5-1 copyright © the mcgraw-hill companies, inc. permission required to reproduce or display...

5-1 Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or display

Powerpoint to accompany

Genetics: From Genes to GenomesThird Edition

Hartwell ● Hood ● Goldberg ● Reynolds ● Silver ● Veres

Chapter5

Prepared by Malcolm D. SchugUniversity of North Carolina Greensboro


Linkage, Recombination, and the Linkage, Recombination, and the Mapping of Genes on ChromosomesMapping of Genes on Chromosomes


Linkage and meiotic recombinationLinkage and meiotic recombination Genes linked together on the same chromosome usually assort Genes linked together on the same chromosome usually assort

together.together. Linked genes may become separated through recombination.Linked genes may become separated through recombination.

MappingMapping The frequency with which genes become separated reflects the The frequency with which genes become separated reflects the

physical distance between them.physical distance between them. Mitotic recombinationMitotic recombination

Rarely, recombination occurs during meiosis.Rarely, recombination occurs during meiosis. In eukaryotes mitotic recombination produces genetic mosaics.In eukaryotes mitotic recombination produces genetic mosaics.

Outline of Outline of Linkage, Recombination, and the Linkage, Recombination, and the

Mapping of Genes on ChromosomesMapping of Genes on Chromosomes


Independent assortment Independent assortment

Genes on different chromosomesGenes on different chromosomesAA

aa

BB

bb

aB

AB

ab

Ab

Gametes


LinkageLinkageTwo genes on same chromosome segregate together.Two genes on same chromosome segregate together.

AA

aa

BB

bb

Gametes

a b

A B A B

a b


Crossing over and linkage Crossing over and linkage Lead to separation of linked genesLead to separation of linked genes

AA

aa

BB

bb

Gametes

a B

A B

A b

a b

x

Parental

Recombinant


Some genes on the same chromosome Some genes on the same chromosome assort together more often than not.assort together more often than not.

In dihybrid crosses, departures from a In dihybrid crosses, departures from a 1:1:1:1 ratio of F1 gametes indicate that the 1:1:1:1 ratio of F1 gametes indicate that the two genes are on the same chromosome.two genes are on the same chromosome.

How we determine if two genes are on the How we determine if two genes are on the same chromosome can be demonstrated by same chromosome can be demonstrated by the the whitewhite and and yellowyellow genes on the X genes on the X chromosome of Drosophila.chromosome of Drosophila. yellowyellow ( (yy+) – yellow body color+) – yellow body color whitewhite ( (ww+) – white eye color+) – white eye color


Linkage at a sex-linked gene• Deviation from 1:1:1:1 ratio of phenotypes for males

• Draw traits on chromosomes and work through the cross

Fig. 5.2


Designations of “parental” and “recombinant” Designations of “parental” and “recombinant” relate to past history.relate to past history.

Parental and recombinant classes are opposite of one another in these two crosses.Parental and recombinant classes are opposite of one another in these two crosses. Similar percentages of recombinant and parental types show that the frequency of Similar percentages of recombinant and parental types show that the frequency of

recombination is independent of the arrangement of alleles.recombination is independent of the arrangement of alleles.


• Genotypes of F1 female revealed by test cross• Parental class outnumbers recombinant class demonstrating linkage.

Linkage in an autosomal gene

Fig. 5.4


Chi square test pinpoints the probability Chi square test pinpoints the probability that ratios are evidence of linkage.that ratios are evidence of linkage.

Transmission of gametes is based on chance events.Transmission of gametes is based on chance events. Deviations from 1:1:1:1 ratios can represent chance Deviations from 1:1:1:1 ratios can represent chance

events OR linkage.events OR linkage. Ratios alone will never allow you to determine if Ratios alone will never allow you to determine if

observed data are significantly different from predicted observed data are significantly different from predicted values.values.

The larger your sample, the closer your observed values The larger your sample, the closer your observed values are expected to match the predicted values.are expected to match the predicted values.

Chi square test measures “goodness of fit” between Chi square test measures “goodness of fit” between observed and expected (predicted) results.observed and expected (predicted) results. Accounts for sample size, or the size of the experimental Accounts for sample size, or the size of the experimental

populationpopulation


Applying the chi square testApplying the chi square test

Framing a hypothesisFraming a hypothesis Null hypothesis – observed values are not Null hypothesis – observed values are not

different from the expected valuesdifferent from the expected values For linkage studies – no linkage is null hypothesisFor linkage studies – no linkage is null hypothesis Expect a 1:1:1:1 ratio of gametes.Expect a 1:1:1:1 ratio of gametes.

Alternative hypothesis – observed values are Alternative hypothesis – observed values are different from expected valuesdifferent from expected values

For linkage studies – genes are linked.For linkage studies – genes are linked. Expect significant deviation from 1:1:1:1 ratio.Expect significant deviation from 1:1:1:1 ratio.


Applying the chi square test to a Applying the chi square test to a linkage studylinkage study

GenotypeGenotype Experiment 1Experiment 1 Experiment 2Experiment 2

A BA B 1717 3434

a ba b 1414 2828

A bA b 88 1616

A BA B 1111 2222

Total Total 5050 100100

ClassClass Observed/ExpectedObserved/Expected Observed/ExpectedObserved/Expected

ParentalsParentals 31 2531 25 62 5062 50

RecombinationRecombination 19 2519 25 38 5038 50


Chi Square – Experiment 1 & 2Chi Square – Experiment 1 & 2

2 = (observed – expected)2

number expected

2 = (31 – 25)2 + (19 – 25)2 25 25

= 2.88

2 = (62 – 50)2 + (38 – 50)2 50 50

= 5.76

Experiment 1

Experiment 2


Chi square table of critical valuesChi square table of critical values


1909 – Frans Janssens observed 1909 – Frans Janssens observed chiasmatachiasmata, , regions in which nonsister chromatids of regions in which nonsister chromatids of homologous chromosomes cross over each homologous chromosomes cross over each other.other.

Thomas Hunt Morgan suggested these were Thomas Hunt Morgan suggested these were sites of chromosome breakage and change sites of chromosome breakage and change resulting in genetic recombination.resulting in genetic recombination.

Recombination results when crossing-Recombination results when crossing-over during meiosis separates linked over during meiosis separates linked

genes.genes.


Reciprocal exchanges between Reciprocal exchanges between homologous chromosomes are the homologous chromosomes are the physical basis of recombination.physical basis of recombination.

1931 – Genetic recombination depends on the reciprocal 1931 – Genetic recombination depends on the reciprocal exchange of parts between maternal and paternal exchange of parts between maternal and paternal chromosomes.chromosomes. Harriet Creighton and Barbara McClintock studied corn.Harriet Creighton and Barbara McClintock studied corn. Curtis Stern studied fruit flies.Curtis Stern studied fruit flies. Physical markers to keep track of specific chromosome partsPhysical markers to keep track of specific chromosome parts Genetic markers were points of reference to determine if Genetic markers were points of reference to determine if

particular progeny were result of recombination.particular progeny were result of recombination.


Genetic recombination between Genetic recombination between carcar and and BarBar genes on the Drosophila X chromosomegenes on the Drosophila X chromosome

Fig. 5.6


Chiasmata mark the sites of recombination.Chiasmata mark the sites of recombination.

Fig. 5.7 a-c


Chiasmata Chiasmata mark the sites mark the sites

of of recombination.recombination.

Fig. 5.5 d-f


Recombination frequencies for pairs of genes Recombination frequencies for pairs of genes reflect distance between them.reflect distance between them.

Alfred H. Sturtevant – Percentage of Alfred H. Sturtevant – Percentage of recombination, or recombination, or recombination frequency recombination frequency (RF)(RF) reflects the physical distance reflects the physical distance separating two genes.separating two genes. 1 RF = 1 map unit (or 1 centiMorgan)1 RF = 1 map unit (or 1 centiMorgan)

Fig. 5.8


Summary of linkage and Summary of linkage and recombinationrecombination

Genes close together on the same chromosome are linked Genes close together on the same chromosome are linked and do not segregate independently.and do not segregate independently.

Linked genes lead to a larger number of parental class Linked genes lead to a larger number of parental class than expected in double heterozygotes.than expected in double heterozygotes.

Mechanism of recombination is crossing over.Mechanism of recombination is crossing over. Chiasmata are the visible signs of crossing over.Chiasmata are the visible signs of crossing over. The farther away genes are the greater the opportunity for The farther away genes are the greater the opportunity for

chiasmata to form.chiasmata to form. Recombination frequencies reflect physical distance Recombination frequencies reflect physical distance

between genes.between genes. Recombination frequencies between two genes vary from Recombination frequencies between two genes vary from

0% to 50%.0% to 50%.


Mapping: Locating genes along a Mapping: Locating genes along a chromosomechromosome

Two-point crosses: Two-point crosses: Comparisons help Comparisons help establish relative establish relative gene positions.gene positions.

Genes are arranged Genes are arranged in a line along a in a line along a chromosome.chromosome.

Fig. 5.9a


Mapping: Locating genes along a Mapping: Locating genes along a chromosomechromosome

Genes are arranged in a line along a chromosome.

Fig. 5.9 b-d


Limitations of two point crossesLimitations of two point crosses

Difficult to determine gene order if two Difficult to determine gene order if two genes are close togethergenes are close together

Actual distances between genes do not Actual distances between genes do not always add up.always add up.

Pairwise crosses are time and labor Pairwise crosses are time and labor consuming.consuming.


Three Point Crosses: A faster more Three Point Crosses: A faster more accurate method to map genesaccurate method to map genes

Fig. 5.10a


Three point crossThree point crossprpr must be in the middle because longest must be in the middle because longest

distance is between distance is between vgvg and and bb

Fig. 5.10b


Analyzing the results of a three point crossAnalyzing the results of a three point cross

Look at two genes at a time and compare to Look at two genes at a time and compare to parental.parental.

Fig. 5.11 a,b


Analyzing the results of a three point crossAnalyzing the results of a three point cross

Fig. 5.11 c,d


252 + 241 + 131 + 1184197

X 100 = 17.7 m.u.vg – b distance

252 + 241 + 13 + 9 4197

X 100 = 12.3 m.u.vg – pr distance

131 + 118 + 13 + 9 4197

X 100 = 6.4 m.u.b – pr distance

Correction for Double Crossovers

131 + 118 + 13 + 9 4197

X 100 = 6.4 m.u.vg – b distance


Interference: The number of double Interference: The number of double crossovers may be less than expected.crossovers may be less than expected. Sometimes the number of observable double Sometimes the number of observable double

crossovers is less than expected if the two crossovers is less than expected if the two exchanges are independent.exchanges are independent. Occurrence of one crossover reduces likelihood Occurrence of one crossover reduces likelihood

that another crossover will occur in adjacent that another crossover will occur in adjacent parts of the chromosome.parts of the chromosome.

Chromosomal interferenceChromosomal interference – crossovers do not – crossovers do not occur independently.occur independently.

Interference is not uniform among Interference is not uniform among chromosomes or even within a chromosome.chromosomes or even within a chromosome.


Measuring interferenceMeasuring interference

Coefficient of coincidence = ratio between Coefficient of coincidence = ratio between actual frequency of dco and expected actual frequency of dco and expected frequency of dco.frequency of dco.

Interference = 1 – coefficient of coincidence.Interference = 1 – coefficient of coincidence.

If interference = 0, observed and expected frequencies are equal.If interference = 1, no double crossovers can occur.


Double recombinants indicate order Double recombinants indicate order of three genes.of three genes.

Fi.g 5.11 a,d


Summary of three point cross analysisSummary of three point cross analysis Cross true breeding mutant with wild-typeCross true breeding mutant with wild-type Analyze F2 individuals (males if sex linked)Analyze F2 individuals (males if sex linked)

Parental class – most frequentParental class – most frequent Double crossovers – least frequentDouble crossovers – least frequent

Determine order of genes based on parentals and Determine order of genes based on parentals and recombinantsrecombinants

Determine genetic distance between each pair of Determine genetic distance between each pair of recombinantsrecombinants

Calculate coefficient of coincidence and Calculate coefficient of coincidence and interferenceinterference


Do Genetic and Physical maps Do Genetic and Physical maps correspond?correspond?

Order of genes is correctly predicted by physical Order of genes is correctly predicted by physical maps.maps.

Distance between genes is Distance between genes is notnot always similar on always similar on physical maps.physical maps. Double, triple, and more crossoversDouble, triple, and more crossovers Only 50% recombination frequency observable in a Only 50% recombination frequency observable in a

crosscross Variation across chromosome in rate of recombinationVariation across chromosome in rate of recombination

Mapping functions compensate for inaccuracies, Mapping functions compensate for inaccuracies, but are not often imprecise.but are not often imprecise.


Genes Genes chained chained

together by together by linkage linkage

relationships relationships are known as are known as

linkage linkage groups.groups.

Fig. 5.13


Are genetic maps and physical maps Are genetic maps and physical maps correlated?correlated?

The order of genes in a genetic map is the same as The order of genes in a genetic map is the same as the order of those same genes along the DNA the order of those same genes along the DNA molecule of a chromosome.molecule of a chromosome.

The physical distance (amount of DNA separating The physical distance (amount of DNA separating genes) is not always the same as the genetic genes) is not always the same as the genetic distance between genes.distance between genes. Factors responsible for differences in physical and Factors responsible for differences in physical and

genetic map distances:genetic map distances: Double, triple, and even more crossoversDouble, triple, and even more crossovers 50% limit on recombination frequency observable in a cross50% limit on recombination frequency observable in a cross Recombination frequency is not uniform across a chromosome.Recombination frequency is not uniform across a chromosome.

Recombination hotspotsRecombination hotspots Recombination desertsRecombination deserts


Tetrad analysis in fungiTetrad analysis in fungi

Model organisms for understanding the Model organisms for understanding the mechanism of recombination because all mechanism of recombination because all four haploid products of meiosis are four haploid products of meiosis are contained in ascuscontained in ascus

Ascospores within ascus germinate into Ascospores within ascus germinate into haploid individuals.haploid individuals. Saccharaomyces cerevisiaeSaccharaomyces cerevisiae – bakers yeast – bakers yeast Neurospora crassaNeurospora crassa – bread mold – bread mold


Saccharaomyces cerevisiaeSaccharaomyces cerevisiae life cycle life cycle

Fig. 5.14 a


Neurospora crassaNeurospora crassa life cycle life cycle

Fig. 5.14 b


Neurospora crassaNeurospora crassa tetrads tetrads


Tetrads can be characterized by the number of Tetrads can be characterized by the number of parental and recombinant spores they contain.parental and recombinant spores they contain.

Fig. 5.15 a


Fig. 5.15 d,e


Linkage is demonstrated by PDs Linkage is demonstrated by PDs outnumbering NPDs.outnumbering NPDs.

Fig. 5.16


How crossovers How crossovers between linked between linked genes generate genes generate

different different tetradstetrads

Fig. 5.17 a-c


Fig. 5.17 d-f


Calculating recombination Calculating recombination frequencyfrequency

NPD + ½ TTotal tetrads

RF = 100


Confirmation that recombination Confirmation that recombination occurs at the four-strand stageoccurs at the four-strand stage

A mistaken ModelRecombination before four-strand stage not consistent with tetrads

containing recombinant spores; would be NPDs instead of Ts

Fig. 5.18


Tetrad analysis demonstrates that Tetrad analysis demonstrates that recombination is reciprocal.recombination is reciprocal.

In a cross between strains with different In a cross between strains with different alleles at two genes, each tetrad contains alleles at two genes, each tetrad contains and two of each type of recombinantand two of each type of recombinant


Ordered tetrads allow mapping a Ordered tetrads allow mapping a gene in relation to the centromere.gene in relation to the centromere.

Fig. 5.20


Segregation patterns in ordered asciSegregation patterns in ordered asci

Fig. 5.21 a


Segregation patterns in ordered Segregation patterns in ordered tetradstetrads

Fig. 5.21 b


Calculating distance to centromereCalculating distance to centromere

% SDS = SDSFDS + SDS

100


Example of genetic mapping by Example of genetic mapping by ordered tetrad analysisordered tetrad analysis

Fig. 5.22


Mitotic recombination can produce Mitotic recombination can produce genetic mosaics.genetic mosaics.

Mitotic recombination is rare.Mitotic recombination is rare. Initiated byInitiated by

Mistakes in chromosome replicationMistakes in chromosome replication Chance exposure to radiationChance exposure to radiation

Curt Stern – observed “twin spots” in Curt Stern – observed “twin spots” in Drosophila – a form of genetic Drosophila – a form of genetic mosaicism.mosaicism. Animals contained tissues with different Animals contained tissues with different

genotypes.genotypes.


Mitotic crossing over between Mitotic crossing over between snsn and and centromere in Drosophilacentromere in Drosophila

Fig. 5.24 a


Essential ConceptsEssential Concepts Gene pairs that are close together on the same chromosome are Gene pairs that are close together on the same chromosome are

linked because they are transmitted together more often than not.linked because they are transmitted together more often than not. The recombination frequency of pairs of genes indicate how often The recombination frequency of pairs of genes indicate how often

two genes are transmitted together. Gene pairs that assort two genes are transmitted together. Gene pairs that assort independently exhibit a recombination frequency of 50%.independently exhibit a recombination frequency of 50%.

Statistical analysis helps determine whether or not two genes Statistical analysis helps determine whether or not two genes assort independently.assort independently.

The greater the physical distance between linked genes, the higher The greater the physical distance between linked genes, the higher the recombination frequency.the recombination frequency.

Genetic maps are visual representations of relative recombination Genetic maps are visual representations of relative recombination frequencies.frequencies.

Organisms that retain all the products of meiosis within an ascus Organisms that retain all the products of meiosis within an ascus reveal the relation between genetic recombination and segregation reveal the relation between genetic recombination and segregation of chromosomes during meiosis.of chromosomes during meiosis.


Crossing over between sn and y gene

Fig. 5.24 b


Twin spots in Twin spots in DrosophilaDrosophilaA form of genetic mosaicism – mistakes in chromosome A form of genetic mosaicism – mistakes in chromosome replication or exposure to radiation that breaks DNA replication or exposure to radiation that breaks DNA

molecules lead to mitotic recombinationmolecules lead to mitotic recombination

Fig. 5.23


Origin of twin spots and yellow spots Origin of twin spots and yellow spots in Drosophilain Drosophila

Fig. 5.24a


Origin of twin spots and yellow spots Origin of twin spots and yellow spots in Drosophilain Drosophila

Fig. 5.24b

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