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BIOL2202 Genetics > Module 4--Genetic Analysis of Simple & Complex Traits > Flashcards

Module 4--Genetic Analysis of Simple & Complex Traits Flashcards

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Biology 101 flashcards
1
Q

What is a model organism?

A

A species with morphology/physiology/genetics/ecology/ suitable for your field of inquiry

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2
Q

What is a good model organism?

A
  • Easy to grow and maintain in the lab
  • Fast growth, relatively short life cycle
  • Easy to perform crosses
  • Small genome size
  • Considerable existing knowledge due to previous work
  • Relatively simple model for a question
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3
Q

What are the contributions made by E. coli?

A
  • Elucidation of universal genetic code
  • Spontaneous nature of mutations
  • Mechanisms of DNA replication, transcription, translation and gene regulation
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4
Q

What is CRISPR?

A

Clustered Regularly Interspaced Short Palindromic Repeats

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5
Q

What is the CRISPR-Cas9 and its application?

A

A DNA editing technique that has been engineered into many eukaryotic model and non-model organisms to induce specific DNA mutation

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6
Q

What is Saccharomyces cerevisiae and its characteristics?

A

It is a single-celled eukaryote and a species of yeast.

Characteristics:

  • Haploid
  • Combines the convenience of bacterium, with the key features of eukaryotes
  • Can be grown easily and can be plated on plates, screened for mutations (like bacteria)
  • 90 minutes to complete cell cycle
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7
Q

Why Saccharomyces cerevisiae is easy to screen for mutation?

A

Because there is only one copy of the gene, there is no need to generate a homozygous state

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8
Q

What are the major contributions made with Saccharomyces cerevisiae?

A
  • Identification of cell cycle genes
  • Mechanisms of recombination
  • Studies on gene interactions
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9
Q

Give an example in which Saccharomyces cerevisiae is used

A

Synthetic gene lethality

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10
Q

What is Caenorhabditis elegans and its characteristics?

A

It is a little worm in the phylum of Nematode

Characteristics:

  • Transparent –> helps trace defined number of cells and cell fate
  • Can be frozen and taken out like bacteria
  • Can feed on E. coli
  • Can be grown in plates
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11
Q

What are the major contributions made with C. elegans?

A
  • Excellent model for development
  • Study of programmed cell death
  • RNA interference
  • Role of microRNAs in development
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12
Q

Give an example in which C. elegans is used

A

Complete cell lineage map of C. elegans nervous system

(allows study on development)

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13
Q

What is Drosophila melanogaster and its characteristics?

A

It is a fruit fly

Characteristics:

  • Easy to rear in the lab
  • Easy to obtain
  • Short life cycle (10 days)
  • Easy to do crosses
  • Large collection of mutants
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14
Q

What are the major contributions made with Drosophila melanogaster?

A
  • 70% of cancer genes have Drosophila counterparts
  • Fundamental aspects of development
  • Discovery of HOX genes
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15
Q

What is Danio rerio and its characteristics?

A

It is a zebrafish

Characteristics:

  • Transparent embryos
  • External fertilization
  • Relatively easy to breed
  • Completes generation in 5-6 months
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16
Q

What are the major contributions made with Danio rerio?

A
  • Development of the eye, pigment cells and embryos
  • Model for some of the human diseases (neuroal disorders)
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17
Q

What is Mus musculus and its characteristics?

A

It is a mouse

Characteristics:

  • Remarkable genetic similarity with humans
  • Models for human diseases
  • Genome sequences are available
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18
Q

What are the major contributions made with mouse?

A
  • Genetic basis of skin colour
  • Testing carcinogens (Ames test)
  • Model for mammalian development
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19
Q

What is Arabidopsis thaliana and its characteristics?

A

It is a flowering plant

Characteristics:

  • Small
  • Easy to grow
  • Short life cycle (5 weeks)
  • Seeds can be collected and stored
  • Complete genome sequence
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20
Q

What are the major contributions made with Arabidopsis thaliana?

A
  • Identification of developmental genes
  • For genome architecture and evolution
  • Plant physiology, environmental effects
  • Population genetics
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21
Q

Genetic analysis is often classified into:

A

Forwand genetic and reverse genetic analysis

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22
Q

What is forward genetic analysis?

A

A mutant is isolated based on a phenotype, and the gene that carries the mutation is identified by mapping

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23
Q

What is reverse genetic analysis?

A

Identify all the genes that are present (genome sequencing) and find out what the genes are actually doing

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24
Q

What is EMS and its function?

A

Ethyl methanesulfonate alkylates guanine which makes the mutated guanine paired up with thymine;

thus at the next round of gene replication, thymine is paired with adenine (point mutation)

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25
Q

How is EMS used?

A
  • Feed flies and worms with EMS/Treat seeds with EMS
  • Analyse the phenotypes in the M2 generation
  • In 1st generation, mutation is generated, but in heterozygous state (only dominant mutations can be detected in M1)
  • In 2nd generation, mutation will segregate into homozygous state and recessive phenotypes can be identified
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26
Q

What are temperature-sensitive allels (ts)?

A

Conditional mutants produced by chemical mutagenesis, which only show the mutant phenotype at the restrictive temperature, and not at the permissive temp.

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27
Q

What is complementation test?

A

Test for allelism

-When two independently isolated mutants (A1A1 and A2A2) display the same phenotype, it finds out whether this is due to mutations in the same gene or due to mutations in different genes

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28
Q

What results do complementation test give?

A
  • If the F1 heterozygotes between the two mutants show the same mutant phenotype (A1A2 = A1A1 = A2A2), the mutations are said to be allelic, i.e. the mutants are not able to complement each other (on same gene)
  • If F1 is wild type, the mutations are in different genes
  • If two mutants are able to complement each other, they are on separate genes
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29
Q

What is epistasis?

A

Phenomenon where the effect of one gene is dependent on the presence of one or more ‘modifier genes’

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30
Q

How is one mutation epistatic to the other mutation?

A

If two different mutants are crossed and the phenotype of the double mutant resembles the phenotype of only one of the mutants

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31
Q

What is additive genetic interaction?

A

When the effects of two mutation are visible in double mutant, which means that the two genes are acting in mutually independent genetic pathways controlling the same phenotype

32
Q

What is suppressor screen?

A

It identifies suppressor mutations which alleviate or revert the phenotype of the original mutation

33
Q

What is enhancer screen?

A

It identifies mutations which exacerbate (or enhance) a phenotype of interest in an already mutant individual

34
Q

What would the F2 ratio between two linked genes (do not assort independently)?

A

Number of recombinants are much less than the expected

35
Q

What process produce recombinant chromosomes?

A

Crossing over

36
Q

What is the maximum frequency of recombination between linked genes?

A

Frequency of recombination between two genes linked on the same chromosome cannot be higher than 50%

-50% = 1:1 = independent assortment = no linkage

37
Q

Recombination rate can be used to:

A

Generate genetic map

e.g. 18% of recombinants = distance between two gene is 18 map units or 18 centimorgans

38
Q

What are genetic markers?

A

Effective reference points to illustrate relative positions in the genome

39
Q

What do molecular markers represent?

A

Differences in the DNA sequences of the two strains used in the crosses to generate F2

40
Q

Give examples of molecular markers (x3)

A
  1. Microsatellite markers
  2. Simple Sequence Length Polymorphism (SSLP)
  3. Variable Number of Tandem Repeats (VNTR)
41
Q

Why repeating sequences can be used as markers?

A

Because repeating sequences often vary between individuals, the variable region is analysed using polymerase chain reaction (PCR)

42
Q

What is genetic linkage?

A

Deviation from the law of independent assortment

43
Q

How is the distance between two linked loci related to the recombination rate?

A

The further apart the two linked loci are, the higher the recombination rate is

44
Q

What is mapping population?

A

F2 or backcross population that is required for recombination mapping

45
Q

What is association mapping?

A

It relies on population history and a history of blocks of inherited alleles linked in cis

46
Q

When is association mapping used?

A

It is used when you want to map genes but you do not have mapping population

47
Q

What fact does association mapping rely on?

A

The alleles of linked genes are likely to be inherited in a linkage block due to population history

48
Q

What is quantitative or simple trait?

A

Trait that shows simple inheritance patterns, in which distribution of phenotype is in classes

49
Q

What is qualitative or complex trait?

A
  • Trait that shows complex inheritance patterns, in which distribution of phenotype is continuous
  • Trait that is affected by many genes and environment
50
Q

How many genes control quantitative trait?

A

1/4n

51
Q

What does this equation mean?

T = μ + g + e

A

T = value of a quantitative trait

μ = population mean

g = deviation from mean due to genetic factors

e = deviation from mean due to environmental factors

52
Q

What does this equation mean?

VT = Vg + Ve

A

VT = total phenotypic variance

Vg = genetic variance

Ve = environmental variance

53
Q

How can Ve, environmental variance, be estimated mathematically?

A

It can be estimated from parental and F1 populations, which are genetically uniform and inbred

Ve = (VA + VB + VF) / 3

VA and VB = two parental populations

VF = F1 population

54
Q

What is broad-sense heritability (H2)?

A

Proportion of the total phenotypic variance that is due to genetic differences among individuals in a population

H2 = Vg / VT

H2 = Vg / (Vg + Ve)

55
Q

What does the value of broad-sense heritability (H2) tell us?

A

If H2 is close to 0, then little to no variability in the population is due to genetic differences among individuals.

If H2 is close to 1, most of the variability in the population is due to genetic differences

56
Q

Will different populations have different broad-sense heritability?

A

Yes because broad-sense heritability is population-specific

57
Q

What are the genetic factors of genetic variance?

A
  1. Effects of individuals alleles
  2. Dominance relationships between alleles
  3. Epistatic interactions between different genes
58
Q

Which genetic factor of the genetic variance can help predict the phenotypes of offspring from the phenotypes of their parent?

A

Effects of individual alleles

59
Q

What are the components of genetic variance?

A
  • Va additive genetic variance = variance due to alleles that act additively
  • Vd dominance variance = variance due to dominance effects at loci contributing to a quantitative trait
  • Vi epistatic variance = variance due to epistatic interactions between (alleles of) different genes
60
Q

What is the equation of genetic variance, Vg?

A

Vg = Va + Vd + Vi

(VT = Va + Vd + Vi + Ve)

61
Q

What is narrow-sense heritability, h2?

A

Proportion of the total phenotypic variance that is due to the additive genetic variance

62
Q

What is the equation of narrow-sense heriability, h2?

A

h2 = Va / VT

63
Q

What does the value of narrow-sense heritability, h2, tell us?

A

If h2 is close to 1, then most of the total phenotypic variance is due to additive genetic variance

64
Q

What is midparent value, TP?

A

Average of the trait values of father and mother

TP = (TM + TF) / 2

65
Q

What is the equation for predicting the outcome of offspring?

A

TO = μ + h2 (TS - μ)

TO = mean of offspring

μ = mean of population

TS = mean of the selected parents

h2 = narrow-sense heritability

66
Q

What is selection differential, S?

A

Difference between the mean of the selected parents and the mean of the population, (TS - μ)

67
Q

What is the response to selection, R?

A

Measurement of how much the mean has changed in one generation, (TO - μ)

68
Q

What is the equation for evoultionary response?

A

R = h2S

69
Q

What is a locus?

A

A gene’s position in a chromosome

70
Q

What is a quantitative trait locus, QTL?

A

The locus for a gene that affects a quantitative trait

71
Q

What technique can be used to map locus for a gene that affects a simple trait?

A

Co-segregation of the mutant phenotype with the genotype

72
Q

How to map QTL?

A

Calculate whether allelic variation is significantly associated with phenotypic variation

73
Q

What is the process of identifying QTLs that affect tomato fruit weight?

A
74
Q

Which RFLP locus is linked to a QTL that affects fruit weight?

A

TG167 RFLP locus on chromosome 2, is linked to a QTL that affects fruit weight

75
Q

What is genome-wide association study (GWAS)?

A

It uses SNPs to track predisposition to disease and other genetic traits

76
Q

In GWAS, can the causative polymorphism be captured definitely?

A

The causative polymorphism may not actually be captured as many SNPs are used (many SNPs may be in linkage blocks)

77
Q

What is the Wellcome Trust Case Control Consortium?

A

Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls

BIOL2202 Genetics (6 decks)

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