Molecular Genetics (Keith Edwards 5-12) Flashcards
What is a molecular marker?
a fragment of DNA associated with a locus. They occur randomly within the genome and can be used for genotyping studies. A good marker can distinguish homozygotes from heterozygotes.
Microsatellites are molecular markers, but what are they?
Also known as SSRs and STSSRs.
Very simple, repetitive sequences (e.g. CACACACACACACACACACACA)
Why are errors common in microsatellites?
DNA polymerase finds it difficult to remember its position along the chain, its like if we were to count the stripes of a very long zebra crossing! They show diversity across every chromosome. SSRs can recognise multiple, different alleles.
How were molecular markers useful when looking at multiple mating in army ants? Paper: Denny et al. (2004).
used microsatellites to see how many drones a queen bred with by examing progeny. Found exceptionally high levels of multiple mating.
What is an SNP?
SNPs- Single Nucleotide Polymorphisms.
Don’t affect cell function.
most common type of variation- highly abundant.
analysis can be automated.
What is a probe?
single-stranded DNA, complementary to the target DNA.
Why are probes great for identifying genetic markers?
- They can be designed for known sequences (Mutants and Wild types)
- They can fluorescently be labelled.
- Allele-specific Oligonucleotide probes can be read by machines (binary- it hybridises or it doesn’t)
- Can use multiple probes for different genes at the same time in a MULTIPLEX assay.
Note: Axiom high density genotyping array
-13 million data points!
In the paper: SNPs in ecological and conservation studies: a test in the Scandinavian wolf population (2005), how were SNPs used?
SNP analysis inferred a strong bottleneck in the recolonisation of wolves in Sweden and Norway.
they were able to individually identify wolves and their relatives, but this was restricted due to their low genetic diversity from a bottleneck.
What did Karl Landsteiner discover in 1901?
He discovered the blood groups and developed blood typing, using antigens, which became a great forensic tool.
What was discovered by chance by Alec Jeffreys?
DNA fingerprinting
sequences he found by chance are longer than microsatellites so are called minisatellite instead. These sequences are highly polymorphic and inherited by offspring. Useful because it can be looked at like a barcode, but requires lots of DNA (N.B. PCR).
What advantages are there to blood typing over the more developed DNA fingerprinting technique?
- Much less DNA is needed
- faster
- degraded samples can still be used
Why do we tend to not use blood typing as much?
It is not necessarily sensitive enough.
When would we use Whole Genome Amplification? (WGA)
Used a lot in environmental genomics.
test for the presence of a species that hasn’t been seen, can’t be cultured or one that we don’t know if it exists.
What three areas of animal and plant breeding uses molecular markers?
Clonal identity
Marker-assisted Selection (MAS)
Genome Selection
What is DUS testing?
In clonal identification, it stands for distinctness, uniformity and stability testing. For anything to be a new variety, it must be stable across generations, be distinctively different from other varieties and share uniform characteristics with that of the same variety.
Clonal identity is about identifying species and varieties, what process can be used to see if a product has been genetically modified?
GMOs can be identified by DNA fingerprinting.
What is MAS?
Marker-assisted selection is often used in farming. DNA markers may be tightly-linked to specific loci, so these markers may reliably predict phenotypes. Markers that tag a gene (e.g. resistance to a pathogen) can be looked for in progeny. This is good for plant breeding as homozygotes can be selected for.
Advantages of MAS over phenotypic selection?
- Simpler and saves resources
- selection at seedling age saves time
- more reliable.
Why is it difficult to predict an offspring’s blood pressure when looking at the parents?
BP is polygenic and influenced by the environment.
2009 study said BP is controlled by 29 loci, but realistically it’s probably more like 50-100 loci!
In MAS, why do markers have to be close (<5cM) to the gene?
To remain linked after recombination. Using a pair of flanking markers can greatly improve reliability.
Note: cM = Centimorgan
How are markers useful for Genomic Selection?
complex traits can’t be tracked by a single marker. Compare the associated markers known to a trait from a control population and apply it to the test population.
E.g. these cows, which produce lots of milk, have more of these certain markers. Can then genotype the unknown population using these markers.
When is genomic selection using molecular markers useful?
- for traits with low heritability.
- for traits which are difficult to measure
- disease susceptibility and resistance traits
- Traits that take a lifetime to measure
What was the first species of Homo?
Homo habilis - evolved in Africa 2mya
Which important lineage decided from habilis?
H.erectus!
Which species gave rise to Homo sapiens?
Homo erectus gave rise to H.sapiens 100,000-200,000ya
Note: H.neanderthalensis may be an intermediate but was probably a coexisting species
Briefly, describe the 2 theories for homo migration
The Out of Africa Theory:
- H.erectus evolved into H.sapiens in Africa and then dispersed worldwide.
- Sapiens had a single origin, wiping out what was before
The Multi-regional Theory:
-H.erectus left Africa and evolved into sapiens in 7 different locations around the world.
What is ‘mitochondrial eve’?
In mtDNA studies, a phylogenetic tree suggests a mitochondrial eve. It is a concept where a group of females or one female, had a particular haplotype which gave rise to the rest of human kind - around 171,500ya.
In studying the Y chromosome, what is thought to be the ‘eve’?
Haplotype A
In studying the Y chromosome, what is deemed the Genghis Khan haplotype?
Haplotype C, because he is thought to of had 1000s of babies.
Which of the 2 theories about Homo migration is supported by molecular markers?
the Out of Africa Theory.
Groups of people can be traced back to see their ‘closeness’ (e.g. Japanese and Chinese).
It is thought that H.sapiens and H.neandarlensis interbred at some point (evident from molecular markers), but why don’t we carry neanderthal DNA?
- It may have lead to sterile offspring
- It may have been involved with the Y chromosome. Differences in immunity genes have been found on the Y chromosome which could have lead to miscarriages. (Fernando Mendez, 2016).
Why is Neanderthal DNA found in 1-4% of Eurasian humans, but not those of African descent?
H.neanderthalensis never lived there.
Discuss the question ‘Are we still evolving?’
- CCR5 ( a chemokine receptor) is a protein found on white blood cells. CCR5 is utilised by viruses that cause AIDS to enter and infect cells.
- Some individuals that are protected from HIV have a mutant CCR5-Δ32. High frequency and wide distribution of the CCR5-Δ32 allele suggest it was selected for in the past (before HIV), it is most frequent in northern Europe but low in Africa and Asia.
- In 1665 the bubonic plague hit the small town of Eyam, who quarantined themselves. The only survivors were those carrying the CCR5-Δ32 mutation.
Some companies can analyse your genetic information (using SNPs), why might this be useful for health services?
- disease risk
- carrier status
- responses to drugs (could save money)
e. g. 7-10% of women with breast cancer can’t activate the drug Tamoxifen. - can target treatments
