Jordans Notes 14

Question 1

what is the biggest consequence of allelic drop out
and null alleles?

Answer 1

calling an individual as homozygous but it is actually heterozygous but one allele wasn’t amplified

false parentage determination etc.

Question 2

What is homoplasy in microsatellites?

Answer 2

where two different individuals have what appears to be the same allele but it may have mutated to be the same length separately

doesn’t necessarily indicate relatedness

Question 3

What is different between sequence level analysis
of genotyping vs sequencing?

Answer 3

sequencing looks at the entire sequence produced
genotyping only looks at single nucleotide substitutions (variants)

Question 4

what is association mapping?

Answer 4

determining whether a genetic variant is associated with a certain trait or disease

Question 5

What 3 types of studies can SNP genotyping be
used for

Answer 5

1. Association mapping (traits)
2. population genetics (including parentage)
3. Evolution/adaptation

Question 6

What does GBS stand for?

Answer 6

Genotyping by sequencing

Question 7

What does RADseq stand for?

Answer 7

Restriction-site-Associated DNA sequencing

Question 8

What does ddRAD stand for?

Answer 8

double digest Restriction-site-Associated DNA sequencing

Question 9

what does using a restriction enzyme digest
achieve?

Answer 9

reduces the genome of all individuals to the same subset

Question 10

What are the 5 steps of GBS?

Answer 10

1. Restriction enzyme digest (reduce genome complexity)
2. Adapters ligate to “sticky ends”
3. PCR amplifies restricted fragments
4. Fragments sequenced by Illumina HiSeq
5. SNPs discovery

Question 11

What do the sticky ends created during restriction
enzyme digest allow?

Answer 11

The ligation of adapters

Question 12

What are the two types of adapters for SNP
genotyping?

Answer 12

barcode adapter and common adapters

Question 13

What are the barcoding adapters for in SNP
genotyping?

Answer 13

sample identification (allows multiplexing)

Question 14

What are the 4 steps of SNP discovery?

Answer 14

1. raw sequences read to select highest quality reads
2. Demultiplexing using barcode adapters
3. high quality reads aligned
4. alignments scanned to find SNPs

Question 15

What are the 8 steps of RADseq?

Answer 15

1. digest
2. ligate first adapters
3. pool DNA and shear randomly
4. ligate second adapters
5. Size select 300bp
6. PCR fragments
7. Sequence with MiSeq
8. SNP discovery

Question 16

What is demultiplexing?

Answer 16

separating different samples from a pooled product using barcode adapters

Question 17

What are three pros of reduced representation
sequencing?

Answer 17

1. greater depth of coverage at restricted loci
2. greater number of samples for the same budget
3. doesn’t require a reference genome

Question 18

4 cons of reduced representation sequencing?

Answer 18

1. large genome=low depth of coverage
2. creating DNA library is expensive
3. association mapping require annotated reference genome
4. needs very high quality DNA

Question 19

Why are SNPs more useful than microsatellites?

Answer 19

more loci examined increases accuracy despite lower variation between alleles
SNPs are usually in coding regions so can determine genomic regions of natural
selection

Question 20

What is used to determine the contribution of a
SNP to a continuous trait?

Answer 20

Quantitative Trait Loci Mapping