Chapter 5: Genetic linkage and chromosome 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 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 Mapping by tetrad analysis Special features of recombination Introduction Genes located on the same chromosome might be expected to be in COMPLETE linkage. As a result of crossing-over over, however, recombinant progeny with genotypes not observed in the parents are observed.
Introduction The probability of recombination increases with genetic distance. Thus recombination rate can be used as a unit of distance between loci and used to build maps. Linkage analysis is very important in genetics. It is often the first step towards isolating genes underlying defined phenotypes including inherited diseases. 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 Mapping by tetrad analysis Special features of recombination Linkage and recombination of genes in a chromosome Mendel s second law: parental p versus recombinant gametes Mendel s second law: parental versus recombinant gametes Syntenic loci may be linked, i.e. F1 s produce more parental than recombinant gametes The recombination rate is the same whether the mutant alleles are in cis or trans in the F1 parent The chi-squared test for linkage Each pair of linked genes has a characteristic ti frequency of recombination Recombination in females versus males
Mendel s second law: parental versus recombinant gametes Linkage and recombination of genes in a chromosome Mendel s second law: parental versus recombinant gametes Syntenic loci may be linked, i.e. F1 s produce more parental than recombinant gametes The recombination rate is the same whether the mutant alleles are in cis or trans in the F1 parent The chi-squared test for linkage Each pair of linked genes has a characteristic ti frequency of recombination Recombination in females versus males Syntenic loci may be linked Syntenic loci may be linked 66.5% parentals 33.5% recombinants
Linkage and recombination of genes in a chromosome Coupling versus repulsion of of syntenic alleles Mendel s second law: parental versus recombinant gametes Syntenic loci may be linked, i.e. F1 s produce more parental than recombinant gametes The recombination rate is the same whether the mutant alleles are in cis or trans in the F1 parent The chi-squared test for linkage Each pair of linked genes has a characteristic ti frequency of recombination Recombination in females versus males Repulsion Coupling Coupling versus repulsion of of syntenic alleles 62.3% parentals 37.7% recombinants Linkage and recombination of genes in a chromosome Mendel s second law: parental versus recombinant gametes Syntenic loci may be linked, i.e. F1 s produce more parental than recombinant gametes The recombination rate is the same whether the mutant alleles are in cis or trans in the F1 parent The chi-squared test for linkage Each pair of linked genes has a characteristic ti frequency of recombination Recombination in females versus males
The chi-squared test for linkage Linkage and recombination of genes in a chromosome Mendel s second law: parental versus recombinant gametes Syntenic loci may be linked, i.e. F1 s produce more parental than recombinant gametes The recombination rate is the same whether the mutant alleles are in cis or trans in the F1 parent The chi-squared test for linkage Each pair of linked genes has a characteristic ti frequency of recombination Recombination in females versus males Each pair of linked genes has a characteristic frequency of rec. 98.6% parentals 1.4% recombinants Linkage and recombination of genes in a chromosome Mendel s second law: parental versus recombinant gametes Syntenic loci may be linked, i.e. F1 s produce more parental than recombinant gametes The recombination rate is the same whether the mutant alleles are in cis or trans in the F1 parent The chi-squared test for linkage Each pair of linked genes has a characteristic ti frequency of recombination Recombination in females versus males
Recombination in females versus males Drosophila Other organisms (including mammals) 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 Mapping by tetrad analysis Special features of recombination Genetic mapping Hypothesis (Sturtevant & Morgan) Test 1: recombination between genes results from a physical exchange between een chromosomes (Stern, 1936) Test 2: Crossing-over takes place at the 4-strand stage of meiosis Frequency of recombination versus map distance: Haldane s mapping function Hypothesis (Sturtevant & Morgan) Recombination is due to an exchange of segments between homologous chromosomes in the process called crossing-over over, manifested physically as a chiasma The likelihood of a crossing-over over between two loci depends on their distance on the chromosome, thus explaining variable recombination rates => should allow mapping
Hypothesis (Sturtevant & Morgan) Genetic mapping Hypothesis (Sturtevant & Morgan) Test 1: recombination between genes results from a physical exchange between een chromosomes (Stern, 1936) Test 2: Crossing-over takes place at the 4-strand stage of meiosis Frequency of recombination versus map distance: Haldane s mapping function Recombination results from a physical exchange between homologues Genetic mapping Hypothesis (Sturtevant & Morgan) Test 1: recombination between genes results from a physical exchange between een chromosomes (Stern, 1936) Test 2: Crossing-over takes place at the 4-strand stage of meiosis Frequency of recombination versus map distance: Haldane s mapping function
Crossing-over takes place at 4- strand stage of meiosis Crossing-over takes place at 4- strand stage of meiosis Genetic mapping Hypothesis (Sturtevant & Morgan) Test 1: recombination between genes results from a physical exchange between een chromosomes (Stern, 1936) Test 2: Crossing-over takes place at the 4-strand stage of meiosis Frequency of recombination versus map distance: Haldane s mapping function Frequency of recombination (FR) versus map distance (MD) FR (%): proportion of recombinant gametes (two loci) Non-additive (see hereafter) MD (centimorgan = cm): ½ average number of crossing-overs (m) / meiotic cell (between two loci) additive Difference: multiple cross-overs
Frequency of recombination versus map distance Frequency of recombination versus map distance Nota bene Haldane s mapping function
Haldane s mapping function 1 crossing-over => 50% recombinant gametes 0 crossing-over: P 0 =e -m Rec = 0% 1 crossing-over: P1= m 1 e -m /1! Rec = 50% 2 crossing-over: P2 = Rec =?% 3 crossing-over: m = 0xe m 1 m e + 1x 1! m 2 m e + 2x 2! m +... Haldane s mapping function 2 crossing-over g => 50% rec. gam.!! 0 crossing-over: P 0 =e -m Rec = 0% 1 crossing-over: P1= m 1 e -m /1! Rec = 50% 2 crossing-over: P2 = m 2 e -m /2! Rec =?% 3 crossing-over: m = 0xe m 1 m e + 1x 1! m 2 m e + 2x 2! m +...
Haldane s mapping function Haldane s mapping function 0 crossing-over: P 0 =e -m Rec = 0% 1 crossing-over: P1= m 1 e -m /1! Rec = 50% 2 crossing-over: P2 = m 2 e -m /2! Rec = 50% 3 crossing-over: Rec = 50% m = 0xe m 1 m e + 1x 1! m 2 m e + 2x 2! m +... FR = ( m ) ( 2MD e e ) 1 1 = 1 2 2 1 Haldane s mapping function =Haldane s MF Haldane s mapping function Non-syntenic loci are characterized by a RF of 50% Syntenic loci are characterized by a RF 50%
Overview Building linkage maps Multiple two-point crosses 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 Mapping by tetrad analysis Special features of recombination Building linkage maps Three-point crosses Building linkage maps Three-point crosses Parental (most frequent) genotypes Double recombinant (DR) (rarest) genotypes
Building linkage maps Three-point crosses Building linkage maps Three-point crosses Identification of parental genotypes + double-recombinants unambiguously determines locus order => Lz-Su-Gl Lz_Su_Gl LzxSu_Gl Lz_SuxGl LzxSuxGl LzxSuxGl Lz_SuxGl LzxSu_Gl Lz_Su_Gl Building linkage maps Three-point crosses Building linkage maps Examples RF LzxSu = F LzxSu_Gl + F LzxSuxGl RF SuxGl = F Lz_SuxGl + F LzxSuxGl RF LzxGl = F Lz_SuxGl + F LzxSu_Gl RF LzxGl < RF LzxSu + RF SuxGl Ch r. 10 lon ng arm Chr r. 10 sho ort ar rm
Building linkage maps Genetic vs physical map distance Building linkage maps Genetic vs physical map distance 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 Mapping by tetrad analysis Special features of recombination Chromosome interference Lz_Su_Gl LzxSu_Gl Lz_SuxGl LzxSuxGl LzxSuxGl Lz_SuxGl LzxSu_Gl Lz_Su_Gl
Chromosome interference I(nterference) = 1 coefficient of coincidence Coefficient of coincidence = Observed DR / Expected DR Observed DR = F LzxSuxGl Expected DR = RF LzxSu x RF SuxGl Chromosome interference Positive interference first crossing-over reduces probability to have a second one in the vicinity => fewer observed than expected DR The rule in many genomes (at low resolution) => Kosambi s mapping function Negative interference First crossing-over increases probability to have second one in the vicinity => more observed than expected DR Observed as a result of gene conversion at very high resolution Kosambi s mapping function Chromosome interference Positive interference first crossing-over reduces probability to have a second one in the vicinity => fewer observed than expected DR The rule in many genomes (at low resolution) => Kosambi s mapping function Negative interference First crossing-over increases probability to have second one in the vicinity => more observed than expected DR Observed as a result of gene conversion at very high resolution
Chromatid interference Positive: First crossing-over involving specific nonsister chromatids decreases probability for their involvement in second one Would increase 4-strand DC Would push FR > 50% Never observed 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 Mapping by tetrad analysis Special features of recombination The lod score Definition Mapping in human and animal Compute likelihood of the observations under H1, i.e. FR 50%. (Find value of FR that maximizes likelihood of the data) => L1 Compute likelihood of the observations under H0, i.e. FR = 50% => L0 Lod score = log 10 L1/L0 Maximum likelihood and lod scores
The lod score Properties Mapping in human and animal Can be added across ( 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 of 3 (prior probability of linkage is low 1/50) Allows for unknown phase, incomplete penetrance, Maximum likelihood and lod scores The lod score Properties Can be added across ( 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 of 3 (prior probability of linkage is low 1/50) Allows for unknown phase, incomplete penetrance, 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 Mapping by tetrad analysis Special features of recombination
Mapping by tetrad analysis Unordered tetrads Mapping by tetrad analysis Unordered tetrads Non-syntenic loci PD = NPD Mapping by tetrad analysis Unordered tetrads Syntenic loci PD >> NPD Mapping by tetrad analysis Unordered tetrads MD = ( 1 2 ) ( [ TT ] 2 [ NPD ] ) + 4 [ NPD ] x 100 Total _ N _ tetrads
Gene centromere mapping in ordered tetrads Gene centromere mapping in ordered tetrads First vs second- division segregation Gene centromere mapping in ordered tetrads Gene centromere mapping in mammals: teratocarcinoma FR C_G = ½ (% 2 nd div. segr.) (% 2 nd div. segr.) 66,7% (2/3)
Overview Special features Recombination within genes 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 Mapping by tetrad analysis Special features of recombination Special features Mitotic recombination Somatic mosaics (cancer!)