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QTL And Genetic Markers > Lecture 5 > Flashcards

Lecture 5 Flashcards

1
Q

What is a genome? What are its two components?

A

A genome is all the genetic material (DNA) present in a particular organism. It includes

  • coding and non-coding DNA
  • nuclear and organelle genomes
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2
Q

What is a transcriptome?

A

A transcriptome is all RNA coded by the genome

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3
Q

What is a proteome?

A

a proteome is all proteins coded by the genome

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4
Q

How many protein coding genes are in the mammalian genome? How many RNA & mRNA do the produce? how many proteins/spots in total and per gene does this yield?

A 
~21,000 protein coding genes
~70,000-100,000 RNA due to alternative start, stop or splicing
~45,000 coding mRNA
~5 proteins per gene
~100,000 proteins total
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5
Q

How many genes on average does a single tissue express?

A

30-40%

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6
Q

how many different cell types with different compliment mRNA and proteins are there in animals?

A

~252

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7
Q

What does genomics investigate in genomes?

A

Construction of genetic and physical maps

Identification of structural and functional components of the genome (genes and noncoding DNA)

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8
Q

Explain using the google maps example how genetic mapping and mapping by genome sequence are different?

A

If you are trying to get to ANNU:

  • A map of TO will give you a low resolution result, allowing you to see a lot of markers and can be used to get to a general place (genetic map)
  • A map of campus will give you a high resolution result, and you can easily find the building (high resolution physical map)
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9
Q

What is the importance/purpose of accurate and different maps?

A
  • Maps provide the likely order of genes/markers along a chromosome
  • A single map is usually not sufficient
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10
Q

What is mapping?

A

Any method used for determining the location of, and relative distances between, genes on a chromosome

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11
Q

What are two examples of low resolution maps? Using the google maps example what do they allow us to do?

A

Genetic and cytogenetic

allow you to drive from one city to another

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12
Q

What are three examples of High resolution maps? Using the google maps example what do they allow us to do?

A

radiation hybrid, BAC clones and sequencing

allows you to find specific street in the city

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13
Q

What is an examples of an Ultra resolution map? Using the google maps example what do they allow us to do?

A

Complete DNA sequence of the genome

allows you to find a specific house in the city

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14
Q

What two things can a genome map be based on?

A

indirect and direct estimates of the distance between two markers

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15
Q

What are two things you could use for an indirect estimate? What map types are they associated with?

A

Recombination rate for genetic linkage maps

Radiation induced fragmentation for radiation hybrid maps

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16
Q

What can you use for a direct estimate? what map types is this associated with (3)?

A

Physical distances for all of cytogenic, BAC clones and sequencing maps

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17
Q

What is a genetic linkage map?

A

A map of the relative positions of the genetic loci/DNA markers along the chromosome, determined based on recombination frequency between markers

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18
Q

How is distance measured for genetic linkage maps? what recombination frequency usually corresponds with 1cM?

A

Distance is measured in morgans or centimorgans

1cM=1% recombination frequency

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19
Q

Generally, 1cM=1% recombination frequency. How is this different across species? Give two examples of species in Mb (million basepairs)

A

This may correspond to different physical distances in different species, of even different places on the same chromosome.
~0.5Mb in Drosophila
~1Mb in human and bovine

20
Q

Who produced the first genetic map? When? What was it based on?

A

Alfred Sturtevant, 1913
Based on noticeable phenotypic observations and allelic segregation on the physical characteristics of flies such as eye colour, body colour, wing length, etc.

21
Q

What can serve as mapping markers?

A

Any inherited physical or molecular characteristic that differs among individuals and is easily detectable has potential

22
Q

What are the three important features of a marker?

A

Polymorphism (different forms within a population)
Frequency (closer to equal frequency = more info)
Ease and cost of detection (eg microsatellites are too expensive vs. SNPs)

23
Q

Give three examples of DNA based markers for DNA sequence polymorphism

A

Single Nucleotide Polymorphism (SNPs)
Insertions and Deletions (Indel)
Restriction fragment length polymorphism (RFLP)(old)

24
Q

Give an example of a DNA based markers for DNA length variation

A

Microsatellite - parentage test and genetic diversity studies

25
Q

What are microsatellites?

A

Short tandem repeats defined by a variable number of repetitions of 2-3 nucleotide base pairs within a sequence.

26
Q

With microsatellites, is the number of repeats consistent across species?

A

No, it may differ between animals.

27
Q

Give three characteristics of microsatellites.

A
  • Multiallelic - can have many alleles/repetitions in pop’n
  • Codominant - separates the homozygous from heterozygous alleles
  • Low throughput
28
Q

What are SNPs?

A

Single nucleotide polymorphisms are individual point mutations or substitutions of a single nucleotide that do not change the overall length of the DNA sequqnce in that region.

29
Q

What are three characteristics of SNPs?

A
  • SNPs occur at a high frequency throughout the genome.
  • Usually Biallelic
  • Codominant
30
Q

Why is sequencing considered the gold standard?

A

Because it allows both detection of new SNPs and genotyping of known SNPs.

31
Q

Is sequencing low throughput or high throughput?

A

Low Throughput

32
Q

List 10 SNP genotyping techniques.

A 
Hybridization
Primer extension
Oligonucleotide Ligation
Nuclease Cleavage
DNA conformation
Gel Separation
Array
Mass Spectrometry
Plate reader
Chromatography
33
Q

What are the disadvantages of genetic maps?

A
  • Starting genetic maps is easier than finishing them
  • Difficult to produce high resolution maps due to small sample sizes and inability to increase recombination rate (to detect 1% recomb. need to examine >100 offspring)
  • Variation between genetic and physical distances
34
Q

What are two differences between physical maps and genetic maps?

A

Physical maps: measured in bp and based on physical distances between markers
Genetic maps: measured in cM and based on recombination frequency between markers

35
Q

Briefly explain FISH.

A

Fluorescent in situ Hybridization

- a DNA probe is labelled with a fluorescent dye and hybridized to the homologous region on a chromosome

36
Q

What are 4 characteristics of Cytogenic Maps?

A
  • Low resolution
  • Direct physical distances between markers
  • Alignment of different types of maps
  • comparative mapping across different species
37
Q

Explain Radiation Hybrid mapping.

A
  • In vitro radiation-induced chromosome fragmentation and cell fusions to create panels of cells in which fragments of DNA from the irradiated cells become integrated into the chromosomes of the host cells
38
Q

What does RH mapping allow us to do?

A

Allows for rapid increase in the amount of genomic information to produce a high resolution map with gene based markers and integrate different maps

39
Q

How does RH mapping calculate distance?

A

RH mapping uses frequency of co-segregation of two DNA markers to calculate distance between markers. the closer two markers are, the less chance they will be broken by radiation and segregate into different cells.

40
Q

What are 4 advantages of RH maps?

A
  • unique ability to map polymorphic markers (microsatellites, SNPs) and non-polymorphic markers (or genes)
  • Integration of maps (genetic linkage and physical) based on different markers
  • Ability to adjust mapping resolution by changing the radiation dosage (low or high resolution maps; provides distance measure between markers with direct correlation to physical distance (1cR~2-13kbp)
  • Allows creation of comparative maps between different species (pig/mouse)
41
Q

What are comparative maps?

A

Comparative maps are a powerful approach for the expansion of gene maps of less analyzed genomes by transfer of information from well analyzed genomes.

42
Q

How do comparative maps work?

A

The genomic address for a gene from a map poor species can be transferred to a corresponding region of a map rick species. It is based on gene synteny between two species.

43
Q

how can comparative maps be produced?

A

using cytogenic approach (chromosome painting) or RH mapping

44
Q

What is gene synteny?

A

the concept that orthologous genes often show conserved gene order

45
Q

Why do we sequence genomes?

A

to produce a complete catalog/blueprint of the organism for:

  • Rapid identification of genes and proteins
  • identifiaction of regulatory and structural elements of the genome
  • transcriptome, proteome analysis
  • Comparative genetics (evolution, comparing species)

QTL And Genetic Markers (10 decks)

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