Molecular Markers

Question 1

Major advantages of molecular markers against morphological markers

Answer 1

1. practically unlimited in number
2. not affected by the environment and developmental stage
3. selectively neutral

Question 2

6 types of molecular markers

Answer 2

1. restriction fragment length polymorphism (RFLP)
2. random amplified DNA polymorphism (RAPD)
3. amplified fragment length polymorphism (AFLP)
4. simple sequence repeats (SSR)
5. variable number tandem repeats (VNTR)
6. single nucleotide polymorphism (SNP)

Question 3

involves restriction enzyme and hybridization, and variation is caused by differences in the fragment sizes

Answer 3

RFLP

Question 4

A and D of RFLP

Answer 4

A:
robust
reliable
transferable

D:
laborious, time-consuming, expensive
requiring large amounts of DNA
limited polymorphism

Question 5

CAPS

Answer 5

cleaved amplified polymorphic sequences

Question 6

C or D: RFLP

Answer 6

codominant

Question 7

PCR-based marker that uses short oligonucleotide primers

Answer 7

RAPD

Question 8

C or D: RAPD

Answer 8

dominant

Question 9

A and D of RAPD

Answer 9

A:
quick and simple
inexpensive
multiple loci
requiring small amounts of DNA

D:
problem with reproducibility
not transferable across populations

Question 10

combination of RE digestion and PCR

Answer 10

AFLP

Question 11

AFLP steps

Answer 11

RE digestion of the genomic DNA
ligation with restriction half-site-specific adapters
selective amplification
electrophoresis
visualization

Question 12

C or D: AFLP

Answer 12

dominant

Question 13

A and D of AFLP

Answer 13

A:
multiple loci
high polymorphism

D:
requiring large amount of DNA
complicated methodology

Question 14

consists of short nucleotide tandem repeats

Answer 14

SSR

Question 15

C or D: SSR

Answer 15

codominant

Question 16

Why use the tandem repeats?

Answer 16

Because flanking the tandem repeats are conserved regions of DNA across genera (even families) which allows for the development of locus-specific microsatellite primers

Question 17

A and D of SSR

Answer 17

A:
technically simple
robust and reliable
transferable

D:
laborious in primer design
requires PAGE

Question 18

consists of short nucleotide sequences (15-100) present in tandem repeat arrays

Answer 18

VNTR

Question 19

Differentiate SNP and point mutation

Answer 19

a variation is considered a SNP if it occurs at at least 1% of the population, whereas mutations are very rare around 10^-5 to 10^-6.

Question 20

Define GWAS

Answer 20

genome-wide associate studies is used in identifying genes or genomic variants associated with a trait (e.g., a disease) by searching for small variation (SNP) across the DNA of a large group of individuals