Definitions

1
Definitions

• Alternatively fixed alleles
• Dominant vs. co-dominant markers
• Genotype

2
Alternatively fixed alleles

• Two flower species (species 1 and species 2) can
  have one of two features
• Long (L) or short (s) leaves
• Red ( R) or white (w) flowers
• Ten individuals from species 1 have the following
  traits
• LR LR LR LR LR LR LR sR sR sR
• Ten individuals from species 2 have the following
  traits
• sw sw sw sw sw sw sw Lw Lw Lw

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Which one is the alternatively fixed allele?

• Both alleles will differentiate the groups
  (frequencies are significantly different)
• Only one will be diagnostic because alternatively
  fixed
• It is the color of the flower all flowers in
  species 1 are R, all flowers in species 2 are w
  (all implies your sampling size is adequate!!)

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Dominant vs. co-dominant markers

• Flowers are red or white or yellow, DNA sequence
  is agg, agt, agc DNA fragment is 10, 12 0r 14 bp
  long (CO-DOMINANT, we know what alternative
  alleles are)
• Flowers are red or non-red, DNA is agg or not,
  size is 10bp or not. We only see the dominant
  allele and we express it in binary code
  1(present), 0(absent)

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Limitations of co-dominant markers

• Not all non-red flowers are the same, but we
  assume they are (non red flowers can be orange or
  yellow)
• If at one locus we have a dominant A allele and a
  recessive a allele, using a codominant marker we
  would say AAAa but not aa. We know in reality
  AA and Aa are quite different.

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Genotype

• A unique individual as defined by an array of
  genetic markers. (the more markers you have the
  less mistaken identity you will have.
• blonde

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• Blonde
• Blue-eyed

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• Blonde
• Blue-eyed
• Hairy

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• Blonde
• Blue-eyed
• Hairy
• 6 feet tall

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• Blonde
• Blue-eyed
• Hairy
• 6 feet tall
• Missing two molars

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In the case of microbes it will probably be
something like

• Genotype A 01010101
• Genotype B 00110101
• Genotype C 00010101

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Summary of third lesson

• DNA polymorphisms can be diagnostic
• Mutations/Sex/Barriers to mating
• Plant Diseases can be biotic (interaction between
  host and causal agent ), or abiotic
• Many organisms can cause plant diseases, but
  fungi are the No.1 cause
• Diversity of fungi, but all have ideal structure
  for plant infection
• hypha/cord/rhizomorph/infection peg/appressorium
• Sexual vs. asexual reproduction can do both

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Fungi again!

• ASCOMYCETES
• BASIDIOMYCETES
• OOMYCETES (fungus-like, water molds)

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ASCOMYCETES

• Yeasts (fermentation, human mycoses)
• Truffles, morels
• Penicillia (penicillin), Fusaria (potent toxins,
  damping off of seedlings), molds

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Ascus is the sack in which the spores are
contained
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Asci can be placed on a disk (apothecium), many
apothecia can be together in a fruitbody
Morel fruitbody
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Asci can be carried inside a flask (perithecium)
Nectria
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Ploidy is mostly n
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BASIDIOMYCETES

• Mushrooms. mycorrhizal
• Wood decay organisms
• Rusts, Smuts
• Yeasts and damping off

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Toadstools and huitacochle are both basidiomycetes
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Basidium means club, it carries the
basidiospores (dispersion propagules) naked
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Most of their life, they are nn (dikaryons),
some rare ones are diploid
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Oomycetes

• Belong to the kingdom Stramenopila, used to be
  called Chromista
• Phytophthora, Pythium, Saprolegnia

H20
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Hyphae, sporangia, and zoospores of P. ramorum
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Most of their lifecycle they are 2n Have
cellulose in cell wall Not fungi!!, but
look like them because of convergent evolution
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Fungi do not photosynthesize

• Biotrophic mycorrhyzae, rusts
• Endophites clavicipetaceae,
• Necrotrophic most pathogens
• Saprobes primary (involved in litter
  decomposition)

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DISEASE!!

• Symptoms vs. signs e.g. chlorosis vs. fruit-body
• The disease triangle

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host-pathogen-environment

• Susceptibility of individuals or of portions of
  individuals
• Genetic variability
• Basic compatibility (susceptibility) between host
  and pathogen
• Ability to withstand physiological alterations

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Genetic resistance in host
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Cankers by P. ramorum at 3 months from time of
inoculation on two coast live oaks
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host-pathogen-environment

• Basic compatibility with host (virulence)
• Ability to maintain diversity sex vs. no sex
• Size of genetic pool
• Agressiveness (pathogenicity) towards hosts
• Ability to survive without host

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Chlamydospores of P. ramorum
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host-pathogen-environment

• Temperatures
• Shading
• Relative humidity
• Free standing water
• pH and any potentially predisposing factors
• Nutrient status

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Colony diameter (mm) at 13 days
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Presence of free water
Between 6 and 12 hours required for infection of
bay leaves
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Some pathogen roles in natural plant communities

• Selection of individuals best suited for the site
• Maintenance of genetic diversity and stability in
  host plant populations
• Establishment or maintenance of host geographic
  ranges
• Natural succession
• Regulation of stand density, structure, and
  composition

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Human activities affecting disease incidence in
forests

• Introduction of exotic pathogens
• Planting trees in inappropriate sites
• Changing stand density, age structure,
  composition, fire frequency
• Wound creation
• Pollution, etc.

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Effects of fire exclusion