4 gene linkage and genetic mapping. mendel’s laws: chromosomes homologous pairs of chromosomes:...
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Gene Linkage and Genetic Mapping
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
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
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
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
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)
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
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
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
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
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
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
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
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
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
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
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)
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 chips can detect SNPs
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
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
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
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
Tetrad Analysis
• Unlinked genes produce parental and nonparental ditype tetrads with equal frequency
• Linked genes produce parental ditypes at much higher frequency than nonparental ditype
• Gene conversion = identical alleles produced by heteroduplex mismatch repair during recombination
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