Linkage, Recombination, and the Mapping of Genes on …skgjx.whu.edu.cn/Public/upfile/article/... · 2017-06-22 · 5.1 Gene linkage and recombination 5.2 The Chi-square test and

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

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

Chapter 5


5.1 Gene linkage and recombination5.1 Gene linkage and recombination5.2 The Chi5.2 The Chi--square test and linkage analysissquare test and linkage analysis5.3 Recombination: A result of crossing5.3 Recombination: A result of crossing--over during over during

meiosismeiosis5.4 Mapping: Locating genes along a chromosome5.4 Mapping: Locating genes along a chromosome5.5 Tetrad analysis in fungi5.5 Tetrad analysis in fungi5.6 Mitotic recombination and genetic mosaics5.6 Mitotic recombination and genetic mosaics

Sections to studySections to study


5.1 Gene linkage and recombination5.1 Gene linkage and recombination

AaBb

aB

AB

ab

A

b

Gametes

AB: Ab: aB: ab=1: 1: 1: 1

Independent assortmentIndependent assortmentGenes on different Genes on different chromosomeschromosomes


Genetic linkageGenetic linkageTwo genes on the same chromosome segregate together.Two genes on the same chromosome segregate together.

Aa

Bb

Gametes

a b

A B A B

a b

AB: Ab: aB: ab=2: 0: 0: 2


Fig. 5.2

w+: brick-red eyesw: white eyes

y+: brown bodyy: yellow body

Y: Y chromosome

w and y genes are X-linked in Drosophila

Thomas H. Morgan


Autosomal genes can also exhibit linkage

Fig. 5.4


In In dihybriddihybrid crosses, departures from a 1:1:1:1 ratio of crosses, departures from a 1:1:1:1 ratio of F1F1 gametes indicate that the two genes are linked on the gametes indicate that the two genes are linked on the same chromosome.same chromosome.

Testcrosses with one parent homozygous for recessive Testcrosses with one parent homozygous for recessive alleles of both genes can help determine if linked.alleles of both genes can help determine if linked.

Parental class outnumbers recombinant class Parental class outnumbers recombinant class demonstrates linkage.demonstrates linkage.

A nonA non--2:0:0:2 segregation pattern of 2:0:0:2 segregation pattern of F2F2 progenies progenies indicates genetic recombination.indicates genetic recombination.

Summary of linkageSummary of linkage



Fig. 5.2

w+: brick-red eyesw: white eyes

y+: brown bodyy: yellow body

Y: Y chromosome

T. H. Morgan’s experiment


Fig. 5.3


For genes w and y:

Recombinant frequency (RF) = Recombinant classes/Total classes


Parental and recombinant classes are opposite of one another in Parental and recombinant classes are opposite of one another in these two crosses.these two crosses.

Similar percentages of recombinant and parental types show Similar percentages of recombinant and parental types show that the frequency of recombination is independent of the that the frequency of recombination is independent of the arrangement of alleles.arrangement of alleles.

Fig. 5.3


Two questions Morgan faced:Two questions Morgan faced:

1. What was the source of gene separation?

2. Why did the recombinant frequency vary?

1.3% versus 37.2%w——mw——y

w y+F1 femalesw+ y

4 genotypes(gametes)


1909 1909 –– FransFrans A. A. JanssensJanssens reported reported chiasmatachiasmata, regions in , regions in which which nonsisternonsister chromatidschromatids of homologous of homologous chromosomes cross over each other during prophase of chromosomes cross over each other during prophase of the first meiotic division.the first meiotic division.

Frans A. Janssens(1865-1924)

5.3 Recombination: A result of crossing-overduring meiosis


MorganMorgan’’s explanation:s explanation:

centromere

centromerechromatid

chiasmachiasma

Morgan suggested Morgan suggested chiasmatachiasmata were the sites of were the sites of chromosome breakage and exchange resulting in chromosome breakage and exchange resulting in genetic recombination.genetic recombination.


AAaa

BB

bb

Gametes

a B

A B

A b

a b

x

Parental

Recombinant


Experimental evidence of reciprocal chromosomal Experimental evidence of reciprocal chromosomal exchange in genetic recombinationexchange in genetic recombination

Reported in 1931 Reported in 1931 –– Genetic recombination depends on Genetic recombination depends on the reciprocal exchange of parts between maternal and the reciprocal exchange of parts between maternal and paternal chromosomes.paternal chromosomes. Harriet CreightonHarriet Creighton and and Barbara McClintockBarbara McClintock’’s work on corn.s work on corn.

Curt SternCurt Stern’’s work on fruit flies.s work on fruit flies.


Curt SternCurt Stern (1902(1902--1981), UC 1981), UC BerkeleyBerkeley

Identification of Identification of physical physical markersmarkers to keep track of to keep track of specific chromosome parts specific chromosome parts enabled researchers to test enabled researchers to test the idea.the idea.

Genetic markersGenetic markers were were points of reference to points of reference to determine if particular determine if particular progeny were result of progeny were result of recombination.recombination.

5-19Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or displayFig. 5.6

Genetic recombination between Genetic recombination between carcar and and BarBar genes on genes on the the DrosophilaDrosophila X chromosomeX chromosome


ChiasmataChiasmata mark the sites of recombinationmark the sites of recombination

Fig. 5.7 a-c


Fig. 5.7 d-f


Crossing over occurs after chromosome replication

Fig. 5.18 mod


MorganMorgan’’s three proposals:s three proposals:

w y

m

Linked genes exist in Linked genes exist in a linear ordera linear order along the chromosome.along the chromosome. A variable amount of exchange (A variable amount of exchange (crossing overcrossing over) occurs between ) occurs between

any two genes during gamete formation.any two genes during gamete formation. The closer two genes are, the less likely a genetic exchange wilThe closer two genes are, the less likely a genetic exchange will l

occur between them.occur between them.


Alfred H. Sturtevant was the first to realize that one can use data about how often genes separate to map their relative locations.

5.4 The mapping of genes along a chromosome

y w m

The percentage of recombination, or recombination frequency (RF) reflects the physical distance separating two genes.

RF = Recombinant classes/Total classes


(y min) (w — min)— w) +35.4% 34.5%0.5%

yellow – white 0.5%white – miniature 34.5%yellow – miniature 35.4%

(y

35.4

0.5 34.5y w m

Recombinationfrequency


Fig. 5.8

1% RF (1% recombinant progeny)1% RF (1% recombinant progeny)= 1 = 1 map unitmap unit ((m.um.u..), or 1 ), or 1 centimorgancentimorgan ((cMcM))


Mapping genes by two-point crosses

Fig. 5.9


Limitations of twoLimitations of two--point crossespoint crosses

Each cross only involves two genes at a time. Each cross only involves two genes at a time. PairwisePairwisecrosses are timecrosses are time-- and laborand labor--consuming.consuming.

Difficult to determine gene order if two genes lie very Difficult to determine gene order if two genes lie very close.close.

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


ThreeThree--point crosses: A faster and more accurate point crosses: A faster and more accurate method to map genesmethod to map genes

Fig. 5.10 a

5-30Copyright © The McGraw-Hill Companies, Inc. Permission required to reproduce or displayFig. 5.10 a

vg b RF=(252+241+131+118)100/ 4197=17.7 m.u.

vg pr RF=(252+241+ 13 +9 ) 100/ 4197=12.3 m.u.

b pr RF=(131+118+ 13 + 9) 100/ 4197=6.4 m.u.


Fig. 5.10 b

vg b distance: 17.7 m.u.

vg pr distance: 12.3 m.u.

b pr distance: 6.4 m.u.


Inferring the location of a crossover eventInferring the location of a crossover event

Fig. 5.11


Fig. 5.11

vg b distance should be adjusted: RF=(252+241+13+9+131+118+13+9)100/ 4197=18.7 m.u.

Original calculation:RF=(252+241+131+118)100/ 4197=17.7 m.u.


Fig. 5.11

The predicted probability of the double crossovers:

12.3% (vg pr) 6.4% (b pr)=0.79%

The actual probability of the double crossovers:(13+9) / 4197=0.52%


Interference: The number of double crossoversInterference: The number of double crossoversis less than expectedis less than expected

The two crossovers are not independent events.The two crossovers are not independent events. Occurrence of one crossover reduces likelihood that another Occurrence of one crossover reduces likelihood that another

crossover will occur in adjacent parts of the chromosome.crossover will occur in adjacent parts of the chromosome. Chromosomal interferenceChromosomal interference: : The phenomenon of chromosomal

crossovers not occurring independently. Interference is not uniform and may vary even for different Interference is not uniform and may vary even for different

regions of the same chromosome.regions of the same chromosome.


Coefficient of coincidenceCoefficient of coincidence is the ratio between actual is the ratio between actual frequency of frequency of dcodco and expected frequency of and expected frequency of dcodco..

Measuring interferenceMeasuring interference

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

Coefficient of coincidence = frequency observed / frequency expected

1- 0.66 = 0.34

For the three-point cross: 0.52% / 0.79%=0.66


Summary of threeSummary of three--point cross analysispoint cross analysis

Cross true breeding mutant with wildCross true breeding mutant with wild--type.type. Analyze F2 individuals (males if sex linked).Analyze F2 individuals (males if sex linked).

Parental class Parental class –– most frequentmost frequent Double crossovers Double crossovers –– least frequentleast frequent

Determine order of genes based on parental and Determine order of genes based on parental and recombinant classes.recombinant classes.

Determine Determine genetic distancegenetic distance between each pair of between each pair of recombinants.recombinants.

Calculate Calculate coefficient of coincidencecoefficient of coincidence and and interferenceinterference..


Genes chained Genes chained together by together by linkage are linkage are known as known as linkage groupslinkage groups

Fig. 5.13 A genetic map of the fruit fly


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


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

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

distances: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


Fig. 5.1

Linkage and recombination of X-linked disease-causing genes in humans


Human colorblindness and two forms of hemophilia are X-linked traits

Fig. 5.26


Did Gregor Mendel encounter gene linkage?



5.5 Tetrad analysis in fungi

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

AscosporesAscospores within within ascusascus germinate into haploid germinate into haploid individuals.individuals. SaccharomycesSaccharomyces cerevisiaecerevisiae –– the bakerthe baker’’s yeasts yeast NeurosporaNeurospora crassacrassa –– the bread moldthe bread mold


SaccharomycesSaccharomyces cerevisiaecerevisiae life cyclelife cycle

Fig. 5.14 a


NeurosporaNeurospora crassacrassa life cyclelife cycle

Fig. 5.14 b


Tetrads are generated from sporulation

Diploid MATa/

Haploid

Starvation

Tetrad

Ascus wall


Heterozygote (a/ bud3::TRP1/+)

Haploid(a BUD3)( BUD3)(a bud3::TRP1)( bud3::TRP1)

A tetrad

Tetrad analysis


Tetrad dissection microscope


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

Fig. 5.15 a


Fig. 5.15 b,c


Fig. 5.15 d,e

When PD=NPD, two genes are unlinked, or linked but lie far apart.


When PD significantly outnumbers NPD,When PD significantly outnumbers NPD,two genes are linkedtwo genes are linked

Fig. 5.16


How crossovers between linked genes generate different tetrads ?

Fig. 5.17 a-c


Fig. 5.17 d-f


How to calculate RF in tetrad analysis?

RF = (3+1/2 70)/200 100= 19 m.u.

NPD + ½ TTotal tetrads

RF = 100

Fig. 5.16


5.6 Mitotic recombination and genetic mosaics5.6 Mitotic recombination and genetic mosaics

Recombination occurs Recombination occurs during mitosis.during mitosis.

Discovered in 1936 by an Discovered in 1936 by an early early DrosophilaDrosophila geneticist, geneticist, Curt SternCurt Stern..

Initiated by DNA breaks Initiated by DNA breaks caused by replication errors caused by replication errors or exposures to radiation. or exposures to radiation.

Rare events, less than 10Rare events, less than 10--66..


Twin spots in Twin spots in DrosophilaDrosophila

Fig. 5.23

Twin spotsTwin spots: Adjacent patches of tissue that differ both : Adjacent patches of tissue that differ both from each other and from the surrounding tissue.from each other and from the surrounding tissue.

Detected in the female Detected in the female heterozygotesheterozygotes..

Female sn+ y /sn y+


Mitotic crossing over between Mitotic crossing over between snsn and and centromerecentromere results in twin spotsresults in twin spots

Fig. 5.24 a


Crossing over between sn and y gene results in single spot

Fig. 5.24 b


Mitotic recombination in yeast cellsADE2

ade2

ADE2 ADE2

ade2

Centromere Crossover

ADE2 ade2

ADE2 ade2

White sector Red sector

Mitosis

Whitecolony

Fig. 5.25


Mitotic recombination

Crossovers are initiated byCrossovers are initiated by Mistakes in chromosome replication.Mistakes in chromosome replication. Exposures to radiation that break DNA.Exposures to radiation that break DNA.

A powerful tool for the study of development. May play a role in cancer formation.


Mitotic recombination can contribute to cancer

Retinoblastoma


Figure A

Retinoblastoma gene RB Wild-type RB+ gene encodes a protein that regulates

retinal growth and differentiation Mitotic recombination during retinal growth in an RB+

/RB- heterozygote may produce an RB-/RB- daughter cell.


Genes close together on the same chromosome are Genes close together on the same chromosome are linked and do not segregate independently.linked 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 than expected in double heterozygotesheterozygotes..

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

for for chiasmatachiasmata to form.to form. Recombination frequenciesRecombination frequencies between two genes vary between two genes vary

from 0% to 50%.from 0% to 50%. Linkage is never 100%.Linkage is never 100%. No matter how tightly two No matter how tightly two

genes are linked, you will find some recombination if genes are linked, you will find some recombination if you observe enough individuals.you observe enough individuals.

Summary

Documents

Linkage, Recombination, and the Mapping of Genes on …skgjx.whu.edu.cn/Public/upfile/article/... · 2017-06-22 · 5.1 Gene linkage and recombination 5.2 The Chi-square test and