Jordans Notes 13

Question 1

What increases the mutation rate of microsatellite
loci?

Answer 1

The higher the number of repeat units, the greater the chance of slippage

Question 2

What is multiplexing for microsatellite analysis?

Answer 2

pooling multiple different loci in a single reaction to save money

Question 3

How are individual loci recognised during
multiplexing?

Answer 3

fluorescent tags

Question 4

If different microsatellite loci have large differences
in fragment size, what process should be done?

Answer 4

multiplexing should be done after PCR to give each loci a good chance to be amplified

Question 5

How are microsatellite alleles determined in
Geneious?

Answer 5

fluorescent peaks compared to size standard

Question 6

what can be mistaken as an allele in microsatellite
analysis?

Answer 6

stutter may look like a peak

tallest peak is the true allele!

Question 7

What will the microsatellite peaks look like in a
heterozygote?

Answer 7

The shortest length allele will have the tallest peak

Question 8

What are the 6 issues with microsatellite analysis?

Answer 8

1. Only 5 different fluorescent tag colors (need 8-20 loci)
2. Allelic drop out
3. null alleles
4. stutter calling
5. homoplasy
6. species specific (usually)

Question 9

How to get around the shortage of fluorescent tag
colors in microsatellite analysis

Answer 9

can assign the same tag color to different loci as long as they don’t have overlapping potential allele sizes

Question 10

What is allelic dropout

Answer 10

Where the PCR fails to amplify some alleles due to multiplexing issues or low DNA