Genetics: From genes to genomes - Chapter 5: Basic principles: how traits are transmitted

*Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or displayPowerPoint to accompanyGenetics: From Genes to GenomesFourth EditionLeland H. Hartwell, Leroy Hood, Michael L. Goldberg, Ann E. Reynolds, and Lee M. SilverPrepared by Mary A. BedellUniversity of Georgia*Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5CHAPTERBasic Principles: How Traits Are TransmittedCHAPTERPART ILinkage, Recombination and the Mapping of Genes on Chromosomes5.1 Gene Linkage and Recombination5.2 The Chi-Square Test and Linkage Analysis5.3 Recombination: A Result of Crossing-Over During Meiosis5.4 Mapping: Locating Genes Along a Chromosome5.5 Tetrad Analysis in Fungi5.6 Mitotic Recombination and Genetic MosaicsCHAPTER OUTLINEGene linkage and recombinationGenes linked together on the same chromosome usually assort togetherLinked genes may become separated by recombinationTwo themes in this chapter:Further apart two genes are, the greater the probability of recombinationRecombination data can be used to generate maps of relative locations of genes on chromosomesCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Detecting linkage by analyzing the progeny of dihybrid crosses: X-linked genesSyntenic genes – genes located on the same chromosomeTwo X-linked genes in Drosophila with recessive allelesw+ (red eyes) and w (white eyes)y+ (brown body) and y (yellow body)Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Note that in this cross:F1 males get their only X chromosome from their mothersF1 females are dihybrids Fig. 5.2aDetecting linkage by analyzing the progeny of dihybrid crosses: X-linked genes (cont)Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.2bCompare allele configurations in F2 to P generationDeviation from 1:1:1:1 segregation in F2 indicates the genes are linkedNote that in this cross involving X-linked genes, only the F2 male progeny were countedDesignation of "parental" and "recombinant" relate to past historyNote that the parental configurations in these two crosses are opposite of each otherCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.3Autosomal genes can also exhibit linkageDetect linkage by generating a double heterozygote and crossing to homozygous recessive (testcross)Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.4Chi square test pinpoints the probability that ratios are evidence of linkageDeviations from 1:1:1:1 ratios can represent chance events or linkageChi square test measures "goodness of fit" between observed and expected valuesNull hypothesis – observed values are no different from expected valuesIn linkage studies, the null hypothesis is no linkageIf genes are linked, expect 1:1:1:1 ratio in F2 progenyChi-square test can reject the null hypothesis, but it cannot prove a hypothesisCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Information needed for the chi-square testUse data from breeding experimentTotal number of progenyHow many classes of progenyNumber of offspring observed in each classCalculate number of offspring expected in each class if there is no linkage (1:1:1:1 segregation)Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Applying the chi-square testCalculate the chi-squareConsider degrees of freedom (df) in the experimentdf = N – 1 (where N is the number of classes)Determine a p value using chi-square value and df Probability that the deviation from expected numbers had occurred by chanceUse table 5.1 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Applying the chi-square test to see if genes A and B are linkedCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Experiment 1: Experiment 2: Fig. 5.5Critical chi-square valuesCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Use p value of 0.05 as cutoffChi-square values that lie in the yellow region of this table allow rejection of the null hypothesis with >95% confidenceIf null hypothesis is rejected, then linkage can be postulatedTable 5.1Recombination: A result of crossing-over during meiosisFrans Janssens – 1909, observed chiasmata at chromosomes during prophase of meiosis IT. H. Morgan – suggested chiasmata were sites of chromosome breakage and exchangeH. Creighton and B. McClintock (corn) and C. Stern (Drosophila) – 1931, direct evidence that genetic recombination depends on reciprocal exchanged of chromosomesPhysical markers were used to identify specific chromosomesGenetic markers were used as points of reference for recombinationCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Evidence that recombination results from reciprocal exchanges between homologous chromosomesCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.6Recombination during meiosis I visualized by light microscopy Early prophase Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.7 Leptotene and zygotene DiploteneRecombination during meiosis I visualized by light microscopy (cont)Terminalization – movement of chiasmataCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.7Anaphase – chromosome separation occurs after chiasmata reach the telomeresTwo recombinant and two parental gametes are producedRecombination frequencies are the basis of genetic mapsA. H. Sturtevant – proposed that recombination frequencies (RF) could be used as a measure of physical distance between two linked genes1 percent recombination = 1 RF = 1 map unit (m.u.) – 1 centiMorgan (cM)Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.8Properties of linked versus unlinked genesCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Table 5.2Mapping genes by comparisons of two-point crossesLeft-right orientation of map is arbitraryMost accurate maps obtained by summing many small intervening distancesCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.9Limitations of two point crossesDifficult to determine gene order if two genes are close togetherActual distances between genes do not always add upPairwise crosses are time and labor consumingCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Three point crosses provide faster and more accurate mappingTestcross of triply-heterozygous F1Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.10Analyzing the results of a three-point crossTestcross progeny have four sets of reciprocal pairs of genotypesMost frequent pair has parental configuration of allelesLeast frequent pair results from double crossoversExamination of double crossover class reveals which gene is in the middleCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.10Inferring the location of crossover eventExamine numbers of progenyCompare configuration of alleles at two genes at a time to parental configurationCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.11aInferring the location of crossover events (cont)Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.11b-dGenetic map deduced from three-point cross in Figure 5.10Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.10bCorrection for double crossoversCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*This calculation isn't accurate because it fails to account for double crossoversCorrect calculation that accounts for double crossoversInterference: The number of double crossovers may be less than expectedChromosomal interference – occurrence of crossover in one portion of a chromosome interferes with crossover in an adjacent part of the chromosomeNot uniform between chromosomes or within a chromosome Compare observed and expected frequencies of double crossovers (DCO)Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Calculation of interference in the three-point cross in Figure 5.10Expected probability of double crossovers is the product of the single crossover frequencies in each intervalProbability of single crossover between vg and pr is 0.123 (12.3 m.u.)Probability of single crossover between pr and b is 0.064 (6.4 m.u.)If interference = 0, crossovers in adjacent regions occur independently of each otherIf interference = 1, no double crossovers occur Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Calculation of interference in the three-point cross in Figure 5.10 (cont)Expected probability of double crossoversObserved proportion of double crossoversCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Do genetic maps correlate with physical reality?Order of genes revealed by genetic mapping corresponds to the actual order of genes along the chromosomeActual physical distance (amount of DNA) does not always show direct correspondence to genetic distanceDouble, triple, and more crossovers50% limit on observable recombination frequencyNon-uniform recombination frequency across chromosomesMapping functions compensate for some inaccuraciesRecombination rates differ between speciesCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Drosophila melanogaster has four linkage groupsCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.13When many genes per chromosome have been mapped, a linkage group is synonymous with a chromosomeTetrad analysis in fungiTwo model organisms for understanding mechanisms of recombinationSaccharomyces cerevisiae – bakers yeastNeurospora crassa – bread moldAll four haploid products of each meiosis are contained within an ascus (sac)Ascospores (haplospores) can germinate and survive as viable haploids that divide by mitosisTetrad - four ascospores in a single ascusHaploid strains of opposite mating type (a and α) can be mated and the resulting diploid induced to undergo meiosisCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*The life cycle of Saccharomyces cerevisiae Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.14aThe life cycle of Neurospora crassa Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.14bGenetic analysis in fungiPhenotype of haploid fungi is direct representation of their genotypeMutations in haploids can affect appearance of cells and ability to grow under certain conditionshis4 mutant; recessive, unable to grow in absence of histidineHIS4; dominant, grows in presence or absence of histidinetrp1 mutant; recessive, unable to grow in absence of tryptophanTRP1; dominant, grows in presence or absence of tryptophan Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Generation of diploid yeast cells that are heterozygous for two unlinked geneshis4 TRP1 (a) x HIS4 trp1 (α)  his4/HIS4; trp1/TRP1 (a/α)Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.15aMeiosis can generate three kinds of tetrads:Parental ditype (PD)his4 TRP1 (a) x HIS4 trp1 (α)  his4/HIS4; trp1/TRP1 (a/α)Parental ditype (PD) - all spores with parental allele configurations (0/4 recombinants)Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.15bMeiosis can generate three kinds of tetrads:Nonparental ditype (NPD)his4 TRP1 (a) x HIS4 trp1 (α)  his4/HIS4; trp1/TRP1 (a/α)Nonparental ditype (NPD) - all spores with nonparental allele configuration (4/4 recombinants) Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.15cMeiosis can generate three kinds of tetrads:Tetratype (T)his4 TRP1 (a) x HIS4 trp1 (α)  his4/HIS4; trp1/TRP1 (a/α)Tetratype (T) - four kinds of spores (2/4 recombinants)Two have parental allele configurationsTwo have recombinant allele configurationsCrossover between centromere and closest geneCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.15dTetrad analysis of unlinked genesWhen genes are unlinked, number of PD = number of NPDCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.15eTetrad analysis of linked genesWhen genes are linked, number of PD >> number of NPDCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.16How crossovers between linked genes generate different tetradsCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.17How crossovers between linked genes generate different tetrads (cont)Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.17How crossovers between linked genes generate different tetrads (cont)Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.17Calculating recombination frequencies in tetrad analysisCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*For the cross in Figure 5.16:Evidence that recombination takes place at the four-strand stageCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.18Evidence for exception to the rule that recombination is reciprocalMeiotic recombination almost always generates equal numbers of both kinds of recombinant progeny (2:2 segregation)Rare tetrads will segregate 3:1, 1:3, 4:0, or 0:4Implications of this for molecular mechanisms of recombination discussed in chapter 6Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.19Neurospora form ordered tetradsCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.20Undergo meiosis I and II as usual, but a single round of mitosis after 2nd meiotic division – produces octadAscus is very narrow and spindle forms parallel to long axisTwo genetically identical ascosporesare next to each otherArrangement of chromatids can be inferred from position of ascosporesTwo segregation patterns in ordered asci: First-division segregation patternCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.21aTwo segregation patterns in ordered asci: Second-division segregation patternNumber of second division tetrads is used to calculate the distance between a gene and a centromereGene – centromere distance = divide percentage of second division tetrads by 2 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.21bOrdered tetrads help locate genes in relation to the centromereNeurospora cross thr+ arg+ x thr arg  tetrads in 7 genotype classes Centromere – thr distance: Centromere – arg distance:Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.22aDetermining linkage with ordered tetradsNeurospora cross thr+ arg+ x thr arg  tetrads in 7 genotype classesIf thr and arg are linked, PD >> NPDPD = 72 + 1 = 73 >> NPD = 1 + 2 = 3 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.22aCalculating map distance with ordered tetradsCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*arg – thr distance:This calculation doesn't account for double crossovers Fig. 5.22bRules for tetrad analysis in ordered and unordered tetradsCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Table 5.3Mitotic recombination can produce genetic mosaicsRare occurrence through:Mistakes in chromosome replicationChance exposure to radiationCan be observed in yeast and multicellular organismsDifferent genotypes in different cellsHave major repercussions to human healthC. Stern (1936), inferred existence of mitotic recombination from observations of "twin spots" in DrosophilaPatches of somatic tissue that have different genotypesCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Twin spots are a form of genetic mosaicismDouble heterozygous Drosophila females y sn+/y+ snyellow (y) mutant – yellow bodywildtype (y+) – brown bodysinged (sn) mutant – short and curled bristleswildtype (sn+) – long and straight bristlesCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.23Origin of twin spots in DrosophilaCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.24aOrigin of yellow spots in DrosophilaCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.24bSectored yeast colonies can arise from mitotic recombinationDiploid ADE2/ade2White colonies are wildtypeRed sectors are ade2/ade2Size of sector indicates when recombination took placeCopyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display Hartwell et al., 4th ed., Chapter 5*Fig. 5.25