More Questions for Chapter 8: mapping

1
More Questions for Chapter 8 mapping 8, 9,
13, 15
2
Uses for Gene Mapping

• Find genes (quantitative trait loci) that are
  associated with traits of economic importance.
• Use genetic markers for marker assisted
  selection.
• Discover genes causing major physiological
  defects.
• Develop comparative maps.

3
Types of Mapping

• Genetic linkage map
• linear description of markers/genes on a given
  chromosome with markers closer being inherited
  together more often.
• Physical Map
• The physical location on the chromosome - two
  types - Cytogenetic and physical

4
Linkage Mapping
A genetic linkage map shows the relative
locations of specific genes and DNA markers along
the chromosome. Any inherited physical or
molecular characteristic that differs among
individuals and is easily detectable in the
laboratory is a potential genetic marker.
5
Constructing a Genetic Linkage Map

• Two markers located near each other on the same
  chromosome will tend to be passed together with
  no crossover.
• Frequency of crossovers allows the researcher
  the ability to estimate distance between the
  markers.

6
Diagram of Crossing Over Between Non-Sister
Chromatids of Homologous Chromosomes
Non-Recombinant
Non-Recombinant
Recombinants
7
Diagram of Crossing Over Between Non-Sister
Chromatids of Homologous Chromosomes
Crossover occurs, but not between the two genes
of interest, so the combination of alleles
remains unchanged.
Crossover occurs between the two genes of
interest and causes two gametes to receive a new
combination of alleles and two gametes to receive
an unchanged allele combination.
8
Diagram of Crossing Over Between Non-Sister
Chromatids of Homologous Chromosomes
Crossover occurs, but not between the two genes
of interest, so the combination of alleles
remains unchanged.
Crossover occurs between the two genes of
interest and causes two gametes to receive a new
combination of alleles and two gametes to receive
an unchanged allele combination.
9
Diagram of Crossing Over Between Non-Sister
Chromatids of Homologous Chromosomes
When there is no recombination of alleles, we
refer to this as a noncrossover (NCO), when there
is a single recombination we call it a single
crossover (SCO).
What about double recombinations?
10
Paired Homologous Chromosomes
We need to observe three genes, each with two
distinct alleles, if we are to keep track of
double recombinations.
11
Diagram of Double Cross Over Between Non-Sister
Chromatids of Homologous Chromosomes
When there are two recombinations we call it a
double crossover (DCO).
12
Using Three Point Cross Analysis to Map Genes

• What criteria must be met to use 3 point mapping?
  
• Genotype of organism producing crossover gametes
  must be heterozygous at all loci being mapped.
• Phenotypes of offspring must accurately reflect
  the genotype of the gametes.
• Large numbers of offspring must be produced in
  order to get a representative sample of all
  crossover classes.

What is the first step in determining the order
of genes on a chromosome? Determine the
arrangement of alleles along each of the
homologous chromosomes in a heterozygous parent.
13
Using Three Point Cross Analysis to Map Genes
How do we determine which is correct?
14
Using Three Point Cross Analysis to Map Genes
Need to determine which offspring are from NCO
gametes.
Which offspring are from NCO gametes?
15
Using Three Point Cross Analysis to Map Genes
16
Using Three Point Cross Analysis to Map Genes

• What is the next step in determining the order of
  genes on a chromosome?
• Find the arrangement of alleles for the
  offspring from double crossover gametes.
• Imperically try different orders of the genes to
  determine which order will result in an allele
  combination found in the double crossover
  offspring.

17
Using Three Point Cross Analysis to Map Genes
18
Using Three Point Cross Analysis to Map Genes

• What is the next step in determining the order of
  genes on a chromosome?
• Find the arrangement of alleles for the
  offspring from double crossover gametes.
• Imperically try different orders of the genes to
  determine which order will result in an allele
  combination found in the double crossover
  offspring.

pr
v
bm
v
bm

?
No
DCO



pr


19
Using Three Point Cross Analysis to Map Genes

• What is the next step in determining the order of
  genes on a chromosome?
• Find the arrangement of alleles for the
  offspring from double crossover gametes.
• Imperically try different orders of the genes to
  determine which order will result in an allele
  combination found in the double crossover
  offspring.

pr
v
bm
v
bm

?
No
DCO



pr


pr
v
bm
v
bm

?
Yes
DCO



pr


20
Using Three Point Cross Analysis to Map Genes
21
Using Three Point Cross Analysis to Map Genes

• What is the distance between the genes on a
  chromosome?
• Determine the grand total number of offspring.
• Total the number of offspring for the single
  crossover with the lowest number of offspring and
  then add the total number of DCO offspring.
• Divide this total by the grand total of offspring
  x 100 .
• Do the same for the other SCO.

(SCO offsringDCO offspring)/grand total X 100
recombined
22
Using Three Point Cross Analysis to Map Genes
SCO 8279161 DCO 444286, so (16186)/1109
x 10022.3 SCO 200195395 DCO 444286, so
(39586)/1109 x 10043.4
23
Using Three Point Cross Analysis to Map Genes
24
Physical Mapping

• Cytogenetic map or a physical map
• Several levels of physical mapping
• Chromosome, chromosome arm, band
• specific region within an arm, or
• a certain stretch of bases

25
Cytogenetics Karyotype
26
In Situ Hybridization

• Allows for localization of fragments of DNA by
  in situ hybridization of modified (labeled) DNA
  probe(s) to complementary sites on the chromatin
  fiber.
• ISH probes are labeled
• - radioactive or fluorescent

27
Fluoresecence In Situ Hybridization
DAPI Banding
FISH
28
Ultimate Map
DNA sequence is the ultimate map!
29
Human Genome Project Timeline
30
Comparative Genome Mapping
synteny on the same chromosome
31
http//www.ornl.gov/hgmis/publicat/primer/intro.ht
ml
http//www.nature.com/genomics/human/papers/articl
es.html