1. 4 Gene Linkage and Genetic Mapping

2. Mendel’s Laws: Chromosomes Homologous pairs of chromosomes: contain genes whose information is often non- identical =alleles Different alleles of the same gene segregate at meiosis I Alleles of different genes assort independently in gametes Genes on the same chromosome exhibit linkage: inherited together

4. Gene Mapping Gene mapping determines the order of genes and the relative distances between them in map units 1 map unit=1 cM (centimorgan) Alleles of two different genes on the same chromosome are cis Alleles of two different genes on different homologues of the same chromosome are trans

5. Gene Mapping Gene mapping methods use recombination frequencies between alleles in order to determine the relative distances between them Recombination frequencies between genes are proportional to their distance apart Distance measurement: 1 map unit = 1 percent recombination

7. Gene Mapping Recombination between linked genes located on the same chromosome involves homologous crossing-over = allelic exchange between them Recombination changes the allelic arrangement on homologous chromosomes = recombinant

9. Gene Mapping Genes with recombination frequencies less than 50 percent are on the same chromosome (linked) Two genes that undergo independent assortment have recombination frequency of 50 percent (or more?) and are located on nonhomologous chromosomes or far apart on the same chromosome (unlinked)

11. Recombination Recombination between linked genes occurs at the same frequency whether alleles are in cis or trans configuration Recombination frequency is specific for a particular pair of genes Recombination frequency increases with increasing distances between genes

12. Genetic Mapping Map distance between two genes = one half the average number of crossovers in that region Map distance=recombination frequency over short distances because all crossovers result in recombinant gametes Genetic map = linkage map = chromosome map

13. Genetic Mapping Linkage group = all known genes on a chromosome Physical distance does not always correlate with map distance; less recombination occurs in heterochromatin than euchromatin Locus=physical location of a gene on chromosome

14. Gene Mapping: Crossing Over Crossing-over between genes on homologous chromosomes changes the linkage arrangement of alleles on a single chromosome Two exchanges between the same chromatids result in a reciprocal exchange of the alleles in the region between the cross-over points

16. 16 Example: Trihybrid Mapping Counts from: LSG/lsg x lsg/lsg n=740 Distance L to S: (40+33+4+2)/740 * 100 = 11.2 cM Interference = 1-[f(doubles)/ f(single1) *f(single2)]

17. Gene Mapping: Crossing Over Cross-overs which occur outside the region between two genes will not alter their arrangement Double cross-overs restore the original allelic arrangement Cross-overs involving three pairs of alleles specify gene order = linear sequence of genes

19. Genetic vs. Physical Distance Map distances based on recombination frequencies are not a direct measurement of physical distance along a chromosome Recombination “hot spots” overestimate physical length Low rates in heterochromatin and centromeres underestimate actual physical length

20. Gene Mapping Mapping function: the relation between genetic map distance and the frequency of recombination Chromosome interference: cross-overs in one region decrease the probability of second cross-over Coefficient of coincidence=observed number of double recombinants divided by the expected number

21. Gene Mapping: Human Pedigrees Methods of recombinant DNA technology are used to map human chromosomes and locate genes Genes can then be cloned to determine structure and function Human pedigrees and DNA mapping are used to identify dominant and recessive disease genes

22. Gene Maps: Restriction Endonucleases Restriction endonucleases are used to map genes as they produce a unique set of fragments for a gene EcoR1 cuts ds DNA at the sequence = 5’- GAATTC-3’ wherever it occurs There are >100 restriction endonucleases in use, and each recognizes a specific sequence of DNA bases

24. Gene Maps: Restriction Enzymes Differences in DNA sequence generate different recognition sequences and DNA cleavage sites for specific restriction enzymes Two different genes will produce different fragment patterns when cut with the same restriction enzyme due to differences in DNA sequence

26. Gene Maps: Restriction Enzymes Polymorphism= relatively common genetic difference in a population Changes in DNA sequence = mutation may cause polymorphisms which alter the recognition sequences for restriction enzymes = restriction fragment length polymorphisms (RFLPs)

28. Gene Maps: Restriction Enzymes RFLPs can map near or in human genes Genetic polymorphism resulting from a tandemly repeated short DNA sequence = simple tandem repeat polymorphism (STRP) Most prevalent type of polymorphism is a single base pair difference = simple- nucleotide polymorphism (SNP) DNA chips can detect SNPs

29. Human Gene Mapping Human pedigrees can be analyzed for the inheritance pattern of different alleles of a gene based on differences in STRPs and SNPS Restriction enzyme cleavage of polymorphic alleles differing RFLP pattern produces different size fragments by gel electrophoresis

31. 31 Tetrad Analysis Meiotic spores held in asci (ascospores) Allows recovery of all products of meiosis Two types Unordered tetrads (yeast) Usually allows gene to gene map distances Under rare circumstances, gene to centromere Ordered tetrads (neurospora) Usually allows gene to centromere map distance

32. 32 Unordered Tetrads Four kinds of tetrads Parental ditype (AB, AB, ab, ab) Non-parental ditype (Ab, Ab, aB, aB) Tetra-type (AB, Ab, aB, ab) When genes tightly linked only parentals seen When genes unliked parentals and non-parentals equal tetratypes: gene-centromere X-over gene-centromere map possible (1 gene @ cen)

33. 33 Unlinked Genes in Tetrads

34. 34 Linked Genes in Tetrads Also three tetrad types seen parental ditypes: no X-overs (2 str doubles) non-parental ditypes: 4 str double X-overs tetratypes more complicated single X-overs 3 strand double X-overs Formula for Map distance: [(1/2 TT’s + 3 NPD’s)/total asci] * 100 applies only to unordered tetrads

35. 35 Linkage and Tetrads

36. 36 22 Ordered Tetrads Neurospora Tetrads: two kinds First Division Segregation (FDS) occurs in absence of recombination two versions (rotationally equivalent) Second Division Segregation (SDS) occurs with gene-centromere X-overs four versions (rotationally equivalent) Gene-Centromere distance (1/2 SDS)/total asci * 100 applies only to ordered tetrads

37. 37 Ordered Tetrads

38. Recombination: Holliday Model Homologous recombination: single-strand break in homologues pairing of broken strands occurs branch migration: single strands pair with alternate homologue nicked strands exchange places and gaps are sealed to form recombinant by Holliday junction-resolving enzyme