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 inversely 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 greater than 50 percentand 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. 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

18. 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

19. 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

20. 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

21. 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

23. 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

25. 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)

27. Gene Maps: Restriction Enzymes • RFLPs can map 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

28. 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

30. Gene Mapping: Tetrad Analysis • In Neurospora, meiotic cell division produces four ascospores; each contains a single product of meiosis • Analysis of ascus tetrads shows recombination of unlinked genes • Tetrad analysis shows products of single and double 2, 3 and 4 strand cross-overs of linked genes

32. Tetrad Analysis • In tetrads when two pairs of alleles are segregating, 3 possible patterns of segregation: -parental ditype (PD): two parental genotypes -nonparental ditype (NPD): only recombinant combinations -tetratype (TT): all four genotypes observed

34. Neurospora: Meiotic Segregation • Products of meiotic segregation can be identified by tetrad analysis • Meiosis I segregation in the absence of cross-overs produces 2 patterns for a pair of homologous chromo-somes • Meiosis II segregation after a single cross-over produces four possible patterns of spores

36. Tetrad Analysis • Unlinked genes produce parental and nonparental ditype tetrads with equal frequency • Linked genes produce parental ditypes at much higherfrequency than nonparental ditype • Gene conversion = identical alleles produced by heteroduplex mismatch repair during recombination

37. 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