Module 4--Genetic Analysis of Simple & Complex Traits Flashcards
What is a model organism?
A species with morphology/physiology/genetics/ecology/ suitable for your field of inquiry
What is a good model organism?
- 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
What are the contributions made by E. coli?
- Elucidation of universal genetic code
- Spontaneous nature of mutations
- Mechanisms of DNA replication, transcription, translation and gene regulation
What is CRISPR?
Clustered Regularly Interspaced Short Palindromic Repeats
What is the CRISPR-Cas9 and its application?
A DNA editing technique that has been engineered into many eukaryotic model and non-model organisms to induce specific DNA mutation
What is Saccharomyces cerevisiae and its characteristics?
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
Why Saccharomyces cerevisiae is easy to screen for mutation?
Because there is only one copy of the gene, there is no need to generate a homozygous state
What are the major contributions made with Saccharomyces cerevisiae?
- Identification of cell cycle genes
- Mechanisms of recombination
- Studies on gene interactions
Give an example in which Saccharomyces cerevisiae is used
Synthetic gene lethality
What is Caenorhabditis elegans and its characteristics?
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
What are the major contributions made with C. elegans?
- Excellent model for development
- Study of programmed cell death
- RNA interference
- Role of microRNAs in development
Give an example in which C. elegans is used
Complete cell lineage map of C. elegans nervous system
(allows study on development)
What is Drosophila melanogaster and its characteristics?
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
What are the major contributions made with Drosophila melanogaster?
- 70% of cancer genes have Drosophila counterparts
- Fundamental aspects of development
- Discovery of HOX genes
What is Danio rerio and its characteristics?
It is a zebrafish
Characteristics:
- Transparent embryos
- External fertilization
- Relatively easy to breed
- Completes generation in 5-6 months
What are the major contributions made with Danio rerio?
- Development of the eye, pigment cells and embryos
- Model for some of the human diseases (neuroal disorders)
What is Mus musculus and its characteristics?
It is a mouse
Characteristics:
- Remarkable genetic similarity with humans
- Models for human diseases
- Genome sequences are available
What are the major contributions made with mouse?
- Genetic basis of skin colour
- Testing carcinogens (Ames test)
- Model for mammalian development
What is Arabidopsis thaliana and its characteristics?
It is a flowering plant
Characteristics:
- Small
- Easy to grow
- Short life cycle (5 weeks)
- Seeds can be collected and stored
- Complete genome sequence
What are the major contributions made with Arabidopsis thaliana?
- Identification of developmental genes
- For genome architecture and evolution
- Plant physiology, environmental effects
- Population genetics
Genetic analysis is often classified into:
Forwand genetic and reverse genetic analysis
What is forward genetic analysis?
A mutant is isolated based on a phenotype, and the gene that carries the mutation is identified by mapping
What is reverse genetic analysis?
Identify all the genes that are present (genome sequencing) and find out what the genes are actually doing
What is EMS and its function?
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)
How is EMS used?
- 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
What are temperature-sensitive allels (ts)?
Conditional mutants produced by chemical mutagenesis, which only show the mutant phenotype at the restrictive temperature, and not at the permissive temp.
What is complementation test?
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
What results do complementation test give?
- 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
What is epistasis?
Phenomenon where the effect of one gene is dependent on the presence of one or more ‘modifier genes’
How is one mutation epistatic to the other mutation?
If two different mutants are crossed and the phenotype of the double mutant resembles the phenotype of only one of the mutants
What is additive genetic interaction?
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
What is suppressor screen?
It identifies suppressor mutations which alleviate or revert the phenotype of the original mutation
What is enhancer screen?
It identifies mutations which exacerbate (or enhance) a phenotype of interest in an already mutant individual
What would the F2 ratio between two linked genes (do not assort independently)?
Number of recombinants are much less than the expected
What process produce recombinant chromosomes?
Crossing over
What is the maximum frequency of recombination between linked genes?
Frequency of recombination between two genes linked on the same chromosome cannot be higher than 50%
-50% = 1:1 = independent assortment = no linkage
Recombination rate can be used to:
Generate genetic map
e.g. 18% of recombinants = distance between two gene is 18 map units or 18 centimorgans
What are genetic markers?
Effective reference points to illustrate relative positions in the genome
What do molecular markers represent?
Differences in the DNA sequences of the two strains used in the crosses to generate F2
Give examples of molecular markers (x3)
- Microsatellite markers
- Simple Sequence Length Polymorphism (SSLP)
- Variable Number of Tandem Repeats (VNTR)
Why repeating sequences can be used as markers?
Because repeating sequences often vary between individuals, the variable region is analysed using polymerase chain reaction (PCR)
What is genetic linkage?
Deviation from the law of independent assortment
How is the distance between two linked loci related to the recombination rate?
The further apart the two linked loci are, the higher the recombination rate is
What is mapping population?
F2 or backcross population that is required for recombination mapping
What is association mapping?
It relies on population history and a history of blocks of inherited alleles linked in cis
When is association mapping used?
It is used when you want to map genes but you do not have mapping population
What fact does association mapping rely on?
The alleles of linked genes are likely to be inherited in a linkage block due to population history
What is quantitative or simple trait?
Trait that shows simple inheritance patterns, in which distribution of phenotype is in classes
What is qualitative or complex trait?
- Trait that shows complex inheritance patterns, in which distribution of phenotype is continuous
- Trait that is affected by many genes and environment
How many genes control quantitative trait?
1/4n
What does this equation mean?
T = μ + g + e
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
What does this equation mean?
VT = Vg + Ve
VT = total phenotypic variance
Vg = genetic variance
Ve = environmental variance
How can Ve, environmental variance, be estimated mathematically?
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
What is broad-sense heritability (H2)?
Proportion of the total phenotypic variance that is due to genetic differences among individuals in a population
H2 = Vg / VT
H2 = Vg / (Vg + Ve)
What does the value of broad-sense heritability (H2) tell us?
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
Will different populations have different broad-sense heritability?
Yes because broad-sense heritability is population-specific
What are the genetic factors of genetic variance?
- Effects of individuals alleles
- Dominance relationships between alleles
- Epistatic interactions between different genes
Which genetic factor of the genetic variance can help predict the phenotypes of offspring from the phenotypes of their parent?
Effects of individual alleles
What are the components of genetic variance?
- 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
What is the equation of genetic variance, Vg?
Vg = Va + Vd + Vi
(VT = Va + Vd + Vi + Ve)
What is narrow-sense heritability, h2?
Proportion of the total phenotypic variance that is due to the additive genetic variance
What is the equation of narrow-sense heriability, h2?
h2 = Va / VT
What does the value of narrow-sense heritability, h2, tell us?
If h2 is close to 1, then most of the total phenotypic variance is due to additive genetic variance
What is midparent value, TP?
Average of the trait values of father and mother
TP = (TM + TF) / 2
What is the equation for predicting the outcome of offspring?
TO = μ + h2 (TS - μ)
TO = mean of offspring
μ = mean of population
TS = mean of the selected parents
h2 = narrow-sense heritability
What is selection differential, S?
Difference between the mean of the selected parents and the mean of the population, (TS - μ)
What is the response to selection, R?
Measurement of how much the mean has changed in one generation, (TO - μ)
What is the equation for evoultionary response?
R = h2S
What is a locus?
A gene’s position in a chromosome
What is a quantitative trait locus, QTL?
The locus for a gene that affects a quantitative trait
What technique can be used to map locus for a gene that affects a simple trait?
Co-segregation of the mutant phenotype with the genotype
How to map QTL?
Calculate whether allelic variation is significantly associated with phenotypic variation
What is the process of identifying QTLs that affect tomato fruit weight?
Which RFLP locus is linked to a QTL that affects fruit weight?
TG167 RFLP locus on chromosome 2, is linked to a QTL that affects fruit weight
What is genome-wide association study (GWAS)?
It uses SNPs to track predisposition to disease and other genetic traits
In GWAS, can the causative polymorphism be captured definitely?
The causative polymorphism may not actually be captured as many SNPs are used (many SNPs may be in linkage blocks)
What is the Wellcome Trust Case Control Consortium?
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls
