download lab. handouts download lab. #3 and print out 3 files: quiz #2 marks posted on webpage

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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 mapslinkage 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


CC ABC ABC

BB

c ABcc ABc

A A

C AbCC AbC

bb

c Abcc Abc

aa

Trihybrid GametesTrihybrid Gametes


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 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 +/+ +/+


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/+


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


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


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



ParentalParental

ParentalParental

268

268

1448= 18.5 %


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


+ + + 94 + + + 94

v + ct 3 v + ct 3

+ cv + 5 + cv + 5

14481448



ParentalParental

ParentalParental

191

191

1448= 13.2 %


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


+ + + 94 + + + 94

v + ct 3 v + ct 3

+ cv + 5 + cv + 5

14481448



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 ?


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


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 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


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

http://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


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


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


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


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.


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 chromosomegenes 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


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


http://www.ndsu.nodak.edu/instruct/mcclean/plsc431/linkage/linkage5.htm











download lab. handouts download lab. #3 and print out 3 files: quiz #2 marks posted on webpage

Documents

p ab aabb

r ab aabb

ab r gametes

p aabb

r aabb

cross aabb x aabb ab

b dihybrid

linkage of genes