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.
