(04) Markers and Maps Flashcards
1
Q
(JUST READ THIS)
(Mapping of Animal Genomes)
- A major goal of Animal Genomics is to determine the location, molecular nature and function of genes responsible for desirable as well as undesirable traits.
- A genome map presents the linear order of genes and other genetic loci along a chromosome.
- They depict the structure of the genome in a way that enables researchers to navigate around and efficiently identify the loci and genes responsible for traits of interest.
A
2
Q
(Genes and Genomes)
• The number of genes in a genome is being derived in large part from whole genome sequencing projects.
- It changes all the time, usually downward, but
– Yeast has ~ _____.
– Drosophila ~ 13,000.
– Humans and other mammals have ~ 22,000. - Mammalian genomes have ~ ______ bp DNA.
- There is a gene on average every _____ bp in a mammalian genome.
- Repetitive elements may comprise over _____ of the human genome.
A
- 6,000; 13,000; 22,000
- 2.5 - 3 billion
- 80,000
- two-thirds
3
Q
(The Facts of Genetics and Genomics)
- What is absolutely necessary to have hope of identifying the positions of genes that contribute to health and disease traits?
- What do they provide?
(JUST READ THIS)
• Example: The canine narcolepsy gene Hcrtr2 (hypocretin receptor 2) was identified by co-segregation of the phenotypic trait with genetic markers. The gene codes for a hypocretin cell receptor in the hypothalamus region of the brain. The mutated Hcrtr2 gene is known to cause narcolepsy in three different breeds of dogs.
A
- a map of the relative positions of DNA markers along all the chromosomes
- landmarks from which to identify unique positions on chromosomes
4
Q
(Genetic (DNA) Markers)
- Genetic markers define a segment of DNA by its what?
- What allows the maternally and paternally inherited chromosomes of an individual to be distinguished?
- Highly markers include the commonly used what? Usually found where?
- What else are very common? but they are less what?
A
- its unique sequence and location on a chromosome
- polymorphisms in DNA sequence (markes ie locus with mutliple alleles)
- microsatellites ( (CA)n or (GAAA)n; introns
- single nucleotide polymorphisms (SNPs) (1/1500 bp), polymorphic (biallelic)
5
Q
Look at image - what is it?
What is variable between individuals?
A
- Microsatellite
- number of repeats
6
Q
What is this?
For these to be useful what do you need to be able to do?
A
- whoops
- identify the flanking region
7
Q
(Meiosis and Recombination)
- meiotic crossing over (recombination) occurs when the what?
- There is typically at least ___ recombination per chromosome per meiosis
- What is the basic for genetic linkage maps?
A
- four chromatides are lined up during gametogenesis
- one
- the measurement of recombination rates between markers along the chromosomes
8
Q
(Meiosis and Recombination)
What will dictate how often a recombination occurs between these markers?
- Farther apart they are - the ____ likely it is that recombination will happen (and the opposite)
So what does this mean?
(don’t think recessive dominant here - just markers)
A
- the physical distance between A and B
- more
- The proportion of the recombinants that you see (AB and aB) is proportional to how close A and B are
9
Q
- Recombination rates are a measure of _____
- What is the unit of recombination?
- This equals about how many bp of DNA?
- So basically the distance is the ____ of recombination
A
- genetic distance
- centi Morgan (cM)
- 1 Million
- percent
10
Q
(Reference Families)
- Reference Families used for constructing genetic linkage maps must of of what size? To enable what?
- i.e. a large number of ______ is needed to detect the difference between a recombination rate of .25 and .30
- What is created for this purpose?
- If you have a family of 200, how many meitoic events does this represent?
A
- At least 100; to enable sufficient statistical confimation of the extent of linkage between the markers
- meioses
- a mutli-generation pedigree
- 400
11
Q
- does 6013 or 4974 have more different alleles at this loci?
A
- 4974
12
Q
(Statistical Proof of Linkage of Loci)
- so you have taken a bunch of that binding data and now need to figure out what are close based on the recombination data - this is going to be tough - so what do you use to make it easier? what is it?
What does it depend upon?
A
- the LOD score - a test statistic used in analyses for the co-inheritance of loci
- the number of meioses (more you do the more likely you are to see recombinants - especially at low percentages); polymorphism of the markers (informative - look below); number of recombinants; recombination frequency
- informative - how much info the type gives you (lets say a male is AB and female CD - this is max informative (will know which allele it is and what parent it came from): However if a male is AA and female is AA this isn’t informative at all - also Ab Ab isn’t that helpful)
13
Q
(Physical Maps)
- Fluorescent in situ hyridization (FISH) is used to do what?
- What is at the heart of this procedure?
- What two things can the DNA probes be?
- The chromosomes are counterstained to accomplish what?
CAN BASICALLY VISUALIZE WHERE A LINKAGE GROUP IS ON A CHROMOSOME
A
- visually located genetic loci on chromosomes
- complementary base pairing (hybridization)
- Can be a genomic DNA clone (containing gene of interstet) or a population of genomic DNA clones derived from whole chromosomes or chromosomal segments
- give the cytogenetic position of the FISHed marker
14
Q
(Integrated Genome Maps)
- What do integrated genome maps combine?
- For pigs, cattle, sheep, chickens, horses, dogs, cats
- ____ - _____ microsatellite markers have been mapped
- a similar number of genes have been FISHed (or mapped by another technique called radiation hybrid mapping)
- All chromosomes are covered with what? How many linkage groups?
A
- the info of linkage and physical maps
- 500-2000
- highly informative markers
- a few linkage groups
15
Q
- Info as to the position, relative order of markers and sequence differences between species is the field of what?
A
comparative genomics
