Gene Linkage and Genetic Mapping

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 betweenthem • 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. 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 • EcoR1cuts 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 = mutationmay 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 chipscan detectSNPs

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. 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. 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. Unlinked Genes in Tetrads

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. Linkage and Tetrads

36. 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 22

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