L10

Question 1

what is the advantage of PCR based markers

Answer 1

markers based on PCR are faster, cheaper, and automatable

Question 2

true or false, PCR can amplify only DNA with primer on it

Answer 2

true

Question 3

what are the characteristics of PCR

Answer 3

• simple, cheap, fast, automatable
• amplification in vitro of small DNA region (1 kb of 3M)
• sequence of primers (20-25 bp) define target region, need 2 primers facing each other
• exponential process- product doubles per cycle
• fragment amplified can be up to 2 kb (20-30 possible)
• extremely sensitive: small starting sample needed
• uses thermostable polymerase

Question 4

true or false, primers only work across very closely related species

Answer 4

true

Question 5

true or false, primers > 20 bases typically bind to one site per genome

Answer 5

true

Question 6

true or false, PCR replaced southern blots, partly replaced library construction to clone genes, replaced cloning to get templates for sequencing, means of manipulating DNA

Answer 6

true

Question 7

true or false PCR partly replaced plasmid DNA preps to analyze cloned inserts

Answer 7

true

Question 8

true or false, PCR extension requires exact match at the 3’ end of the primer but not at the 5’ end, they are tolerated readily

Answer 8

true

Question 9

what are the types of microsatellites

Answer 9

SSR
SSLP
STR

Question 10

microsatellite properties

Answer 10

• tandem repeats of 1-6 nucleotides
• interspersed frequently throughout the genome
• highly polymorphic between individuals

Question 11

define polymorphic

Answer 11

multiple forms of a single gene that can exist in an individual or among groups of individuals

Question 12

true or false, microsatellites are very polymorphic

Answer 12

true

Question 13

what are SNPs

Answer 13

single nucleotide polymorphisms

Question 14

true or false, SNPs 1 base different per 1200 bp for any tw human chromosomes, these markers are capable of the most dense genetic map

Answer 14

true

Question 15

true or false, SNPs offer potential for extremely high throughput

Answer 15

true

Question 16

true or false, SNPs are less polymorphic than microsatellites, max 4 alleles per site, usually only 2 common, thus much lower information content per SNP than per microsatellite

Answer 16

true

Question 17

true or false, need to know location and sequence of many variants within species in advance,

Answer 17

true

Question 18

what are the two methods which are used to analyze SNP

Answer 18

1. ) each feature is a 25 mer oligonucleotide synthesized in situ, make four oligonucleotides per SNP, identical except with G,C,T or A in the central position of 25 mer, fluorescent labeled probes can be made from whole genome DNA or amplified subsets of DNA and hybridized to array, fluorescence per feature measured by laser microscopy
2. ) isolate genomic DNA, anneal oligos adjacent to SNPs, add 4 fluorescently labelled dideoxynucleotides + polymerase to copy next base, denature, anneal to microarray containing the complementary oligos, score to color to read SNP at each site