlLzxSu_GlLz_SuxGlLzxSuxGlLzxSuxGlLzxSuxGlLz SuxGlLz_SuxGlLzxSu_GlLz Su GlLz_Su_Gl
Building linkage mapsg g pThree-point crosses
RFLzxSu = FLzxSu_Gl + FLzxSuxGl
RF = F + FRFSuxGl = FLz_SuxGl + FLzxSuxGl
RFLzxGl = FLz_SuxGl + FLzxSu_Gl
RFLzxGl < RFLzxSu + RFSuxGl
Building linkage mapsg g pExamples
m
Chr
ng a
rm
r. 10
–lo
n
–sho
r. 10
ort ar
Ch
rm
Building linkage mapsg g pGenetic vs physical map distance
Building linkage mapsg g pGenetic vs physical map distance
OverviewIntroductionLinkage and recombination of genes in a g gchromosomePrinciples of genetic mappingBuilding linkage mapsChromosome and chromatid interferenceGenetic mapping in human and animal pedigreesMapping by tetrad analysisSpecial features of recombination
Chromosome interference
Lz_Su_GlLzxSu GlLzxSu_GlLz_SuxGlLzxSuxGlLzxSuxGlLzxSuxGlLz SuxGlLz_SuxGlLzxSu_GlLz Su GlLz_Su_Gl
Chromosome interference
I(nterference) = 1 – coefficient of coincidencecoincidenceCoefficient of coincidence = Observed DR / E pected DRDR / Expected DRObserved DR = FLzxSuxGlu
Expected DR = RFLzxSu x RFSuxGl
Chromosome interferencePositive interference
first crossing-over reduces probability to have a second one in the vicinity=> fewer observed than expected DRThe rule in many genomes (at low resolution) => The rule in many genomes (at low resolution) => Kosambi’s mapping function
Negative interferencegFirst crossing-over increases probability to have second one in the vicinity
> b d th t d DR=> more observed than expected DRObserved as a result of gene conversion at very high resolution
Kosambi’s mapping function Chromosome interferencePositive interference
first crossing-over reduces probability to have a second one in the vicinity=> fewer observed than expected DRThe rule in many genomes (at low resolution) => The rule in many genomes (at low resolution) => Kosambi’s mapping function
Negative interferencegFirst crossing-over increases probability to have second one in the vicinity
> b d th t d DR=> more observed than expected DRObserved as a result of gene conversion at very high resolution
Chromatid interference
Positive:First crossing-over involving specific non-First crossing-over involving specific non-sister chromatids decreases probability for their involvement in second onefor their involvement in second oneWould increase 4-strand DCWould push FR > 50%Would push FR > 50%Never observed
OverviewIntroductionLinkage and recombination of genes in a g gchromosomePrinciples of genetic mappingBuilding linkage mapsChromosome and chromatid interferenceGenetic mapping in human and animal pedigreesMapping by tetrad analysisSpecial features of recombination
The lod scoreDefinition
Compute likelihood of the observations under H1 i e FR ≤ 50% observations under H1, i.e. FR ≤ 50%. (Find value of FR that maximizes likelihood of the data) => L1likelihood of the data) => L1Compute likelihood of the b ti d H0 i FR 50% observations under H0, i.e. FR = 50%
=> L0Lod score = log10 L1/L0
Mapping in human and animal pp gpedigrees
Maximum likelihood and lod scores
The lod scoreProperties
Can be added across pedigrees ( log of product of prob = sum of logs)Sequential test:
> 3: reject H0< -2: accept H0-2 < z < 3: collect more data
Baysian justification of very stringent threshold Baysian justification of very stringent threshold of 3 (prior probability of linkage is low ∼ 1/50)Allows for unknown phase incomplete Allows for unknown phase, incomplete penetrance, …
Mapping in human and animal pp gpedigrees
Maximum likelihood and lod scores
The lod scoreProperties
Can be added across pedigrees ( log of product of prob = sum of logs)Sequential test:
> 3: reject H0< -2: accept H0-2 < z < 3: collect more data
Baysian justification of very stringent threshold Baysian justification of very stringent threshold of 3 (prior probability of linkage is low ∼ 1/50)Allows for unknown phase incomplete Allows for unknown phase, incomplete penetrance, …
OverviewIntroductionLinkage and recombination of genes in a g gchromosomePrinciples of genetic mappingBuilding linkage mapsChromosome and chromatid interferenceGenetic mapping in human and animal pedigreesMapping by tetrad analysisSpecial features of recombination
Mapping by tetrad analysispp g y yUnordered tetrads
Mapping by tetrad analysispp g y yUnordered tetrads
Non-syntenic lociPD = NPDPD NPD
Mapping by tetrad analysispp g y yUnordered tetrads
Syntenic lociloci
PD >> NPD
Mapping by tetrad analysispp g y yUnordered tetrads
Gene centromere mapping in pp gmammals: teratocarcinoma
OverviewIntroductionLinkage and recombination of genes in a g gchromosomePrinciples of genetic mappingBuilding linkage mapsChromosome and chromatid interferenceGenetic mapping in human and animal pedigreesMapping by tetrad analysisSpecial features of recombination