Molecular Markers

1
Molecular Markers

• DNA PROTEINS
• mtDNA often used in systematics in general, no
  recombination uniparental inheritance
• cpDNA often used in systematics in general, no
  recombination uniparental inheritance
• Microsatellites tandem repeats genotyping
  population structure
• Allozymes variations of proteins population
  structure
• RAPDs short segments of arbitrary sequences
  genotyping
• RFLPs variants in DNA exposed by cutting with
  restriction enzymes genotyping, population
  structure
• AFLPs after digest with restriction enzymes, a
  subset of DNA fragments are selected for PCR
  amplification genotyping

2
Genetic analysis requires variation at loci,
variation of markers (polymorphisms)

• How the variation is structured will tell us
• Does the microbe reproduce sexually or clonally
• Is infection primary or secondary
• Is contagion caused by local infectious spreaders
  or by a long-disance moving spreaders
• How far can individuals move how large are
  populations
• Is there inbreeding or are individuals freely
  outcrossing

3
CASE STUDY

• A grou

A stand of adjacent trees is infected by a
disease How can we determine the way trees are
infected?
4
CASE STUDY

• A grou

A stand of adjacent trees is infected by a
disease How can we determine the way trees are
infected? BY ANALYSING THE GENOTYPE OF THE
MICROBES if the genotype is the same then we
have local secondary tree-to-tree contagion. If
all genotypes are different then primary
infection caused by airborne spores is the
likely cause of Contagion.
5
CASE STUDY

• A grou

WE HAVE DETERMINED AIRBORNE SPORES (PRIMARY
INFECTION ) IS THE MOST COMMON FORM OF
INFECTION QUESTION Are the infectious spores
produced by a local spreader, or is there a
general airborne population of spores that may
come from far away ? HOW CAN WE ANSWER THIS
QUESTION?
6
If spores are produced by a local spreader..

• Even if each tree is infected by different
  genotypes (each representing the result of
  meiosis like us here in this class).these
  genotypes will be related
• HOW CAN WE DETERMINE IF THEY ARE RELATED?

7
HOW CAN WE DETERMINE IF THEY ARE RELATED?

• By using random genetic markers we find out the
  genetic similarity among these genotypes
  infecting adjacent trees is high
• If all spores are generated by one individual
• They should have the same mitochondrial genome
• They should have one of two mating alleles

8
WE DETERMINE INFECTIOUS SPORES ARE NOT RELATED

• QUESTION HOW FAR ARE THEY COMING FROM? .or
• HOW LARGE IS A POPULATION?
• Very important question if we decide we want to
  wipe out an infectious disease we need to wipe
  out at least the areas corresponding to the
  population size, otherwise we will achieve no
  result.

9
HOW TO DETERMINE WHETHER DIFFERENT SITES BELONG
TO THE SAME POP OR NOT?

• Sample the sites and run the genetic markers
• If sites are very different
• All individuals from each site will be in their
  own exclusive clade, if two sites are in the same
  clade maybe those two populations actually are
  linked (within reach)
• In AMOVA analysis, amount of genetic variance
  among populations will be significant (if
  organism is sexual portion of variance among
  individuals will also be significant)
• F statistics Fst will be over ) 0.10 (suggesting
  stongt structuring)
• There will be isolation by distance