Download Lecture #4

Definitions
• Alternatively fixed alleles
• Dominant vs. co-dominant markers
• Genotype
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
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!!)
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)
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 AA=Aa but not aa. We know in reality
AA and Aa are quite different.
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
• Blonde
• Blue-eyed
• 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
In the case of microbes it will
probably be something like
• Genotype A= 01010101
• Genotype B= 00110101
• Genotype C= 00010101
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
Fungi… again!
• ASCOMYCETES
• BASIDIOMYCETES
• OOMYCETES (fungus-like, water molds)
ASCOMYCETES
• Yeasts (fermentation, human mycoses)
• Truffles, morels
• Penicillia (penicillin), Fusaria (potent
toxins, damping off of seedlings), molds
Ascus is the sack in which the
spores are contained
Asci can be placed on a disk
(apothecium), many apothecia
can be together in a fruitbody
Morel fruitbody
Asci can be carried inside a flask
(perithecium)
Nectria
Ploidy is mostly
n
BASIDIOMYCETES
• Mushrooms. mycorrhizal
• Wood decay organisms
• Rusts, Smuts
• Yeasts and damping off
Toadstools and huitacochle are
both basidiomycetes
Basidium means “club”, it carries
the basidiospores (dispersion
propagules) naked
Most of their life, they are
n+n (dikaryons), some rare
ones are diploid
Oomycetes
• Belong to the kingdom Stramenopila, used
to be called Chromista
• Phytophthora, Pythium, Saprolegnia
H20
Hyphae, sporangia, and zoospores of P. ramorum
Most of their lifecycle
they are 2n
Have cellulose in cell
wall
Not fungi!!, but look
like them because of
convergent evolution
Fungi do not photosynthesize
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Biotrophic: mycorrhyzae, rusts
Endophites: clavicipetaceae,
Necrotrophic; most pathogens
Saprobes: primary (involved in litter
decomposition)
DISEASE!!
• Symptoms vs. signs; e.g. chlorosis vs. fruitbody
• The disease triangle
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
Genetic resistance in host
Length of lesion Proportion of stem
(mm)
girdled (%)
Nicasio\
China Camp
42.5a
40.5a
0.71a
0.74a
San Diego
27.8b
0.41b
Ojai
Interior live
oak
(Maricopa)
25.0b
14.1b
0.47b
0.33b
Cankers by P. ramorum at 3 months
from time of inoculation on two coast
live oaks
host-pathogen-environment
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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
Chlamydospores of P. ramorum
93
100
0.1
Pr75 Qa Monterey
Pr87 Am Marin
Pr86b Am Marin
Pr86a Am Marin
Pr84 Soil Marin
Pr82 Vo Marin
Pr80 Vo Marin
Pr72 Rh Alameda
Pr65 Qp Santa Cruz
Pr58 Vo Marin
Pr50 Qa Sonoma
Pr201b Rh Santa Cruz
Pr201a Rh Santa Cruz
Pr47b Qa Sonoma
Pr47a Qa Sonoma
Pr35 Qa Sonoma
Pr28 Ld Sonoma
Pr24 Qa Sonoma
Pr22 Qa Sonoma
Pr20 Qa Sonoma
Pr19 Qa Napa
Pr16 Qa Santa Cruz
Pr13 Qa Santa Cruz
Clone group
Pr11b Qa Monterey
Pr11a Qa Monterey
Pr10 Ld Monterey
Pr08 Qa Napa
Pr06 Qa Marin
Pr05 Ld Marin
Pr04 Qk Marin
Pr03 Ld Marin
Pr88 Uc Sonoma
Pr89 Uc Sonoma
Pr90 Qa Marin
Pr91 Uc Sonoma
Pr97 Qa Napa
Pr102 Qa Marin
Pr103 Ld Marin
Pr104 Ld Marin
Pr107 Uc Sonoma
Pr110 Uc Marin
Pr112 Uc Marin
Pr113 Uc Marin
Pr114 Uc Marin
Pr115 Uc Marin
Pr116 Uc Marin
Pr136 Uc Marin
Pr156 Ld Oregon
Pr157 Ld Oregon
Pr158 Ld Oregon
PrJL3.1 Ss Sonoma
PrSDC21.6 Ss Sonoma
Pr36 Qa Sonoma
Pr27 Qa Marin
Pr57 Ld Santa Clara
Pr70 Vo Marin
Pr159 Ld Oregon
Pr52a Rh Santa Cruz
67
Pr52b Rh Santa Cruz
89
PrCoen Rh Santa Cruz
PrJL3.5.3 Ss Sonoma
96
Pr106 Uc Sonoma
Pr71 Qa Sonoma
Pr01 Qa Marin
PrE9/95 Rh Germany
PrE16/99 Vb Germany
PrE12/98 Rh Germany
PrE104 Water Germany
European group
PrE69082 Rh Germany
PrE9/3 Water Germany
PrE14/98-a Rh Germany
Pl33 Cl Del Norte
Pl16 Soil Josephine
P. lateralis
Pl27 Tb Del Norte
(outgroup)
host-pathogen-environment
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Temperatures
Shading
Relative humidity
Free standing water
pH and any potentially predisposing factors
Nutrient status
Colony diameter (mm) at 13 days
Presence of free water
Between 6 and 12 hours required
for infection of bay leaves
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
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.
Effects of fire exclusion