M1 L5

Question 1

PCR-RFLP

Answer 1

restriction enzymes recognize specific sequence in DNA & cut at that site
- if there is a mutation within cut site = Eco R1 does not recognize it = no cut site

Question 2

PCR-RFLP typically use what kind of sequences

Answer 2

palindromic

Question 3

leptin

Answer 3

obese gene

Question 4

how many alleles does sequencing always use

Answer 4

2

Question 5

disadvantage of sequencing

Answer 5

very expensive
slow if need to sequence lots of animals

Question 6

what do SNPs identify?

Answer 6

alleles

Question 7

KASP

Answer 7

uses fluoresence technology to do allele specific PCR to find out genotype
- uses common reverse prime but has 2 diff forward primers
- amount of fluorescence from each colour is plotted on a graph

Question 8

KASP colours (3)

Answer 8

FAM= blue (only A)
HEX = red (only C)
FAM + HEX = AC heterozygote

Question 9

SNP array

Answer 9

used to genotype many SNPs in 1 individual
- microbeads are attached to short probe that is complementary to DNA sequence
- probe will stop right before SNP position & bring in fluorescence colour for whatever the next allele is

Question 10

GWAS

Answer 10

looks for association between SNP & trait of interest

Question 11

what is the go to method for sequencing

Answer 11

SNP array

Question 12

manhattan plot

Answer 12

height of peak shows stronger association
- could be SNP in coding or non-coding region but do not know what chromosome it is on

Question 13

microsatellite markers

Answer 13

expansion contraction polymorphism
- repeated sequences of microsatellites that use siz to associate with a specific allele

Question 14

T or F: mistakes made by polymerase are kept but do not cause a large effect

Answer 14

T

Question 15

if a 3rd repeat is added to microsatellite marker, how many bp longer is it?

Answer 15

2

Question 16

advantages & disadvantages of microsatellite markers

Answer 16

A: more alleles, easy to compare (do not need all on 1 gel) easy to PCR

D: not as abundant as SNPs, will not be causative mutation so need to look further

Question 17

T or F: microsatellite markers are found in all eukaryotes

Answer 17

T

Question 18

PIC

Answer 18

polymorphic info content
- value used to measure informativeness of a genetic marker for linkage studies

Question 19

why do microsatellites have higher PICs than SNPs?

Answer 19

bc they have a larger number of alleles

Question 20

PIC values for SNP vs microsatellite

Answer 20

SNP: 0.2-0.5
microsatellites: 0.5-0.90

Question 21

3 technologies used to map traits - why?

Answer 21

mapping, individual identification, paternity diagnosis & marker assisted selection
- they all have high PIC

Question 22

parentage testing

Answer 22

can only exclude a sire, not determine with 100% accuracy
- harder if sire is related

Question 23

marker assisted selection

Answer 23

uses markers, linkage & mapping together to select for a trait
- use marker to select for a trait if we know that marker is linked to the trait

Question 24

T or F: marker assisted selection is used in both animals and humans

Answer 24

F - only animals

Question 25

3 rules to marker assisted selection

Answer 25

1) must be linked to trait (don’t know gene)
2) use DNA or RNA
3) polymorphic trait

Question 26

a stronger linkage between marker & trait =

Answer 26

less chance of recombination = the goal

Question 27

why is MAS beneficial (2)

Answer 27

can be used when traits are difficult & expensive to measure (fertility/lowly heritable traits)

Question 28

genomic markers are associated with ( ), not ( )

Answer 28

QLTs, single markers

Question 29

T or F: there is always a possibility of recombination with linkage

Answer 29

T

Question 30

advantages & disadvantages of MAS

Answer 30

A: faster selection process (select animals before developmental stage if have a linked marker), ideal for traits with low heritability, can test for trait if have DNA, can examine traits that can only be measured after selection has occured

D: hitch hiking of undesired trait if linked to that marker, need a larger population to establish marker is present in all populations, does not look at mutation, just uses something near the mutation -> better to have actual mutation for selection

Question 31

T or F: if allele #s are closer together = less chance of recombination

Answer 31

T

Question 32

LOD score

Answer 32

compares likelyhood for linkage vs non-linkage

Question 33

what LOD score proves linkage?

Answer 33

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