CHAPTER 4 Gene Linking and Genetic Mapping A gene s sequence does not always reveal its function 4 1 Linked alleles tend to stay together in meiosis Thomas Hunt Morgan found that genes close enough together in the same chromosome typically transmit together a phenomenon known as linkage Drosophilia white wings However this linkage is incomplete and results in recombination via crossing over The probability of recombination between two genes serves as a measure of genetic distance between the genes and allows the construction of a genetic map Parental combinations alleles same as parental configuration coupling or cis configuration Recombinations are repulsion or trans configuration The degree of linkage is measured by the frequency of recombination recombinants total If recombination frequency 50 linked recombination frequency 50 unlinked The frequency of recombination is the same for coupling and repulsion heterozygotes The frequency of recombination differs from one gene pair to the next If the recombination frequency is smaller then the genes are more closely linked Recombination does not occur in Drosophilia males crossing over is prevented 4 2 Recombination results from crossing over between linked alleles Each chiasma results from breaking and rejoining of chromatids during meiosis The theory of crossing over is that each chiasma results in a new association of genetic markers The unit of distance in a genetic map is called a map unit I mu 1 recombination One map unit is also called a centimorgan cM crossover frequency of 2 A double crossover between the same pair of chromatids is not detected no recombination The map distance equals average number of crossovers that take place in the region per cell The recombination frequency indicates how much recombination is actually observed The first measures crossing over the second measures recombination Map units and recombination frequencies are the same when the gene is so short 10 recombination or less that there is no possibility of double crossovers A linkage group is all the known genes in a chromosome The number of linkage groups is the same as the haploid number of chromosome of the species Physical distance is often but not always correlated with map distance Crossing over is less frequent in heterochromatin gene poor near centromeres than in euchromatin so small distance in genetic map over large chromosome distance No matter how far apart two genes may be the max frequency of recombination between any two genes is 50 4 3 Double crossovers are revealed in three point crosses In any genetic cross the two most frequent types of gametes with respect to any pair of genes are non recombinant these provide the linkage phase cis versus trans of the alleles of the genes in the multiply heterozygous parent The effect of double crossing over is to interchange members of the middle pair of alleles between the chromosomes Two strand double crossover double recombination three strand double crossover one double recombinant and two single recombinants four strand double crossover 4 singles The two reciprocal products resulting from any crossover s are expected to appear in approx equal frequencies among the progeny Interference decreases the chance of multiple crossing overs Interference is where a crossover in one region of a chromosome reduces the probability of a second crossover in a nearby region Over short genetic distances interference nearly complete The coefficient of coincidence is the observed number of double recombinant chromosomes divided by the expected number Degree of interference i 1 coeff For Drosophilia at around 10 map units no double crossovers exist coeff 0 interference 1 4 4 Polymorphic DNA sequences are used in human genetic mapping Complications in human gene mapping genes of genetic diseases are rare many mutant genes are recessive hard to detect number of offspring in family is typically small no testcrosses DNA sequences of two corresponding positions of two genes from two people differ 1 1000 bp A genetic different that is relatively common in a population is called a polymorphism Single nucleotide polymorphisms abundant in human genome most common genetic diff Identifying nucleotide at each SNP is possible through the use of DNA microarrays SNP chips enable the SNP genotype to be determined with nearly 100 accuracy SNPs in restriction sites yield restriction fragment length polymorphisms RFLPs Some polymorphisms in DNA are detected by means of a type of enzyme called a restriction endonuclease which cleaves double stranded DNA molecules wherever a particular short sequence of bases is present Ex EcoRI cleaves DNA sequence GAATTC Any difference in DNA sequence that alters a cleavage site also changes the length of the DNA fragments produced by cleavage with the corresponding restriction enzyme Differences in DNA fragment length produced by presence or absence of cleavage sites in DNA molecules are known as restriction fragment length polymorphisms RFLP can form by mutation that changes a base sequence resulting in loss gain of cleavage site Simple sequence repeats SSRs often differ in copy number An SSR is a genetic polymorphism resulting from differences in the number of copies of a short DNA sequence that may be repeated many times in tandem at particular site in a chromosome There is an average of one SSR 2kb of human DNA In genetic mapping phenotype of a person in DNA polymorphism is the pattern of gel bands DNA polymorphisms are the principal types of genetic markers used in genetic mapping in human pedigrees 60 MORE recombination in females than in males 1 cM million bp Gene dosage can differ owning to copy number polymorphisms CNPs CNP is a variation where substantial portions of the genome are duplicated or deleted The extra missing copies of the genome in CNPs detected by means of hybridization with oligonucleotides in DNA microarrays Current SNP chips include a million oglionucleotide probes to detect known CNPs CNPs are 1kb average 200 300kb 300 450 Mb CNPs in alpha and beta hemoglobin genes are associated with resistance to malaria CNPs in an HIV 1 receptor gene CCL3 are associated with resistance to AIDS 4 5 Tetrads contain all four products of meiosis In some species of fungi each tetrad is contained in a sac like ascus containing four ascospores Ascus producing organisms are haploid so genotype is expressed in phenotype and they produce large numbers of progeny making it easy to estimate