Linkage,Recombination,

andCrossingOver
Mendelsaid..
 Heterozygous
for two traits
GgRr

Independent segregation

Gametes:

GR; Gr; gR; gr;

25% each

Phenotypes:
YeRoYeWrGrRoGrWr
9 3 3 1
ButsometimesGenes
DoNot
AssortIndependently
 THOMASHUNTMORGAN
TraitsinMorganscross
Theyellowbodyallele(y)isrecessivetothegraybody
allele(y+)
Thewhiteeyedallele(w)isrecessivetotheredeyed
allele(w+)
Theminiaturewingallele(m)isrecessivetothe
normalwingedallele(m+)

5
 MORGANsEXPERIMENTS

Both the white eye gene (w) (recessive) and a gene

for miniature wings (m) (recessive) are on the X
chromosome.

Morgan (1911) crossed a female white miniature

(w w / m m) with a wild-type male (w^ m^/ Y).

In the F1, all males were white-eyed with miniature

wings (w m/Y), and all females were wild-type for eye
color and wing size (w^ m^/w m).
MORGANs EXPERIMENTS

F1 female have genotype w w^/ m m^ red/normal

possible gametes (w m) (w m^) (w^ m) (w^ m^)
25% each if independent segregation is true
males have genotype (w m) white/miniature

thus F2

(w m) (w m) 25% white/miniature
(w m^) (w m) 25% white/normal
(w^ m) (w m) 25% red/miniature
(w^ m^) (w m) 25% red/normal
F2, the most frequent phenotypes for both sexes
were the phenotypes of the parents in the original
cross (white eyes with miniature wings, and red eyes
with normal wings).

Non-parental phenotypes (white eyes with normal

wings or red eyes with miniature wings) occurred in
about 37% of the F2 flies.

Well below the 50% predicted for

independent assortment
 MORGANSPROPOSAL

Duringmeiosisallelesofsomegenes
assorttogetherbecausetheyarenear
eachotheronthesamechromosome.
Recombinationoccurswhengenes
areexchangedbetweenX
chromosomesoftheF1females
BATESON&PUNNETT,1905
Traitsofsweetpeas
Flowercolorcanbe
eitherpurpleorred
Purpleisdominantto
red
Pollenshapecanbe
eitheroblongorround
Oblongisdominant
toround
12
 BATESON&PUNNETT,1905

Purple,long(PPLL)xred,round(ppll)
F1 offspringarepurple,long(PpLl)
F2 (crossingPpLl xPpLl;gametesPL Pl pL pl)
possessfourdifferentphenotypes

14
 F2 generation
Theobservedratiois
15.6:1.0:1.4:4.5
Theexpected ratio
9:3:3:1>>> isNOTseen!
Parental phenotypeswereoverrepresented
Nonparental phenotypeswereunderrepresented
evidencethatthetwogenesdonotassortindependently
Thenatureoftheirphysicallinkagewasnotapparent
toBatesonandPunnett atthistime
Thegenesarephysicallylinkedonthesame
chromosome

15
 Linkage,Recombination,and
CrossingOver

Genesthatareonthesame
chromosometravelthroughmeiosis
together;however,allelesof
chromosomallylinkedgenescanbe
recombinedbycrossingover.
 LinkagePhases:
CouplingandRepulsion
 KeyPoints
Linkagebetweengenesisdetectedasa
deviationfromexpectationsbasedon
MendelsPrincipleofIndependent
Assortment.
Thefrequencyofrecombinationmeasures
theintensityoflinkage.Intheabsenceof
linkage,thisfrequencyis50percent;forvery
tightlinkage,itisclosetozero.
CrossingOverOccursinProphaseof
MeiosisI
 KeyPoints
Recombinationiscausedbyaphysicalexchange
betweenpairedhomologouschromosomesearlyin
prophaseofthefirstmeioticdivisionafter
chromosomeshaveduplicated.

Atanyonepointalongachromosome,theprocess
ofexchange(crossingover)involvesonlytwoofthe
fourchromatidsinameiotictetrad.

LateinprophaseI,crossoversbecomevisibleas
chiasmata.
 CrossingOver

MAX 50% recombination

 Multiple
Crossovers
 ChromosomeMapping

Linkedgenescanbemappedona
chromosomebystudyinghowoften
theirallelesrecombine.
AChromosome
Map
GeneticMapDistances

Thedistancebetween
twopointsonthe
geneticmapofa
chromosomeisthe
averagenumberof
crossoversbetween
them.
Recombination
Mappingwitha
TwoPoint
Testcross
 TheRecombinationFrequency
betweenvg andb is18%
Thisisequalto18mapunits,
or18centiMorgans (cM)on
thegeneticmap.
RecombinationMappingwitha
ThreePointTestcross
CalculationofMapDistances
 DeterminingtheGeneOrder
Thereare3possiblegeneorders
1. sc ec cv
2. ec sc cv
3. ec cv sc

Thetwomostcommonclassesaretheparentals.
Amongtherecombinantclasses,the2rareclasses
representthedoublecrossovers.

Thegenethatisswitchedinthedoublecrossoverclasses
comparedtotheparentalisthemiddlegene(inthiscase,
ec).
 Map unit = centimorgan

gene A and B 30% RF

gene A and C 10% RF

gene B and C 20% RF

A C B

35
CalculationofMapDistances
 InterferenceandtheCoefficientof
Coincidence
Assumingindependence,theexpected
frequencyofdoublecrossoversis0.091
0.105=0.0095.
Theobservedfrequencyofdoublecrossovers
was2/3248=0.0006.
Acrossoverinoneregioninhibitedacrossover
nearby.
RecombinationFrequencyand
GeneticMapDistance
RecombinationFrequencyandGenetic
MapDistance
 Chiasma
Frequencyand
GeneticMap
Distance
 KeyPoints
Thegeneticmapsofchromosomesarebasedonthe
averagenumberofcrossoversthatoccurduring
meiosis.

Geneticmapdistancesareestimatedbycalculating
thefrequencyofrecombinationbetweengenesin
experimentalcrosses.
 KeyPoints
Recombinationfrequencieslessthan20percent
estimatemapdistancedirectly;however,
recombinationfrequenciesgreaterthan20percent
underestimatemapdistancebecausemultiple
crossovereventsdonotalwaysproducerecombinant
chromosomes.

Anaverageofonechiasmaduringmeiosisis
equivalentto50centiMorgansofgeneticmap
distance.
 GeneticDistance
andPhysicalDistance
 KeyPoints
InDrosophila,genescanbelocalizedonmapsofthepolytene
chromosomesbycombiningrecessivemutationswith
cytologicallydefineddeletionsandduplications.

Adeletionwillrevealthephenotypeofarecessivemutation
locatedbetweenitsendpoints,whereasaduplicationwill
concealthemutantphenotype.

Geneticandcytologicalmapsarecolinear;however,genetic
distancesarenotproportionaltocytologicaldistances.
LinkageAnalysisinHumans

Pedigreeanalysisprovides
waysforlocalizinggeneson
humanchromosomes.
Therelationbetweenphysicalandgeneticdistances
isnotconstantacrossthegenome.

Chiasma countsinhumanmalemeiosisshowan
averageof49crossoverspercell(Morton etal.,
1982).
Sinceeachcrossovergives50% recombinants,the
chiasma countimpliesatotalmalegeneticmap
lengthof2450cM.
Chiasmata aremorefrequentinfemalemeiosisand
thetotalfemalemaplengthis4296cM (excluding
theX).Thusoverthe3000Mbautosomal genome,1
malecM averages1.05Mband1femalecM averages
0.70Mb;thesexaveraged figureis1cM =0.88Mb.
Genes on
human X
chromosome

48
 KeyPoints
Linkagebetweenhumangenescanbedetectedby
analyzingpedigrees.

Pedigreeanalysisalsoprovidesestimatesof
recombinationfrequenciestomapgenesonhuman
chromosomes.
 KeyPoints

Pedigreeanalysisalsoprovidesinformationoflinkage
betweengeneticmarkersanddiseases.
 I:2alleles a;b
I;1alleles c;d

II;1alleles a;c
II;2alleles a;d
II;3alleles b;d

II;4/II;5/II;6alleles e;f

III;1alleles c;e
I;1/II;1/III;1 III;2alleles a;f
Allsharethediseaseandthecallele;thusthe III;3>>III;6allelecnot
calleleisinlinkagewiththedisease. present (absent inparents)
 I:2alleles a;b
I;1alleles c;d

II;1alleles a;c
II;2alleles a;d
II;3alleles d;b

II;4/II;5/II;6alleles e;f

I;1/II;1/III;1/II;3/III;6 III;1alleles c;e

All sharethedisease but not thecallele; III;2alleles a;f
thus thecalleleis not inlinkage withthedisease. III;6alleles b;f
Nail Patella syndrome: (NPS) is a
rare genetic disorder with
abnormalities of bone, joints,
fingernails and kidneys. NPS is
characterized by absent or under-
developed kneecaps and thumbnails.
It is estimated to occur in 1/50,000
newborns.
LinkageBetweentheABO andNail
PatellaLoci
CalculationoftheRecombination
Frequency
4/13offspring(31%)in
thispedigreeare
recombinant.

Combiningdatafrom
manypedigrees,the
geneticdistancebetween
theABO andNPS1 lociis
10cM.

Molecularmarkerscan
alsobemapped.
LODscore: Ingenetics,astatisticalestimateof
whethertwolociarelikelytolieneareachother
onachromosomeandarethereforelikelytobe
inheritedtogetherasapackage.

LOD standsforLogarithmoftheodds(tothebase
10).
ALODscoreofthree ormoreisgenerallytakento
indicatethattwogenelociareclosetoeachother
onthechromosome.
ALODscoreofthreemeanstheoddsarea
thousandtooneinfavorofgeneticlinkage.
 HHT Genes

ENG (HHT1, OMIM #187300) 9q34 [McAllister KA et al., 1994]

ACVRL1 (HHT2, OMIM #600376) 12q13 [Johnson DW et al., 1996]

SMAD4 (JPHT, OMIM #175050) 18q21 [Gallione CJ et al., 2004]

 Results II

DAU DEF
=0 =0.1 =0 =0.1

D9S60 2.31 1.79 0.90 0.68

ENG 0.63 0.43 0.00 0.00
D9S61 2.68 2.13 1.20 0.98

D12S361 5.71 1.27 0.73

D12S1635 5.39 1.32 0.89
D12S359 3.79 0.89 0.28

IAC DIT
=0 =0.1 =0 =0.1

D9S60 0.47 0.58 1.16

ENG 1.16 0.82 2.67 1.14
D9S61 3.64 1.09 2.31

D12S361 1.93 1.42 0.27 0.34

D12S1635 1.75 1.28 2.93 2.34
D12S359 0.94 0.65 1.75 0.47
UniversitdiPavia Laboratoriodi
GeneticaMedica
.and if no
linkage is observed

Still an informative
result:
The gene is not
there !!
 Genetic markers
The number of physically observable genes in
humans is very small. Consequently, human
genetic maps based on these were not useful.
The development of genetic loci that could be
observed at the level of DNA was essential to
modern human genetics.
Two alleles (ie, D vs d) needed to be
detected, at the DNA level, to define a DNA
marker locus.
There are several technical solutions to the
observation of DNA differences.
 Genetic markers
In a DNA marker, somewhere in the 100-1000
bp amplified region there must be a DNA
sequence difference (polymorphism)
between individuals.
The most common DNA marker systems
examine the number of repeated units in a
simple sequence repeat motif, such as
CACACACACACACAC.
Individuals can vary considerably in the
number of CA blocks, making these types of
DNA sequences very useful population
markers.
 Genetic markers
Single basepair differences, however, are
much more common in the genome and so
have great potential.
Single basepair differences are often called
SNPs (Single Nucleotide Polymorphisms).
However, the frequency of individuals being
different at a single base is much less than
CACACACA repeat motifs.
Genetic markers are simply signposts along
the chromosomes that are readily detected
and comparable between laboratory
experiments.
 Genetic markers
Ideally, genetic markers should be readily
available at a high density across the genome
(>100,000).
The markers should be easily communicated
between lab groups and easily quality
controlled.
And, the work to obtain the marker information
should be low error and inexpensive.
 Genetic marker map of the mouse
chr 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X
0 48
80 38 57
48
55
167 62 76 182 46
2
1 49 95 105 12 6 1 76
26 8
2 32 2 51 60
1 71 56
46 25 91 83 46 41 81
31 8 2 93 63 64 144 55
79
1 00
-20 36 5 25 18 6 19 0 40 20
12 9
47
55 94 33 1 10 88
22 15 26 36 51 1 19
91 19
73 19 63
84 10 2 1 56
distance from centromere, cM

22 2 05 10 4 1 98 158 5
30 1 31 18 5 10
61 17 8 29 1 47 15 8 3
-40 42
9
14 9 2 5 3 51
54
1 73
8 76
37 11 0
25 3 26 2 41 191
2 30 167 1 05
253 15 5
22 1
58 35 71 99
86 37 71 12
19 8 1 12 2 89 19 34 71
N2 95 1 34
-60 2 24 26 4
78 42 2 23
75 43
98 47
170 15 1 14
2 85 2 49
42
10 2 16 8

-80 14 3
10 6 2 90

2 65
20 6 centromere
-100 chromosome
22 1
markers used (84)
17 markers in process (11)
available markers (55)
-120
SNP genetic marker data
RecombinationandEvolution

Recombinationorthelack
ofitplaysakeyrolein
evolution.
 KeyPoints
Recombinationcanbringfavorablemutations
together.

Chromosomerearrangements,especially
inversions,cansuppressrecombination.

Recombinationisundergeneticcontrol.
 LINKEDorNONLINKED?
Arecombinationfrequencyof50%meansthat
genesareunlinked.Therearetwowaysin
whichgenesmaybeunlinked:
Theymaybeonseparatechromosomes.
Theymaybefarapartonthesamechromosome.
 MULTIPLECROSSOVERS
Ifthegenesareonthesamechromosome,
multiplecrossoverscanoccur.Thefurther
aparttwolociare,themorelikelytheyareto
havecrossovereventstakeplacebetween
them.Thechromatidpairingisnotalwaysthe
sameincrossover,sothat2,3,or4chromatids
mayparticipateinmultiplecrossover.
 Mitoticrecombination
Crossingoverduringmitosiswasfirst
observedbyStern(1936)inDrosophila.
Theallelesinvolvedaresexlinkedandrecessiveto
thewildtype:
Yproducesyellowbodycolorinsteadofwildtypegrey.
Snproducesshort,twistybristles(signed)ratherthan
thewildtypelong,curvedones.Bristlesfollowbody
color(y+/ areblack,andy/yareyellow.
 Mitoticrecombination
Femaleprogenyfromthecross
y+sn/y+snxysn+/Y
Generallyhavewildtypephenotypeofgreybodies
andnormalbristles,correspondingtotheirgenetoype
(y+sn/ysn+).Butexceptions:
Someflieshadpatchesofyellowand/orsignedbristles.This
couldbeexplainedbynondisjunctionorchromosomalloss.
Otherflieshadtwinspots,adjacentregionsofbristles,one
yellowandtheothersigned,amosaicphenotype.The
spotsarereciprocalproductsofthesamegeneticevent,a
mitoticcrossingover.
Mitoticcrossoveroccurredeitherbetweenthecentromere
andthesnlocusorbetweenthesnandtheylocus.
Fig. 13.22 Body surface phenotype segregation in a Drosophila strain

Peter J. Russell, iGenetics: Copyright Pearson Education, Inc., publishing as Benjamin Cummings.
 Fig. 13.23 Production of the twin spot and single yellow spot shown
in Figure 13.22 by
mitotic crossing-over

Peter J. Russell, iGenetics: Copyright Pearson Education, Inc., publishing as Benjamin Cummings.
 MechanismofMitoticCrossingover
Arareeventoccurringonlyindiploidcells,mitotic
crossovercanresultwhenreplicatedchromatidscome
togethertoformastructuresimilartothefourstrand
stageinmeiosis.
Ifthestartinggenotypeisd+e/de+,thetwopossible
orientationsoftheresultingchromatidsare:
Onecellwithd+e+/d+e+,andonewiththede/de.These
aretheonesthatareusefulformapping,becausetherecessive
phenotypecanbeobservedinprogenyofthede/decells.
Reversalofthealleles,de+/d+e.Phenotypically
indistinguishablefromnonrecombinantcells,therearenot
usefulformapping,butarenonethelessderivedfroma
crossoverevent.
 Retinoblastoma
Mostcommonchildhoodeyecancer.
Nonhereditary(sporadic)formoccursinanindividualwith
nofamilyhistoryofthedisease,andaffectsonlyoneeye
(unilateral).
Heteditaryformaffectsbotheyes(bilateral)andusually
occursatanearlieragethansporadic.
Asinglegene(Rb)onchromosome13q14involved.
Inhereditaryretinoblastoma,tumorcellshavemutationsinboth
copiesofthisgene,whileothercellsinthesameindividualare
heterozygous.Thediseaseiscausedbyasecondmutationthat
affectsthenormalRBallele.
Thesecondmutationisoftenidenticaltotheoneontheother
chromosome,strongcircumstantialevidencethatthewildtype
copyofthegeneissomehowreplacedbytheinheritedmutated
allele.Onepossibleexplanationismitoticrecombination.
 Fig. 13.24 Normal mitotic segregation of genes in a theoretical diploid cell with one
homologous pair of chromosomes

Peter J. Russell, iGenetics: Copyright Pearson Education, Inc., publishing as Benjamin Cummings.
 Fig. 13.25 Result of a mitosis of the same cell type as the cell in Figure 13.24 but in
which a rare mitotic crossing-over occurs

Peter J. Russell, iGenetics: Copyright Pearson Education, Inc., publishing as Benjamin Cummings.