markers and forensic genetics - lecture 18 Flashcards
What is a genetic marker?
Some feature in the genome that allows us to differentiate between different alleles
When are genetic markers useful?
- provide information on genetic differences between individuals
- measures diversity
what are copy number variations?
Duplicated areas. Therefore the markers are difficult to detect
what are the 4 markers we will be focusing on?
- RFLP(restriction fragment length polymorphism)
- SSLP ( simple sequence length polymorphism)
- SNP ( single nucleotide polymorphism)
- DNA sequencing
What is the allozyme technique which was used before DNA technology?
- allelic variants of enzymes
- These enzymes differ in electric charge and migrate differently though the gel
- detected with a stain
What are RFLPs?
Restriction fragment length polymorphisms
How is the RFLP marker formed?
DNA cut into fragments by using restriction enzymes.
How is RFLP a good marker?
The fragments differ in length due to the differences in the DNA repeats
What does a VNTR stand for when using RFLP?
Variable Number of Tandem Repeats
What are the two evolutionary traits that can be detected when using RFLPs?
- changes in number of VNTR units
- mutation in restriction site (no longer recognised by enzyme)
When is RFLP used?
Crime scene forensics and paternity testing
What does RADseq stand for?
‘Reduced representation sequencing’
How does RADseq work?
- Use restriction enzymes to get out a piece of DNA sequence
- Sequence
- sequence the individuals and compare
How are ‘simple sequence repeats’ good markers?
Highly polymorphic (highly variable) – reflects very high mutation rates
• Can distinguish many alleles at a locus
- Amplify the region using PCR
What are SNP markers?
- single base differences between alleles at genomic location
How to identify SNP markers?
Sequence the region
what is a haplotype?
A small chromosomal block that is inherited
what is a genealogy
a line of descent traced from an ancestor
What do SNPs do in a genealogy?
differentiate in the genealogy due to haplotypes
What are 3 reasons that mitochondrial markers are important?
- no recombination , so each sequence represents the end point of a lineage
- haploid
- sequences are highly variable
Where can genetic markers been seen to be used prevalently?
- chilean sea bass ( Dissostichus eleginodies)
- Red snapper ( lutjanus campechanus)
- pacific red snapper
- whale meat in Japan
Problems with chilean sae bass after genetic research?
8% are another species, 15% has forge in haplotypes.
Problems with red snapper?
77% of samples in USA were not actually , genetically red snapper
problems with whale meat in Japan?
- some gray whale killed ( very endangered)
- found eight species: baleen whales, sperm whales, beaked whales, killer whales, dolphins, porpoises, plus sheep and horses.
problems with pacific red snapper?
mitochondrial markers determined that 56% are actually species listed as being overfished
Why can RFLP work?
Each person has a different length of Variable Number Tandem Repeats
How can RADseq help identify mutations?
Should also identify mutations in cut sites by the absence of a sequence
