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Bio 361 - Molecular Genome and Genomics > Midterm 1 - Notes 2 (Part 2) > Flashcards

Midterm 1 - Notes 2 (Part 2) Flashcards

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1
Q

What is an example of a genetic marker?

A

Microsatellites

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2
Q

What can microsatellites generate?

A

Genetic maps

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3
Q

How many repetitive motifs in a genomic DNA?

A

10-100 repeats

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4
Q

What can be different between the locus?

A

The number of repeats

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5
Q

What is a typical size of a repeat?

A

2-6 nucleotides

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6
Q

Are microsatellites very abundant?

A

Yes

- they spread through the genome

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7
Q

What are 3 advantages to microsatellites?

A
  1. Very abundant
  2. Unaffected by the environment or development
  3. Easy to detect
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8
Q

What do microsatellites have a high rate of?

A

Mutations

- resulted from a lot of variation

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9
Q

When do most mutations occur?

A

During DNA replication

  • slipped strand misparing
  • mutations add or subtract one repeat unit at a time
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10
Q

What do microsatellites rarely influence?

A

Phenotypes

- they are neutral markers

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11
Q

What happens in uninformed markers?

A

There is no variation

- is only homozygous

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12
Q

What is an informative marker?

A

There is variation

- contains both homozygous and heterozygous

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13
Q

What can a microsatellite inheritance (paternity test) do?

A

It can follow alleles from one generation to another

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14
Q

Why would you need to look at more than one marker when testing for paternity (DNA)?

A

Because it is likely that another man in the population has the same allele

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15
Q

What kind of marker pattern would you expect if the markers are not linked/ not related?

A

2-1-2 segregation pattern

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16
Q

What happens to the recombinant combination as the alleles get further apart?

A

You will get a higher percentage of recombinant combination (and a lower maternal combination)

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17
Q

Cente morgan

A

Is the probability of recombination occurring

- measures genetic distances

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18
Q

Recombinant

A

When you have an A allele in one segment and a B allele in the other segment
- mis-matched pairing

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19
Q

Why do you need many different markers when creating a linkage map?

A

Because if you only have a few all the markers might be on different chromosomes and you will not have any linkages

  • the more markers you have the better the results will be
  • the markers need to be spread out
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20
Q

What happens when the linkage group is 50/50?

A

The linkage will not be included in the linkage map, but it will start a new one

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21
Q

Why was a radioactive (GT)15 probe used?

A

Because CA repeats are very common so it increases the chance of finding a microsatillite
- GT is the complement of CA

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22
Q

What did the radioactive probe allow?

A

It allowed specific stuff to bind to it and light up in order to identify it

23
Q

Polymorphic

A

Are the differences between two organisms

24
Q

What was the genetic map based on?

A

Genotypes

25
Q

What is the reason that markers are not equally distributed?

A

Because they are randomly selected

26
Q

Why could a genetic map have so many gaps?

A

Because the markers could not be equally distributed the genetic distance between them vary and could over count a linkage

27
Q

If you have 12 linkage groups, how many chromosomes should you have?

A

12

28
Q

Why would you have more linkage groups than chromosomes?

A

Because the linkage groups could have a large region and overlap and therefore be counted more than once

29
Q

What is the average genetic distance for a marker?

A

1 marker per 4cM

30
Q

How do you asses the quality of the marker?

A

You would look at the average genetic distance between any 2 markers

31
Q

What is 1 marker per 4cM suitable for mapping?

A

Morphological traits

32
Q

What does it mean when you have more linkage groups than chromosomes?

A

That the linkage groups were too large to connect

- they overlapped

33
Q

Spine present or spine absent is an example of what?

A

Qualitative trait

34
Q

Variation in spine length is an example of what?

A

Quantitative trait

35
Q

Qualitative traits

A

Traits that can be described

36
Q

Quantitative traits

A

Traits that can be represented by a numerical value

37
Q

What kind of phenotypes are in qualitative traits?

A

2-3 define phenotype variants only

38
Q

What kind of phenotypes are in quantitative traits?

A

The phenotypes vary along a gradient

39
Q

What are qualitative traits caused by?

A

A single gene

40
Q

What are quantitative genes caused by?

A

Multiple genes

41
Q

How are qualitative and quantitative traits mapped?

A

The same way as any genetic marker

42
Q

QTL

A

Quantitative Trait Loci

43
Q

What did it mean when 2 genes were completely independent?

A

The 2 groups would be the same with no significance difference

44
Q

What if the marker was close to the gene that effected the phenotype?

A

Then the 2 groups should be a significant difference

45
Q

How can you determine the significance?

A

By finding out the p value

- the smaller the p value the more significant it is

46
Q

What is a big factor on effecting phenotype?

A

Distance

- the further away the more likely it will recombinant

47
Q

LOD

A

Logarithm of odds

48
Q

Logarithm of odds

A

Is the ratio of probability that 2 traits are linked over the probability that they are not
- (linked/not linked)

49
Q

What does LOD > 3 mean?

A

That the chance of no-linkage is less than 1 in 1,000

- it is 1000x more likely that they are linked than that they are not linked

50
Q

What does LOD = 0 mean?

A

That it is equally likely that they are linked or not linked

51
Q

When would you have a high LOD score and a low LOD score?

A
  • High = closer to the gene that contributes to the phenotype
  • Low = further away from the gene that contributes to the phenotype
52
Q

What does a high LOD score mean?

A

That there is high linkage to the gene causing the phenotype

53
Q

What does a genetic map not tell you?

A

Doesnt tell you what the genes are

54
Q

What can a genetic map let you do?

A

It can let you use the genes as a predictor

Bio 361 - Molecular Genome and Genomics (35 decks)

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