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Download Lab. #3 and Print out 3 files:Download Lab. #3 and Print out 3 files:http://www.http://www.munmun.ca/biology/.ca/biology/dinnesdinnes/B2250/B2250.html/B2250/B2250.html
Quiz #2 Marks posted on WebpageQuiz #2 Marks posted on Webpage
Mendelian GeneticsMendelian Genetics
Topics:Topics: -Transmission of DNA during cell division-Transmission of DNA during cell division
Mitosis and MeiosisMitosis and Meiosis
- Segregation - Segregation
- Sex linkage (- Sex linkage (problem: how to get a white-eyed femaleproblem: how to get a white-eyed female))
- Inheritance and probability- Inheritance and probability
- Mendelian genetics in humans- Mendelian genetics in humans
- Independent Assortment- Independent Assortment
- Linkage- Linkage
- Gene mapping- Gene mapping
- 3 point test cross- 3 point test cross
- Tetrad Analysis (mapping - Tetrad Analysis (mapping in fungi)in fungi)- Extensions to Mendelian Genetics- Extensions to Mendelian Genetics
- Gene mutation- Gene mutation
- Chromosome mutation- Chromosome mutation
- Quantitative and population genetics- Quantitative and population genetics
LinkageLinkageChapter 6Chapter 6
- recombination- recombination
- linkage maps- linkage maps
Ch. 6 p. 148 – 165 Prob: 1-5, 7, 8, 10, 11, 14Ch. 6 p. 148 – 165 Prob: 1-5, 7, 8, 10, 11, 14
Linkage of GenesLinkage of Genes
- Many more genes than chromosomes- Many more genes than chromosomes
- Some genes must be linked on the same - Some genes must be linked on the same chromosome; chromosome; therefore not independenttherefore not independent
Fig 6-6Fig 6-6
Independent AssortmentIndependent Assortment LinkageLinkage
Fig 6-11Fig 6-11
InterchromosomalInterchromosomal IntrachromosomalIntrachromosomal
Two ways to produce dihybridTwo ways to produce dihybrid
A B a b A b a BA B a b A b a B
A B a b A b a BA B a b A b a B
cis A B AaBb cis A B AaBb A b A b transtrans
a b (dihybrid ) a Ba b (dihybrid ) a B
Gametes:Gametes:
AB AB PP Ab Ab
ab ab PP aB aB
Ab Ab RR AB AB
aB aB RR ab ab
X XPP
ExampleExample
Test CrossTest Cross AaBb X aabb AaBb X aabb
ab Exp. Obs.ab Exp. Obs.
AB AaBb 25 10 AB AaBb 25 10 RR
Ab Aabb 25 40 Ab Aabb 25 40 P P
aB aaBb 25 40 aB aaBb 25 40 PP
ab aabb 25 10 ab aabb 25 10 RR
100 100100 100
How to distinguish:How to distinguish:
ParentalParental high freq. high freq.
RecombinantRecombinant
low freq.low freq.
Example (cont.)Example (cont.)
Gametes: AB Gametes: AB RR
Ab Ab PP
aB aB PP
ab ab RR
Therefore dihybrid:Therefore dihybrid:
A b (trans)A b (trans)
a Ba B
Linkage MapsLinkage Maps
Genes close together on same chromosome:Genes close together on same chromosome:
- smaller chance of crossovers- smaller chance of crossovers
between thembetween them
- fewer recombinants- fewer recombinants
Therefore:Therefore:
percentage recombination can bepercentage recombination can be
used to generate a linkage mapused to generate a linkage map
Linkage mapsLinkage maps
A B large # of recomb. A B large # of recomb.
a ba b
C D small number of recombinantsC D small number of recombinants
c dc d
Linkage mapsLinkage mapsexampleexample
Testcross progeny:Testcross progeny:
PP AaBb 2146 AaBb 2146
RR Aabb 43 Aabb 43
RR aaBb 22 aaBb 22
PP aabb 2302 aabb 2302
Total 4513 1.4 map unitsTotal 4513 1.4 map units
656545134513 = 1.4 % RF= 1.4 % RF
A 1.4 mu BA 1.4 mu B
Additivity of map distancesAdditivity of map distances
separate maps A B A Cseparate maps A B A C
7 27 2
combine maps C A Bcombine maps C A B
2 72 7
or or LocusLocus
A C B (pl. A C B (pl. lociloci))
2 52 5
LinkageLinkage
Deviations from independent assortmentDeviations from independent assortment
DihybridDihybrid gametes gametes
2 parent (noncrossover) 2 parent (noncrossover) commoncommon
2 recombinant (crossover) 2 recombinant (crossover) rarerare
% recombinants a function of distance between% recombinants a function of distance between
genesgenes
% RF = map distance% RF = map distance
GametesGametes
Number of Genes Number of DifferentNumber of Genes Number of Different
GametesGametes
monohybridmonohybrid 1 (Aa) 2 1 (Aa) 2
dihybriddihybrid 2 (AaBb) 4 2 (AaBb) 4
trihybridtrihybrid 3 (AaBbCc) 8 3 (AaBbCc) 8
Three Point Test CrossThree Point Test Cross
AaBbCc X aabbccAaBbCc X aabbcc
ABC ABC
ABc ABc abcabc
AbC AbC
Abc Abc
aBC aBC
aBcaBc
abCabC
abcabc
8 gamete types8 gamete types
TrihybridTrihybrid
Three Point Test CrossThree Point Test Cross
CC ABC ABC
BB
c ABcc ABc
A A
C AbCC AbC
bb
c Abcc Abc
aa
Trihybrid GametesTrihybrid Gametes
Three Point Test CrossThree Point Test Cross
AaBbCcAaBbCc 3 genes: 3 genes:
Possibilities:Possibilities:
1. All unlinked1. All unlinked
2. Two linked; one unlinked2. Two linked; one unlinked
3. Three linked3. Three linked
- order ? - order ? A---B---CA---B---C
B---C---A B---C---A
B---A---CB---A---C
TrihybridTrihybrid
Three Point Test CrossThree Point Test Cross
Three recessive mutants of Three recessive mutants of
DrosophilaDrosophila:: +, v +, v vermilion eyesvermilion eyes
+, cv +, cv crossveinlesscrossveinless
+, ct +, ct cut wingcut wing
P +/+ cv/cv ct/ct X v/v +/+ +/+P +/+ cv/cv ct/ct X v/v +/+ +/+
Three Point Test CrossThree Point Test Cross
P +/+ cv/cv ct/ct x v/v +/+ +/+P +/+ cv/cv ct/ct x v/v +/+ +/+
Gametes + cv ct v + +Gametes + cv ct v + +
FF11 trihybrid v/+ cv/+ ct/+ trihybrid v/+ cv/+ ct/+
Three Point Test CrossThree Point Test Cross
FF11 v/+ cv/+ ct/+ x v/v cv/cv ct/ct v/+ cv/+ ct/+ x v/v cv/cv ct/ct
v cv ctv cv ct
8 gamete types one gamete type8 gamete types one gamete type
8 gamete types8 gamete types
FF11 v/+ cv/+ ct/+ v/+ cv/+ ct/+
v + + 580v + + 580
+ cv ct 592 + cv ct 592
v cv + 45 v cv + 45
+ + ct 40 + + ct 40
v cv ct 89 v cv ct 89
+ + + 94 + + + 94
v + ct 3 v + ct 3
+ cv + 5 + cv + 5
14481448
Parental (most frequent)
Recombinant
8 gamete types8 gamete types
FF11 v/+ cv/+ ct/+ v/+ cv/+ ct/+
v + + 580v + + 580
+ cv ct 592 + cv ct 592
v cv + 45 v cv + 45
+ + ct 40 + + ct 40
v cv ct 89v cv ct 89
+ + + 94 + + + 94
v + ct 3 v + ct 3
+ cv + 5 + cv + 5
14481448
RecombinantRecombinant
RecombinantRecombinant
ParentalParental
ParentalParental
268
268
1448= 18.5 %
8 gamete types8 gamete types
FF11 v/+ cv/+ ct/+ v/+ cv/+ ct/+
v + + 580v + + 580
+ cv ct 592 + cv ct 592
v cv + 45 v cv + 45
+ + ct 40 + + ct 40
v cv ct 89v cv ct 89
+ + + 94 + + + 94
v + ct 3 v + ct 3
+ cv + 5 + cv + 5
14481448
RecombinantRecombinant
RecombinantRecombinant
ParentalParental
ParentalParental
191
191
1448= 13.2 %
8 gamete types8 gamete types
FF11 v/+ cv/+ ct/+ v/+ cv/+ ct/+
v + + 580v + + 580
+ cv ct 592 + cv ct 592
v cv + 45 v cv + 45
+ + ct 40 + + ct 40
v cv ct 89v cv ct 89
+ + + 94 + + + 94
v + ct 3 v + ct 3
+ cv + 5 + cv + 5
14481448
RecombinantRecombinant
RecombinantRecombinant
ParentalParental
ParentalParental
93
93
1448= 6.4 %
Calculate Recombination FractionCalculate Recombination Fraction
1. v - cv R v cv 45 + 891. v - cv R v cv 45 + 89
R + + 40 + 94R + + 40 + 94
268 / 1448 = 18.5 %268 / 1448 = 18.5 %
2. v - ct R + + 94 + 5 2. v - ct R + + 94 + 5
R v ct 89 + 3 R v ct 89 + 3
191/1448 = 13.2 %191/1448 = 13.2 %
3. ct - cv R ct + 40 + 3 3. ct - cv R ct + 40 + 3
R + cv 45 + 5 R + cv 45 + 5
93/1448 = 6.4 %93/1448 = 6.4 %
Three point test crossThree point test cross
Observations:Observations:
all 3 RF < 50 % 3 genes on same chrall 3 RF < 50 % 3 genes on same chromosomeomosome
vv----------cvcv largest distance largest distance ctct in middle in middle
map map vv--------------ctct--------------cvcv = = cvcv--------------ctct--------------vv
13.2 + 6.4 = 19.6 > 18.5 !! Why ?13.2 + 6.4 = 19.6 > 18.5 !! Why ?
Three Point Test CrossThree Point Test Cross
P +/+ ct/ct cv/cv x v/v +/+ +/+P +/+ ct/ct cv/cv x v/v +/+ +/+
gametesgametes + ct cv v + + + ct cv v + +
FF11 trihybrid v + + trihybrid v + +
+ ct cv+ ct cv
Three Point Test CrossThree Point Test Cross
Double crossover class rarest:Double crossover class rarest:
vv-----cv-cv
P v + + v +P v + + v +
P + ct cv + cvP + ct cv + cv
R v ct + v +R v ct + v +
R + + cv + cvR + + cv + cv
XX XX XX XX
Three Point test crossThree Point test cross
1. Double crossovers not counted in v--cv RF1. Double crossovers not counted in v--cv RF
2. Double crossovers generate P types (with2. Double crossovers generate P types (with
respect to v--cv)respect to v--cv)
3. Double crossovers not detected as3. Double crossovers not detected as
recombinantsrecombinants
Consequence:Consequence:
underestimate of v----cv map distanceunderestimate of v----cv map distance
Greater distance of genes Greater distance of genes greater error greater error
Double recombinant class:Double recombinant class:
(3 + 5) x 2 = 16(3 + 5) x 2 = 16
268 + 16 = 284268 + 16 = 284
284/1448 = 19.6284/1448 = 19.6
NOTE: double crossovers detectedNOTE: double crossovers detected
because of middle gene (ct)because of middle gene (ct)
Mapping FunctionMapping Function
Genes close together on chromosomeGenes close together on chromosome
-RF good estimate of map distance-RF good estimate of map distance
Genes far apart on chromosomeGenes far apart on chromosome
- RF underestimates true map distance due- RF underestimates true map distance due
to undetected multiple crossoversto undetected multiple crossovers
Mapping FunctionMapping Function m = avg. # crossovers per meiosism = avg. # crossovers per meiosis
(linear with true map distance)(linear with true map distance)
if m = 1 (1 cross over for every meiosis)if m = 1 (1 cross over for every meiosis)
then 50 % recombinants producedthen 50 % recombinants produced
Therefore:Therefore:
map units (mu) = m x 50map units (mu) = m x 50Gamete TypesGamete Types
FF11 A BA B
a b a b AaBbAaBb
gametes A B AB Parentalgametes A B AB Parental
a b a b ab ab ParentalParental
A b A b Ab RecombAb Recomb..
a B a B aB RecombaB Recomb..
Mapping FunctionMapping Function
Mapping function: Mapping function:
- relates RF to true map distance - relates RF to true map distance
(better estimate for genes separated by(better estimate for genes separated by
large distances)large distances)
m = -ln (1 - 2RF) mu = m x 50m = -ln (1 - 2RF) mu = m x 50
Mapping function
Mapping FunctionMapping Function
0
10
20
30
40
50
60
0 50 100 150 200
True Map Distance (m x 50)
Ob
serv
ed
RF
(%
)
m = -ln(1 - 2RF)m = -ln(1 - 2RF)
Mapping FunctionMapping Functionexampleexample
1. RF = 18.5 % m = 0.46 mu = 23.11. RF = 18.5 % m = 0.46 mu = 23.1
2. RF = 6.4 % m = 0.137 mu = 6.82. RF = 6.4 % m = 0.137 mu = 6.8
Summary:Summary:
- short distances: use RF- short distances: use RF
- long distances: use mapping function- long distances: use mapping function
LinkageLinkage
Other Points:Other Points:
1. No crossing over in male 1. No crossing over in male DrosophilaDrosophila
male: AaBb A B male: AaBb A B gametes AB, ab gametes AB, ab
a ba b
use female dihybrid: AaBb x aabbuse female dihybrid: AaBb x aabb
O OO O
LinkageLinkage
2. Linkage of genes on the X chromosome:2. Linkage of genes on the X chromosome:
AaBb x --AaBb x --YY
O OO O
Male progeny:Male progeny:
AB AB YY
Ab Ab Y male progeny directY male progeny direct
aB aB Y measure of female Y measure of female meioticmeiotic
ab ab Y productsY products
Fungal GeneticsFungal Genetics
Fungi:Fungi: important organisms in the ecosystemimportant organisms in the ecosystem
- decomposers- decomposers
- pathogens- pathogens
important for humansimportant for humans
- food- food
- pathogens- pathogens
(Biology 4040 – Mycology)(Biology 4040 – Mycology)
Fun Facts About FungiFun Facts About Fungihttp://www.herbarium.usu.edu/fungi/funfacts/factindx.htm
FungiFungi
Neurospora crassaNeurospora crassa(bread mold)(bread mold)
Morphological mutantsMorphological mutants
Biochemical mutants (one gene, one enzyme)Biochemical mutants (one gene, one enzyme)
Linkage MapLinkage Map
Neurospora crassa Neurospora crassa Linkage group ILinkage group I
Fungus Life CycleFungus Life Cycle
vegetative stage haploidvegetative stage haploid
+, - mating types+, - mating types
brief diploid stage brief diploid stage meiosis meiosis
++
--
nn
nn2n2n
meiosismeiosis ++
--
nn
nn
sporesspores
Gamete PoolGamete Pool
Gametes: Products of many meiosesGametes: Products of many meioses
all pooled togetherall pooled together
A BA B
a b AB AB ab ab AB aba b AB AB ab ab AB ab
P A BP A B ab ab AB ab ab ab AB ab AbAb AB AB GameteGamete
P P a ba b AB AB aBaB ab ab AB AB ab ab AB AB poolpool
R R a Ba B ab AB AB ab ab AB AB ab
R R A bA b
Tetrad AnalysisTetrad Analysis
Some Fungi and algae: 4 products of a Some Fungi and algae: 4 products of a singlesingle
meiosis can be recoveredmeiosis can be recovered
Advantages:Advantages:
1. haploid organism - no dominance1. haploid organism - no dominance
2. examine a single meiosis - test cross not needed2. examine a single meiosis - test cross not needed
3. small, easy to culture3. small, easy to culture
4. Tetrad Analysis - map gene to centromere4. Tetrad Analysis - map gene to centromere
Ascus with ascosporesAscus with ascospores
Tetrad AnalysisTetrad Analysis
Types of Tetrads:Types of Tetrads:
1. Unordered - 4 products mixed together1. Unordered - 4 products mixed together
2. Ordered (linear) - 4 products lined up, each2. Ordered (linear) - 4 products lined up, each
haploid nucleus can be tracedhaploid nucleus can be traced
back through meiosisback through meiosis
3. Octads - mitotic division after meiosis3. Octads - mitotic division after meiosis
8 products (2 x 4)8 products (2 x 4)
Linear Linear Tetrad AnalysisTetrad AnalysisLife Cycle:Life Cycle:
aa
++
HaploidHaploid
aa
++
aa++
DiploidDiploid
4 4 haploid haploid productsproducts
aa
++
aa
++
Mating: Mating: a x + a x + a /+ a /+
n n 2nn n 2n
+ = a+ = a++
MeiosisMeiosis
Linear Linear Tetrad AnalysisTetrad Analysis
8 h8 haploidaploid sporesspores
4 4 haploid haploid productsproducts
aa
aa
+
+
aaaaaaaa
++++
mitosismitosis
(Octad)(Octad)
Linear Tetrad AnalysisLinear Tetrad Analysis
Two types of asci:Two types of asci:
1. no crossover----> first division segregation (M1. no crossover----> first division segregation (M II))
2. crossover between 2. crossover between
gene and centromere-----> second division gene and centromere-----> second division
segregation (Msegregation (MIIII))
Mapping gene to centromereMapping gene to centromere
aa
++aa
++
First DivisionFirst Divisionaaaaaaaa++++++++
No No CrossoverCrossover
First division segregationFirst division segregation
AAAAAAAA
aaaaaaaa
meiosis
Mapping gene to centromereMapping gene to centromere
aaaa++++
aaaa++++aaaa++++
Second divisionSecond division
crossovercrossover
Second division segregationSecond division segregation
AAAAa**a**a**a**
A**A**A**A**aaaa
** recombinant
11stst and 2 and 2ndnd Division segregation Division segregation
aa
++aa
++
First DivisionFirst Divisionaaaaaaaa++++++++
No No CrossoverCrossover
aaaa++++
aaaa++++aaaa++++
Second divisionSecond division
CrossoverCrossover
Mapping gene to centromereMapping gene to centromere
a + a + + aa + a + + a
a + a + + aa + a + + a
a + + a a +a + + a a +
a + + a a +a + + a a +
+ a a + a ++ a a + a +
+ a a + a ++ a a + a +
+ a + a + a+ a + a + a
+ a + a + a+ a + a + a
43 43 3 4 3 4 Total = 10043 43 3 4 3 4 Total = 100I II
MMII = 86 = 86
MMIIII = 14 = 14
Mapping gene to centromereMapping gene to centromere
MMII = 86 M = 86 MIIII = 14 = 14
14/100 = 14 % of meioses showed a crossover14/100 = 14 % of meioses showed a crossover
½ ½ of the crossover products of the crossover products
recombinantrecombinant
RF = RF = ½ ½ x 14 % = 7 % x 14 % = 7 % aa
7 m.u.7 m.u.
Unordered Tetrad AnalysisUnordered Tetrad Analysis
1. still products of a single meiosis1. still products of a single meiosis
2. can not map gene to centromere2. can not map gene to centromere
3. linear tetrads can be analyzed as unordered3. linear tetrads can be analyzed as unordered
4. map distance between linked genes4. map distance between linked genes
XXaa bb aa++ bb++ aa bb
aa++ bb++meiosismeiosis
n n 2nn n 2n
Unordered TetradsUnordered Tetrads
Three kinds of unordered tetrads:Three kinds of unordered tetrads:
aa bb
aa++ bb++a ba ba ba baa++bb++
a a bb++
a a bb++
aa++bbaa++bb
a ba ba a bb++
aa++bb
aa++bb++
PDPD NPDNPD TT
1. Parental Ditype1. Parental Ditype
2. Nonparental Ditype2. Nonparental Ditype
3. Tetratype3. Tetratype
meiosismeiosis
aa++bb++
a ba b
a ba b
aa+ + bb++
aa+ + bb++
a ba b
a ba b++
aa+ + bb++
aa+ + bb
a ba b++
a ba b++
aa+ + bb
aa+ + bb
PDPD
TT NPDNPD
Unlinked genes PD = NPDUnlinked genes PD = NPD
XXaa bb ++ ++
aa bb
++ ++
meiosismeiosis aa
bb++
++
a/+, b/+a/+, b/+
PDPD
NPDNPD
a ba b
a ba b
aa+ + bb++
aa+ + bb++
a ba b++
a ba b++
aa+ + bb
aa+ + bb
Unordered TetradsUnordered TetradsUnlinked Genes: PD = NPDUnlinked Genes: PD = NPD
Linked Genes: PD >> NPDLinked Genes: PD >> NPD
NPD----> all products recombinantNPD----> all products recombinant
T--------> T--------> ½ ½ products recombinant products recombinant
PD-----> all parental typePD-----> all parental type
PD = 58PD = 58
RF = RF = ½ ½ T + NPD T = 40 T + NPD T = 40
T + NPD + PD NPD = 2T + NPD + PD NPD = 2
RF = 0.22 22 m.u.RF = 0.22 22 m.u.
Tetrad AnalysisTetrad Analysis
Types of Tetrads:Types of Tetrads:
1. Ordered (linear)1. Ordered (linear):: map gene to centromere map gene to centromere
2. Unordered2. Unordered: map genes: map genes
Linkage: SummaryLinkage: Summary
• Recombination: generates variationRecombination: generates variation
(inter and intrachromosomal)(inter and intrachromosomal)
• Genetic maps:Genetic maps:
- genes linked on the same chromosome- genes linked on the same chromosome
- location of new genes relative to genes - location of new genes relative to genes
already mapped already mapped
Linkage: SummaryLinkage: Summary
• Hunting for genes (Human Diseases)Hunting for genes (Human Diseases)
- genetic markers: DNA variation- genetic markers: DNA variation
- co-inheritance with diseases using pedigree- co-inheritance with diseases using pedigree
informationinformation
- recombinants used to estimate linkage- recombinants used to estimate linkage
- MUN Medical Genetics- MUN Medical Genetics
• Association - test if a disease and a marker allele show Association - test if a disease and a marker allele show correlated occurrence correlated occurrence in a populationin a population
• Linkage – test if disease and a marker allele show correlated Linkage – test if disease and a marker allele show correlated transmission transmission within a pedigreewithin a pedigree
Linkage vs. AssociationLinkage vs. Association
3,41,3
1,3
3,3
2,3
1,4 2,2
3,4
2,4 4,4
AssociationAssociation
4,4 1,1
1,4
2,4 3,41,2
LinkageLinkage
1,2 3,3
1,3
1,4 1,4 1,43,43,4
Genetic linkage in humansGenetic linkage in humans
Nail- patella syndrome
Rare disease inherited as a dominant
Genetic linkage in humansGenetic linkage in humans
ABO Blood group marker:ABO Blood group marker:
Alleles: A, B, OAlleles: A, B, O
Genotypes: OO, AO, BO, ABGenotypes: OO, AO, BO, AB
Two Genes: N-P syndrome; Blood GroupTwo Genes: N-P syndrome; Blood Group
Evidence for linkageEvidence for linkage
Genetic linkage in humansGenetic linkage in humans
http://www.ndsu.nodak.edu/instruct/mcclean/plsc431/linkage/linkage5.htm