Complex Traits Flashcards

1
Q

Relationship between alleles at one locus

A

Can lead to non-mendelian genetics patterns

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2
Q

Mendle

A

Discovered how alleles at one gene can be dominant or recessive

Did Aa X Aa – go t phenotypic ratio in offspring were predictable

3:1 Phenotypic ratio

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3
Q

3:1 F2 phenotypic ratio in Monohybrid cross

A

Pattern of inheritance = Mendelian Inheritance –> extends to corsses with heterozygosity at 2 loci

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4
Q

F2 phenotypic ratio in Dihybrid cross AaBb X AaBb

A

Get phenotypic ratio 9:3:3:1

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5
Q

Non-mendelian inheritance

A

When phenotypic ratios deviate from 3:1

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6
Q

Non-Mendeian inheritnace at one locus (At one gene)

A
  1. Incomplete dominance
  2. Co-dominance
  3. maternal Effects + Cytoplasmic Inheritance
  4. Sex Influence + Sex-linked
  5. Lethal Alleles
  6. Conditional Allele
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7
Q

Complex (Quanatative traits)

A

Demonstrate continuous phenotypic variation + do not behave according to Mendelian Genetics

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8
Q

Mendelian Inheritance

A

Monohybrid (Aa X Aa)
GR – 1:2:1
PR – 3 Dom: 1 recessive

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9
Q

Incomplete dominance

A

Relationship between 2 alleles were Aa is intermediate between either homozygote

Example:
P = Purple
p = White

PP = Purple
pp = white
Pp = Violat – mid between purple and white

Pp X Pp – PR –> 1 Purple: 2 Violate: 1 White = deviation from 3:1 = Non-mendelian inheritance

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10
Q

Degree of Dominace (h)

A

Describes the degree to which the phenotype of the heterozygote resembles the phenotype of a homozygous parent

Range from 0 - 1

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11
Q

Meaning/finding Degree of dominance

A

You need to define one homozygous phenotype as h = 1

Ex. Flowers
Red – H = 1
White – h = 0

h= 0.5 – midpoint pink
h > 0.5 – Darker pink
h < 0.5 – lighter pink

***need to define one of the homozygotes as h = 1

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12
Q
A

Answer: C – Incomplete dominance where h = 0.7

Black – h = 1 (given in question)
White – h = 0
Dark grey = closer to black = h >0.5 –> h = 0.7

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13
Q

Expressivity

A

When phenotypes vary between individuals with a particular genotype
- There is a wide range of phenotypes for a single genotype

High expresivity = there is a BIG range of phenotypes

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14
Q

Expressivity example – Polydactalism

A = dominant to a

AA or Aa = extra digits
aa = normal # of digits

A

Aa genotypes – have some with just extra small nub and some with many more fingers = wide range of phenotypes but individuals all have the same genotype
- There is a wide range of phenotypes for a single genotype

A = have polydactalism
aa = normal
A = extra digits

Degrees of polydactalism can vary

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15
Q
A

Autosomal Dominant with incomplete penetrance

Extect II - 1 to show the traut because offspring is affected but they don’t

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16
Q

Expressivity + Incomplete dominance

A

Expressivity (range of phenotypes) can sometimes explain incomplete penetrance – if you have high expresivity = have very wide range of phenotypes –> if have wide range then you can have a very low end phenotype – since it is very low end it might not be detected but then can have offspring with detected trait
- High expresivity is one way to explain incomplete penetrance

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17
Q

Penetrance

A

The proportion of individuals with a particular genotype that also express the associated trait

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18
Q

Incomplete penetrance

A

When some individuals with a particular genotype express the trait while others do not

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19
Q

Calculating penetrance example

A

Here 90% – because 9 out of 10 individuals with the genotype have the trait

To solve:
Need to find the genotypes of individuals – look at who NEEDS to have the genotype then look at how many out of those actually have the trait

with trait/ # with genotype

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20
Q

Co-dominance

A

relationship where Aa includes phenotypes of AA and aa
***Example – Red + White –> Red and white spots

Example – Blood types

AA –> Type A – Have A antigen on RBC surface
BB –> Type B – Have B antigen on RBC surface
AB – Type AB (CO-DOMINANT) –> produce BOTH A and B antoigen (Have both AA and BB phenotype NOT a intermediate one)

AB X AB –> Get 1 AA:2AB :1BB Phenotypeic ratio –> Non-mendelian ratio

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21
Q

Blood type adding in i allele

A

KNOW – AB is co-dominant BUT both are dominant to i

i = no antigen – ii = type O
Type A = AA or Ai
Type B = BB or Bi

Have multiple allles in gene = can make it harder to predict outcome of cross = interupts mendelian inheritance pattern

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22
Q

Having multiple alleles per gene + mendelain inheritance

A

Have multiple alleles in gene = can make it harder to predict outcome of cross = interupts mendelian inheritance pattern

Example –
Type A = AA or Ai
Type B = BB or Bi

Without knowing the genotypes (AA or Ai) = don’t know outcome of the cross

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23
Q

Allele context

A

Allelic relations = need context –> Allele is only dominant to another allele BUT if comparing to another allele that might change

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24
Q

Blood transfusions

A

Type A = doesn’t have B antigen = sees B as a foreign = have immune response producing anti-B antigen = essential that the person with Type A doesn’t get blood with B allele
- Can’t get B or AB
- Can only get A or O

Type B = recognizes A as foreign
- Requires B or O

Type AB = have A and B = no immune response to Type A, Type B ot Type O
- Can accept blood from all blood types –> Universal accpetor

Type O = No Antigen = reocgnizes A and B as foreign
- All other types can accept Type O = universal donor
- Can only get type O

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25
Q

Affect of Recessive Lethal Alleles

A

Lead to death when homozygous –> Lethal Alleles can lead to missing or reduced #s of genotypes

In monohybrid cross with recessive lethal alleles = have fewer offspring overall

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26
Q

Example Recessive lethal – Agouti in mice

A

Y = yellow – dominant to y
y = No yellow

Yy = Yellow
yy = no yellow
YY = death

Yy X Yy
GR – 1 YY: 2 Yy: 1 yy

PR – 2:1 – 2 yellow: 1 non-yellow because YY will never develop

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27
Q

Findoing probability in recessive lethal
+ Example

A

Can take out the one that dies = change the probability of all others

Ff X Ff

1 FF – dead
2 Ff – short
2 ff – tall

Because 1 FF is dead = only 3 pffspring – 1/3 is tall

F = dominat for achodrolasia BUT recessive for lethal (becaise need 1 F for short BUT need two F for dead)

***Doesn’t matter which you assign F or f – gives same results

F = dominant for acondroplasia – only need 1 copy (one copy in Ff = have achsdrolplasia)
F = recssive for lethal because need two copies (FF = dead)

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28
Q

Why ressive lethal if the allele is also dominant

A

Y = lethal

Y = dominant to y for agouti – because Yy is yellow (heterozygout has phenotype of Y)

BUT

Y = recessive for lethality because need 2 of them – only die if YY

Yy = alive –> y is dominant for lethality
Yy = alive and yy = alive BUT YY is dead = y is dominat for lethality because Yy is like yy

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29
Q

Recessive lethal phenotypic ratio in monohybird

A

2:1

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30
Q

Recessive Lethal Example 2 – Tail in cats

A

S = truncated tails and is dominat to s

SS = leads to spindal development probelms and is embryonic lethal

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31
Q

Organelle inheritance

A

Organelles contain mtDNA or cpDNA that can influence a trait
- Unpredictable organelle inheritance may lead to differences in trait expression

In mitosis – different quanityoes of organelle is ingerited = mtDNA and cpDNA is not inherited according to mendelian ratios = not predictable

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32
Q

What passes on cytoplasmic componenets

A

IN mammals egg cells (female gametes) pass on all cytoplasmic components – mtDNA is inherited through mothers

Paternal mtDNA is activley elimanted in zygote

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33
Q

Affect of organelle inheritance

A

Unpredictable organelle inheritance may lead to differences in trait expression

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34
Q

Characteristics of cytoplasmically inherited traits

A
  1. Present in Males and Females
  2. Usually inherited from one parent – usually the maternal parent
  3. Reciprical crosses give different results
  4. Exhibit extemsive phenotypic varaition even within a single family
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35
Q

Can there be paternal inheritance of mtDNA

A

Called Paternal leakage – sometimes –> rare exception NOT general rule
- 17 examples of paternal mtDNA in children

Possibilities for how – defects in the ability to eliminate paternal mtDNA

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36
Q

Maternal affects Genes

A

Found genes that encode regulatory RNAs that are passed to the offspring in the cytoplasm of the egg

RULE: Mother’s genotype detemrines the offspring’s phenotype

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37
Q

Maternal effects

A

Moms envirnment to offspring –> envirnment can alter gene expression in offspring that givs rise to phenotype that are reuslt of the materal envirnment

Different envirnment can alter phenotypic ratios in offspring

BUT the mosther’s genotype detemrines the offsrpings phenotype

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38
Q

Sex limits vs. Sex influences traits

A

BOTH – caused by genes on autosomes = both males and females can transmitt the trait but the trait is only expressed on one sex
- Can be on sex chromosmes (then it will also be sex linked and sex-influenced/sex limited) OR can be on autosomes

Sex limit = trait is ONLY expressed in one sex

Sex influence = trait is mostly expressed on one sex

Can be caused by genes on autsomes – sometimes they are also sex-linked
- Sex linked if they are on sex chromsomes

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39
Q

Example Sex limited – Precocious puberty

A

P = Early puberty – dominant mutations in autosomal gene encoding hormone receptor can lead to early puberty in boys –> lead to early puberty in boys only

p = normal puberty

Mutation in AUTOSOME – both males and females can pass down but only have trait in males

pp (normal female) X Pp (Early puberty male)
- Gives Normal female, Normal Female, Early male, andnormal male (SEE IN IMAGE)
- Get gametes with pX from mom, and PX PY, pX, pY from dad (because get P on auatsome and get sex chromsomes)

OR

pp (normal male) X Pp (Normal female)
- Daughters and half sons have normal pubey, Half sons have early puberty

Shows both males and femals can pass down trait but only males show the trait

NOT sex linked because when do reciprical cross = we get the same ratios (get 2 normal females, one early male, and one normal male) –> because same ratios = NOT sex linked traits = both can transmit the trait but only males present the trait

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40
Q

Example of sex influenced – male pattern baldness

A

Mutations in an AUTOSOMAL locus on chr. 21 can lead to hair loss in men, and to a lesser degree women. sex influenced (but not sex-linked)

Sex influneced because can see trait in women but not sex linked because on autosome

Males:
HH = have hair
Hh = have balding
hh = bald

Females (have the same alleles BUT do not see hair loss to full degree):
HH = normal
hh = have thinning of hair BUT not bald in same way that males will be

***Inherited on autosomes = not sex linked

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41
Q

Sex linked male pattern baldness

A

Varaints on gene on X chromosome leads to hair loss in men but not wome (Sex linked because on X chrosmomes AND sex limited because only in men)
Xh = hair loss in men
xH = no hair loss (full hair)

xhxH or xHxH = full hairs

Sex linked – on sex chromosome vs. Sex infulenced is on autosomes

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42
Q

Conditional alleles

A

Influence mendelian ratios –> Allels that ONLY show phenotype in certain envirnments
- Only present their phenotype under certain envirnmments
- Conditional on envirnment
Ex. Siemmese cats – temperature sensitive alleles

cs = non-functional at high temperatures but functional at low temp

CS = WT – can produce melasis = get full color

CS is dominant to cs

cs at low temp expressed = can produce pigment but at high temp not expressed = cannot produce pigment –> expression is dependent on envirnment

Siemesse cats = cscs –> can make tyrosnine to get pigment at low temperature but not at high –> when they are born they are born all white because at high tempeture in the womb = no tryosinase = no pigemnt –> as they grow their expremities cool but their body stays warm = extremeisties get opigment because of cooling and body stays white because warm (warm areas stay white)

This is conditional allele because expression of the allele depends on the envirnmen

cs = Temperature sensative allele
- The extremities = get cold = have color
- The core stays warm = no color
- ALL cells have the alelle but its not expressed in all
- When first born = all white because wamr in the womb = no color

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43
Q

Conditional alleles can be

A

Lethal –> means that they are lethal only under certain conditions = have conditional lethal allele

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44
Q

Example conditional lethal allele – favism

A

X-linked recessive mutation –> mutation prevents G6P dehydrogenase
- Mutation in Glu-6-P dehydrogenase = reduced glutathione = RBCs are not protected against oxydants = cells undergo hemylysis = can lead to death
- Leads to low glutathione, an antioxidant that protects red blood cells
- Hemolysis can occur if oxidant loads are too high

Trigger for increase in oxidants = fava beans + antimalarial drugs + some antibiotics + henna

Most people homozygous for mutation are fine BUT only have health issues if oxidants level increases = conditional lethality

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45
Q

Allele frequencey for favism varaint

A

Offers protection against malaria
- Individuals that have favism allele = protected against malaria
- Increase in malarua alleles = increase in allele frequncey of favism vraints

May explain why some cultures use chickpeas instead of fava beans

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46
Q

Given X-inactivation – why do Turner (XO) or Klinfelder (XXY) syndromes exist

A

At certain times during embryonic development both X chromsomes are needed
- finally a cell with select 1 at random for X chromsome inactivation

ALSO sometimes there is expresion of certain genes from teh condensed X chromosome

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47
Q

Common mechanism in XY females

A

Androgen insensitivity syndrome

Low response to testostrone

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48
Q

Overproducing testosterone

A

XX with congential Adrenal Hyperplasia – genetic variants can cause an overproduction of testosterone

XX individuals with CAh can be:
1. Typicaly female
2. Typical male
3. Cmbined male and female charachteristics

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49
Q

XX males

A

XX can develope as males if SRY targets are activated errenously – if have recombination between X and Y chrosmoems that adds SRY to X chromsome
- Recombination doesn’t normally happen between X and Y chrosmomes but sometimes mistakes happen

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50
Q

Sex chromomomes across biology

A

Not always X and Y

Ex. Lots of repriles and bird and some invertabrates
Female = ZW (heteroganetic –> can make gamated with Z or W chromsomes)
Male = ZZ (homogametic –> can only make one type of gamete)

Still have sex chrosmomes but not called X and Y called Z and W

Ex. 2 – Some Invertabrates
Female = XX
Male = XO (1 X only)

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51
Q

Extreme sex chromsomes

A

Some species take sex chromosomes to the extreme

Ex. Platapus
Female = XX, XX, XX, XX, XX
Male = XY, XY, XY, XY, XY

Have 5 sets of sex chromosomes

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52
Q

Sex + Ploidy

A

Some rely on ploidy rather than specific sex chromsomes

Ex. Bees
Males = Haploid – basically unfertalized gamete becomes male

Females = diploid

Haploids = develope as malel Diploid develop as female

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53
Q

Genic Mating System

A

A single gene determines mating types in some
organisms – the allele of that gene determines Sex
- No sex chromsomes

Ex. Yeast
- Has two mating types – A and Alpha –> mate to form diploid –> controled by a single gene
- The gene = flanked by silent copies of both mating types –> chnages alleles at mating type locus = daughter cells can change mating type

Mating types in yeast:
Saccharomyces cerevisiae: 2 mating types
Tetrahymena thermophila: 7 mating types –> have pheranomes + pheramone receptors that allow this to happen
Cryptococcus neoformans: 2 mating types but
~20 different mating receptors

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54
Q

How are there multiple mating types in yeast

A

Have pheranomes + pheramone receptors that allow this to happen

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55
Q

Drosphila sex determination

A

Female = XX
Male = XY + 3 pairs of autosomes

*The Y chromosome does not determine sex –> Not a gene on Y chromosome that makes male/female
*The ratio of X to autosomes (X:A) determines
the expression of Sxl, a gene that signals the
female sex determination pathway
- Female XXAA – X makes yellow protein and A makes red protein (have no X inactivation – both are active) –> then the proteins make a heterodimer of Yellow and red THEN the left over yellow make a homodimer – the yellow homodimer promotes transcription = female

IF not enogh yellow = no Homodimer = no transcription = male

IF more X = more yellow = homodimer = transcriotion = get gene = female

MALE XYAA
- X still makes yellow and A makes red BUT male makes less yellow because only one X –> NOW there is no yellow for homodimer = no transcription = male

SXL expression = female development
NO SXL = male development

56
Q

Hermphradism in some species

A

Some species – individuals are both male and female = hermaphradism

Ex 1 – C. Elengans – self-fertile females (hermaphradites as male and females for repredouction)

Ex 2 – Flowers – hermaphrodites
- They prefer to out mate BUT will self-fertalize (self mate) –> it is better to make seeds than to not make seeds at all

57
Q

Use of C.Elengans

A

Model system for development – are hermaphrodites

58
Q

Envirnmental Sex determination

A

Sex can be triggered by envirnment

Ex. Lizards + Aligators
- Dveelopment of sex in egg = based on temperatire egg is reared at
- Warmer = get more males; colder = get more females

HERE = have G X E –> All genes are there to make males and females its just what gets activated

Ex 2 - Clownfish – sequntial hermaphradies

59
Q

Clownfish sex

A

They are seuqntial hermaphridites – they switch –> NOT always male and female – same indiviodual can concert to female

  • Switch between male and female
  • The largest fish in the school is female, all others are male
  • If something happens to the female, the largest male turns into a
    female
60
Q

Mole salanders

A

Unisexual – all female
- They steal sperm from other species –> don’t use genetics just activates to make eggs
- Eggs have varaible ploidies
- Sometimes DNA from sperm is present
- This is how they reproduce

To make eggs, the female steal sperm from other salamander species –> This triggers the females to make eggs
(with variable ploidy- mostly 2, but 3 and 4 sets sometimes observed) – Sometimes, the DNA from the sperm is
also present

61
Q

Purple + White –> Pink flowers – what describes the relationship between these allles

A

Incomplete dominance – because see neither purple or white – heterozygoues is a blend of the hoozygous

Co-dominance = see both homozygous

62
Q

Knowing degree of domimance

A

You need to assign one phenotype as h = 1 and one phenotype has h = 0

Ex.
Red h = 1
White h = 0

IF Aa is pink –> h = 0.5
If Aa is closer to red –> h > 0.5

Need to define one as h = 1

63
Q

Incomplete dominance vs. Incomplete penetrance

A

Incomplete penetrance = refers to pedigree when people with genotype don’t show the trait

64
Q

Do indivividulas have high expresivity

A

NO – individuals do not have expresivity – traits have expresivity

65
Q

Recessive lethal alleles (class) – Ex. cats

A

S = spinal defromation
s = normal

Ss = no tail
SS = dead in utero – recessive lethal

S = spinal defect over s but it is recesisve for lethality because 1 copy is not lethal bit 2 copies is lethat
- Dom for spinal development but recessive for lethal
- Spinal development = Ss more like SS than ss = S is dominnat BUT for SS need two copies (Ss is NOT like SS it is like ss for lethality) = S is recessive (need two copies) for lethality

66
Q

Sex limited (lecture)

A

Expressed only in one sex but inheritance is controlled bu sutosomes
- Males and females have the allele but the trait is only expressed in one

Ex. Early puberty in males – Females = have the allele but it is only expressed in males

67
Q

How do you know sex limited/sex associated is NOT sex linked

A

Because for sex limited/sex associated the recipircal cross gives you the same ratio

For Sex linked the reciprical cross gives you two different ratios

68
Q

Variation in complex traits

A

Complex traits demonstrate continuous phenotypic variation – do not fit into tidy discrete categories
- NOT ALWAYS BELL CURVE

***Complex traits do not behave according to Mendelian Genetics predictions

69
Q

Use of continuous traits

A

Help us understand mechanism pathways

70
Q
A

1 – Sex linked (X chrosmome) and Sex limited (ONLY in men)
2 – Sex assicated/sex influenced
3 – Sex limited (ON autosome BUT only in boys)
4 – Sex limited
5 – Sex linked + Sex limited (women do not have postsates)

Sex linked = ON sex chromosomes (if on X or Y = Sex linked)
Sex limited = can be on autosomes OR sex chromoeomes

71
Q

Maternal Effects Gene

A

Maternals Genotype determined the offspring phenotype – MEANS that no matter the phenotype of mom or genotype of kid the kid will have the phenotyp assicated with genotype of the mom
- Kid genotype doesn’t matters – mom genotype is what matters

Example –

D = Dextral
d - Sinistral

IF Mom is D_–> All kids are dextra (Because mom genotype has D)

If mom is dd –> ALL kids are Sinistral EVEN if they have Dd genotype
- Because based on mom genotype and mom has dd genotype = kids phenotype is Sinistral even if Dd genotype

72
Q

Maternal Effects example

D = Dextral
d = Sinistral

MOM Dd X Dad Dd

A

ALL kids are Dextral

STILL have 1 DD: 2 Dd: 1 dd BUT the dd kid is still dextra because mom is Dd
- Since mom is Dd = all kids are dextral because kid phenotype us based on mom genotype

Mom = Dd = all offsrping have dominant trait even if they have dd –> genotype of mom gives information on how offspring develope

The mom’s genotype is Dd (gioves dextral phenotype) so the offsrping will show the omindnat trait even if they inherit recssive alleles
- They still show the dominant traiyt even if dd because mom is Dd (gives dominant phenotyype) and its based on mom genotype

73
Q

What causes maternal affects?

A

Encode RNAs found in the egg –> Stuff that ends up in egg (not in the polar bodies) includes Proteins + mitocondria + RNAs that have regulatory function –> egg has RNAs to turn on development
- Matters what is theer to actrivate egen expressuon

***Genotype of mom = affects regulatpry RNAs in egg = affects the phenotype in offspring
- Mom puts regulatory RNA in egg BUT she also can only put her own genotype (If she is gg she can only give g NOT G) – all of the offspring get the regulatory RNA that mom can make
- The reguoatory RNA turns on expression during development
- Regulatory RNA made from DNA of mom

THE offspring can then make regulatory RNA from their own genotype to give to kids (if offspring is dd then they can make regulatory RNA from their offspring) –> They can give different regulatory RNA to their own offspring than they got from their mom

FOUND 11 Maternal Effect genes in humans

74
Q
A

Phenotype ratio 4 Sinstral: 0 –> Mom is dd = mom genotype gives sinistral AND the mom genotype dictates the phenotype of kids (if mom is dd genotype kids all have phenotype associated with dd regardless of their own genotype)
- Since mom is dd –> ALL offsrping show recssive phenotype even though mom shows the Dominnat phenotype BEACAUSE based on mom genotype NOT mom phenotype

75
Q

Rh Factor

A
76
Q
A

G = Grey
g = White
B = Black
b = Red

G_bb –> Grey and red

Answer: 3/16

77
Q

Menelian Dihybrid Cross Genotype and Phenotype Ratios (walks through Dihybrid cross steps)

A

Expected Genotype/phenotype ratio of Dihybrid cross where each indepent gene influencves seperate traits (2 genes = 2 traits)

GR = 9:3:3:1
PR = 9:3:3:1

Example:
R = Round
r = Wrinckled
Y = yellow
y = green

RRYY –> Only produces RY gametes
rryy –> Only produces ry gametes

RRYY X rryy –> Get RrYy (Heterozygous – all show dominant traits)

RrYy = can make 4 types of gametes (RY, Ry, rY, ry) –> because of law of Independent assortment = expect equal frequency of each type of gamete

THEN can use punnet square to find expected genotype and phenotype frequnceies of F2
- Build a punnet square of 4 Gametes by 4 gametes of each parent across tops and sides –> THEN fill in the sopace by combing gametes for each parent

END: 9R_Y_: 3R_yy: 3 rrY_: 1 rryy

When 2 genes infleunce 2 seperate traits phenotype ratio = 9:3:3:1

78
Q

Genotype Ratio Vs. Phenotype Ratio

A

The genotype ratio always stays the same – expect genotype ratios are always the same

Phenotype ratio = Can shift if not independent (if genes are not indepent if they affect one trait)
- Change ratio if you have two genes that affect one traut and are not independent from each other
- If those 2 genes influence 2 seperate traits expected phenotype rations = 9:3:3:1
- Ways genes interact with each other = can change phenotypic ratio

79
Q

2 genes affect the same trait

A

These genes can intercat in different ways to produce novel phenotypes

80
Q

Use of genetic interactions

A

Different types of genetic interactions can sometimes reveal the pathways or molecular mechanisms underlying a trait
- Different types of genetic interactions + how they predict phenotype ratios in a Dihybrid cross can sometimes reveal the pathways or molecular mechanisms underlying a trait

81
Q

2 genes + one trait

A

Polygenic – two genes influencing the same trait (two genes control one trait)

82
Q

Example of Polygenic trait (Two genes one trait)

A

Two genes control one trait – Color in peppers

Two loci - Y and C loci control the production of color

Y+ is dominant to y
C+ is dominnat ti c

Y+C+ = red
Y+cc (dominant at one and recessive at the other) = Peach colored
yyC+
(dominant at one and recessive at the other) = Orange
yycc (recessive for both) = white

IF Y+Y+C+C+ X yycc

F1 – ALL Y+yC+c –> ALL RED

F2 – Y+yC+c X Y+yC+c

F2 expected Genotype Frequncey (Doesn’t change):
9Y+C+: 3Y+cc: 3yyC+: 1yycc

Expected Phenotype Rato:
9 Red: 3Peach: 3Orange:1 White

HERE – 2 genes infleunce the same trait in indendent fashion – expected PR = 9:3:3:1
- Here two Loci are contributing independently because still 9:3:3:1 –> Here they are additive = indepedent = no epistasis

83
Q
A

ANSWER: 3/16

STILL 9:3:3:1 ration but now 2 genes are for the same (for one) trait
9Y+C+: 3Y+cc: 3 yyC+: 1 yycc

Orange = yyC+_

84
Q

Epistasis

A

Genetic interactions where one gene influences (masks) the effect if another gene
- Allele at one gene masks effect at another gene

85
Q

Epistatic gene

A

The gene that does the masking (the gene you end up seeing)

86
Q

Hypostatic gene

A

The gene whose affect is masked (the gene that you do not see)

87
Q

Other meaning of epistasis

A

Also refers to instances where two genes do not contribute equally to a trait – Non-additive effects
- Interacts in a non-additive way

88
Q

Types of epistasis

A
  1. Recessive Epistasis
  2. Dominnat Epistasis
  3. Duplicate Recessive Epistasis
  4. Duplicate Dominant Epistasis
  5. One domiant, One recesisve Epistasis
  6. Non-additive epistasis
89
Q

Recessive Epistatsis

A

When recessive alleles at one locus mask the effects of the alleles at a second locus

Phenotype ratio – 9:4:3

Example – Labs
Coat color is influenced by 2 labs coat color is influenced by 2 genes (Have B locus and Extension locus)
- Extension locus (E locus) – allows color to extend to fur

B = Black (Dom to b)
b = Brown
E = Extends color = get color in fur (Dom to e)
e = no color in fur (ee = yellow)
- ALL ee = yellow lab because can’t extend pigment into coat

Genotypes:
B_E_ – Black
- Black = BB or Bb AND Must have EE or Ee –> B_E_
bb = chocolate lab AND must have EE or Ee (bbE_)
B_ee – Yellow –> The recessive e allele is epistatic to B and b (Bceause if have ee then you can’t know the genotype at B – no mater what is ee will be yellow no matter what is at B locus)
- Yellow lab = _ _ ee –> Can be BB, Bb, bb –> no matter what if ee then it will be yellow

bbE_ – Brown
bbee – yellow

Recessive epistasis because e (which is the recessive allele) makes affects at B – the recessive e allele is epistatsic to B and b
- Recessive epistasis because ee masks phenotype at B locus
- e = epistastic allele
- B loci = hypostastic gene

9B_E_: 3B_ee: 3bbE_: 1 bbee
9 black (Black + can extend): 3 yellow (Black but no extend = yellow): 3 brown (Brown and can extend): 1 yellow (NO extension) –> 9black: 4 yellow: 3 brown
- Different phenotypic ration (9:4:3)

90
Q

Dominant Epistasis

A

When dominant alleles at one locus mask the effects of
the alleles at a second locus
- The dominant Alleles do the masking

Expected Phenotypic ratio – 12:3:1

Example –
Compund A (White) –> Compund B (Green) –> Compound C (Yellow)
- A –> B – need enzyme 1 – W_ = encodes an inhibitor = blocks synthesis of Enzyme 1 = get white – get build up of A (white squash)
- B –> C have enzyme 2 – Y Produces enzume;
- Mutation along the oath = blocks synthesis of compund C = build up of green or white
W = produces an inhibitor to enzyme 1 = No A –> B
- Dominant W = inhibits enzyme 1 = dominant allele masks affect
w = get A –> B
Y = produces an Enzyme 2
y = No enzyme 2 (No B –> C – unable to get enzyme 2 = build up of compund B = stays green)

W_YY, W_yy, W_Yy = ALL stay white because inhibits Enzyme 1 (W blocks A –> B – because block in early step = doesn’t matter what allele you have at Y locus)
- Means that W (dominant W) masks affects at Y locus (If have dominant W = don’t know genotypes at Y locus = Dominant epistasis)

wwyy = green squash –> Need to make compund B = need ww + can’t make B –C = they need yy

wwY_ = yellow squash – need ww to get A –> B and need 1 Y to get B –> C

WwYy X WwYy
9 W_Y_(White) : 3W_yy (White) : 3 wwY_ (Yellow): 1 wwyy (green)
12 white (W_Y_ or W_yy): 3 Yellow: 1 Green

Overall: Dominnat W blocks enzyme 1 = blocks affect of Y Locus (If have W = don’t know genotype at Y Locus – white can be W_Y_ or W_yy – no matter what W means white) –> W shows dominant epistasis to Y gene
- Because if stop A –> B = B –> C doesn’t matter = masks affect of Y locus = dominant epistasis to Y locus

91
Q

Duplicate Recessive Epistasis

A

When recessive alleles at one locus mask the effects of the alleles at a second locus, and the recessive alleles at the second locus mask the effects of the alleles of the first locus
- When the recessive allele of both genes mask the effects of the other
- Effects of 2 genes on the same trait – both demonstarte recessive epistasis

Predicted Phenotyp Ratio – 9:7
Occurs often if have 2 genes in the SAME linear biochemical pathway –> frequentley observed when 2 genes produce enzymes for the SAME linear pathways

Example – Snail shells (Image)

NEED Compound A –> Compund B –> Comound C (compound C = brown)
- A –> B – have enzyme (coded for by A locus) – A = make enzyme for A –> B
- B –> C – have enzyme 2 codeed for by B Locus (B makes Enzyme 2 – Makes B –> C – get Brown)

aa = no A –> B (no enzyme for A –> B = no A –> B - stays white)
- aa = white – masks the affects if alleles at B locus (Masks influence of B – aa is recessive epistatic to B gene)
bb = No B –> C (no enzyme for B –> C – no compound C = stays white)
- bb = white – makes the affect of any genotype at A (Masks influence of A locus = bb is recessive epistatic to A gene)

A_B_ = Brown
A_bb = Whote
aaB_ = whote
aabb = white

***If have either aa or bb or both aabb = will be white

Need enzyme 1 and 2 to make color

Epistasis because if you have white snail you don’t know the genotype of a or b –> could be aa or bb or aabb = don’t know genotype at the B locus if have aa and don’t know genotype at A locus if have bb (because if have bb white no matter what and if have aa then white no matter what = don’t know genotypes at the other locus + since they are both recssive that does the masking = duplicate recssive epistsis

Since both are recessive that do the making = duplicate recessive epistasis

Since if have bb don’t know genotype at A locus and if have aa don’t know genotype at B locus = duplicate epistasis
- aa = masks B (Can be BB, Bb, bb – still white)
- bb = Makes A (Can be AA, Aa, aa – still white)
- Two genes have epistasis = duplicate epistasis

AaBb X AaBb
9A_B_: 3 A_bb: 3 aaB_: 1 aabb
- A_B_ = brown
- A_bb = white (Have Enzyme 1 BUT no enzyme 2 because bb = white)
- aaB_ = white (No enzyme 1 = stays white)
- aabb= white (No enzyme 1 or 2 = white)

Phenotypic Ratio 9Brown: 7 White

92
Q

Duplicate Dominant Epistasis

A

When dominant alleles at one locus mask the effects of the alleles at a second locus, and the dominant alleles at the second locus mask the effects of the alleles of the first locus
- When the dominant allele of each gene masks the effect of the other gene
- Both act in dominant epistatic manner

Common ratio = 15:1

Example – Wheat

Precursor + Gene A –> Pigmemnts

Procursor + Gene B –> Pigmenyt

Get pigmeny by A or B – A and B have redundent functions (A or B = get kerneel color)

aabb – recessive = can’t make precursur to colored kernerl = stays white

A_B_ or A_bb or aaB_ = colored

AaBb X AaBb
9A_B_ (Colored): 3A_bb (Colored): 3aaB_ (Colored): 1 aabb
- Because just need 1 A or 1 B to get color
15 Color: 1 White

93
Q

One Dominant, One Recessive Epistasis

A

When dominant alleles at one locus mask the effects of the alleles at a second locus, and the recessive alleles at the second locus mask the effects of the alleles of the first locus

Common ratio = 13:1

Example
Gene B = produces feather color
B = colored
b = white

Gene B produces feathers color – the B allele produces colored feathers and sis dominant to b = get white feathers

Gene A = encodes inhibitor that blocks color formation
A = dominant to a and epistatic to B locus

bb genotypes = don’t make colored feathers – you can’t determine the genotype at the the A locus if have bb = recessive epistasis
_ _ bb = all not colored = don’t know genotype at A locus if have bb = recessive epistasis

A_ genotypes = don’t make colored feathers –> You can’t determine the genotype at the B locus = dominant epiostasis
A_ bb, A_BB, A_Bb = all no color = can’t know genotype at B locus = dominant epistasis

Colored feather = need B_ and aa (to not have inhibitor –> aaB_)

White feather = can encode inhibitory (A_B_) OR Can encode inhibitor and no color (A_bb) OR not encode inhibitor and no color (aabb)

AaBb (Make color but also have inhibitor – white because have inhibitor even though they can make color) X AaBb
9A_B_ (White): 3A_bb (White): 3aaB_ (Colored): 1 aabb (White)

PR: 13 White: 3 Color

94
Q

Non-Additive epistasis

A

When alleles at different loci do not contribute equally
to a single trait

95
Q
A

Answer: B_E_

bbee –> Yellow
bbE_ –> Brown
B_ee –> Yellow

96
Q
A

Answer: __ee –> ee masks effect at B locus = can’t know the genotyoe at B locus if yellow lab (Could be BB, Bb, bb – no matter what is ee then it will be yellow)

The recessive e allele is epistatic to B and b (Bceause if have ee then you can’t know the genotype at B – no mater what is ee will be yellow no matter what is at B locus)

Recessive epistasis because e (which is the recessive allele) makes affects at B – the recessive e allele is epistatsic to B and b

97
Q
A

Answer: 4/16 (3 + 1 = 4)

9B_E_:3B_ee:3bbE_:1bbee
9 black: 3 yellow: 3 brown: 1 yellow –> 3 + 1 = 4

Phenotype ratio:
9 black: 4 yellow: 3 brown

98
Q
A

Answer: B –> gene that does the masking – masks the effects if color locus

Epistatic gene = gene that does the masking

99
Q

Black, brown, yellow lab example – why is it recessive epistasis

A

Beacause the rcessive allele does the maksing (e allele is recssive to E = recssive allele –> and the e allele is the allele that masks B locus)

e allele (ee) = prevents you from knowing genotyope at B locus – since e is the recssive – it is the recessive that does the maksing = recessive epistasis
- e = recessive to E NOR recessive to B locus

***Recessive epistasis when the recessive alelle does the maksing

Recessive = refering to E to e (e is recssive to E and does the masking)

e is recssive to E and does the making = recessive epistasis

100
Q
A

Answer: Both are white

bb = get A –> B but no B –> C (Stays white – B is white)
aa = no A –> B = white

101
Q

Where is duplicate recessive epistasis common

A

Common in genes with the SAME linear biochemical pathway

102
Q

Loss of function alleles

A

Alleles that are unable to perform the normal function of a gene
- Can’t produce the function

Loss of function is NOT always epistasis

103
Q

Los of function alleles are typicaly

A

Recessive – Because in diploid might have mutation in one copy BUT then you still have the normal copy –> if have loss of function still have the other version that can make the gene
- In diploid = have a backup – other copy can do the job

104
Q
A
105
Q

When is duplicate dominant epistasis common

A

Frequntley observed when genes have redundant functions

106
Q

Expected phenotypic ratios – summary

A
107
Q
A
108
Q
A
109
Q

Additive traits

A

Example

A+ and A- = incompletley dominant

B+ and B- are incompletley dominant where the degree of dominance is h = 0.5

1/16 =

110
Q

Distrbution of Addition Traits

A
111
Q

Calculating the number of loci involved in additive traits

A
112
Q

Practice –

A
113
Q

What can complex traits involve

A

Complex traits can involve polygenic + Additive + Epistatic genes whose relationships can change depending on the environment

114
Q

Goal of Quantitative Genetics

A

A goal of quantitative (complex trait) genetics is to study phenotypic variation in a population and try to parse these effects into the basic compents of dominance, additive, epistatic relationship of one or more genes, and g x e interactions

115
Q

What often controls a single trait

A

Most often a single trait is influenced by multiple genes –> genes can interact in different ways to produce novel phenotypes
- Interactions = produce novel traits

116
Q

Gametes from RrYy

A

RrYy = can make 4 types of gametes (RY, Ry, rY, ry) –> because of law of Independent assortment = expect equal frequency of each type of gamete

117
Q

How do you know expected Phenotype and Genotype ratios

A

Can use punnet square to find expected genotype and phenotype frequencies
- Build a punnet square of 4 Gametes by 4 gametes of each parent across tops and sides –> THEN fill in the sopace by combing gametes for each parent

118
Q

Two genes infleuncing trait independently

A

IF get 9:3:3:1 Phenotypic ratio –> 2 genes infleunce the same trait in indendent fashion
- Here two Loci are contributing independently because still 9:3:3:1 –> Here they are additive = indepedent = no epistasis

Still 9:3:3:1 = additive = they contribute independently = no epistasus

Ex. In pepper color

119
Q
A

Mom genotype = dd –> mom genotype determines the offspring phenotype = all offspring have p
phenotype from dd = all
sinistral

MEG= always 4:0 ratio

120
Q

How do Maternal Effect Genes work?

A

Durring Oogeeniss = make gametes BUT inreality only get 1 viable cell and 3 polar bodies

If mom Has Dd genotype –> The MEG = makes regulatary RNA
- The Regulatory RNA is based on mom genotype –> turns on if she will be Dexttral; or Sinistral (which way it goes is controlled by expression of gene – contriolled by regulatory RNA) – regulatopry RNA needs to be in egg cell
- The gamete will get that regulatpry RNA made based on mom DNA

NOW get two eggs – one can have D and one can have d
- D egg in development is regulated by regulatpory RNA to trin on spinal (based on reg DNA from mom)
- d egg = still has regulatpry RNA –>? stull on on dominnat dextral phenotype ebven though it has d – because of regulatpry RMA – even if genptype ends up being dd –> but has the regulatpry RNA to make it dextral – if the regulatpry RNA is there = get Dextral phenoytype

BUT the daughter cells from these daighter cells = can’t amke regulatpry RNA – they have enough at first (when daughter cell sget from mom) –> enough at first at the start of development to get dextral but can’t pass down to offspring

THEN if dd offspriunf that is dextral because mom id Dd –> dd is dextral but has dd = can’t make regulatpry RNA for dextral ohenotype like their mom gave them = can make dd Regualtopry RNA in kids –> kids get dd regulatpry RNA = kid is all sinstral

Maternal effect = always 4:0 ratio

121
Q
A

Dd = all dextral

***MEG = always 4:0 ratio

122
Q

Gene knockout

A

When genomic DNA is altered so that the expression of a gene is permanetley prevents – detele a gene or alter promister region (reguilatory region) = can’t make that gebe from that copt of the chromosome
- Gene is there but never tirns on

A gene knockout = A loss of function allele

123
Q

Gene Knockout + Loss of function alleles

A

A gene knockout = a loss of function allele

124
Q

Why are most loss of function alleles recessive?

A

Because we have 2 chromsomes – if have loss of function in 1 chrosmomes –> can be active on the other chromsomes – have other one as a backup

125
Q

Loss of function + Dominance

A

Loss of function alleles can be dominant

Example = image
Two wild type – Get normal phenotyp

1 Wt and 1 mutant (1 loss of function allele)
- Normal = can make regulatlry RNA + protein BUT not as miuch – get 1/2 the amount of protein –> might not be enough

Here = end with obesity – there is not enough to get normal phenoyyp – get obsesity

2 loss of function – 2 copies of Knockoiut –> have obese mice

Here – Obesity is cominant because heteropzygous shows obesisty

SHOWS – halpoinsifcincey – when 1 cope of a gene is not enough
- Aa – that one cope of Wt allele = not enough for W-T phenotype –> shows that Loss of function can be dominant

126
Q

Haploinsufficinecey

A

When 1 cope of a gene is not enough
- Aa – that one cope of Wt allele = not enough for W-T phenotype –> shows that Loss of function can be dominant

127
Q

Additive traits

A

Example – Wheat (Red X white wheat)
A+ and A- are incompletley domiant; B+ and B- are incompletley dominant where h = 0.5
- A+A- = middle
- B+B- = middle –> A+A-B+B- = middle

END = see 5 catagpries of color –> NOT 4 like before – We know it is not epistasis because in epistasis it is max 4 catagpries

HERE they thought - what if each + allele contributes 1 unite of color
- A-A-B-B- –> no units of color
- A+A+B+B+ – 4 units of color
- A+A-B+B- – 2 units of color = in the middle

1/16 = lihghtests color (light purple)
1/16 = darlest colro (dark purple)
-
-

***Very common in biology

128
Q

Distribution of additive traits

A

get bell curve becasue additive – if contonous –> bell curve disyrbution

129
Q

Number of a categories for continuous traits

A

2 genes = 5 categories –> based off the # of additive alleles that are there

1A+A+B+B+ – 4 units of color
2A+A+B+B – 3 units of color
A+A-B+B+ – 3 units of color
4 A+A-B+B- – 2 units of color
1 A+A+B-B- – 2 units of color
1A-A-B+B+ – 2 units of color

More genes = start to see continous distrubution of traits (more genes = more catagoreies)

130
Q

How can you determine the number of genes contributing to an additive trait?

A

The proporition of indvioduals at eaitehr end of dirbution = (1/4)^n

n = number of genes
- look at number of indiviuals at the more left or most right caratgories

Ex from wheat

1/16 = white (no alleles); 1/16 = red (4 alleles)
- 1/16 at the ends
1/16 = (1/4)^4
n = 2

Can get the total number of genes that control a trait if you now the number of individuals at the end and the total number of individuals

***If the end numbers are different = pick one end – can solve for both

131
Q

Example – finding the amount of genes that control a trait

A

First need to look at how many out of total (how many out of 256) has extreme phenotype – look at the two ends –> look at the tails (look at the two extremes)

Here ends = 1 indivual (1/256)

1/256 = (1/4)^n

n = 4 –> 4 genes

132
Q

Finding the genotype example

A

Start – subtrarct both homozygous varlues

Here – 20- 0 = 20
Then divide that value by the total number of alleles –> 20/10 = 2

Means each additive allele contributes +2

HERE – have 5 genes
A+A+B+B+C+C+D+D+E+E+ = 20% (most we can make is 20%)
aabbccddee = 0%

most we can make is 20 and least is 0 –> 10 allles total –> 20/10 = 2 00> each allele contributes 2% oil

Each adds 2% = for 8% oil = we need 4 additive alleles

Range = 0- 20
20 - 0 = 20
20 (difference between highest and lowester) /10 (10 allels) = 2

133
Q
A

Can be any combo of 4 alleles – all would give the same phenotype for additive alleles

134
Q
A

bb = recesive eepistasis because b allele is recessive allele and that recessive b allles masks teh effects of A – don’t know genetype of A

A_ = dominant that blocks B locus – dominant A = masks B locus

135
Q
A