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

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

• 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!

• ASCOASCOMYCETES

• BASIDIOBASIDIOMYCETES

• OOMYCETES (fungus-like, water molds)

ASCOASCOMYCETES

• Yeasts (fermentation, human Yeasts (fermentation, human mycoses)mycoses)

• Truffles, morelsTruffles, 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

BASIDIOBASIDIOMYCETES

• Mushrooms. mycorrhizal Mushrooms. mycorrhizal

• Wood decay organismsWood 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 aren+n (dikaryons), some rareones are diploid

Oomycetes

• Belong to the kingdom Stramenopila, used to be called Chromista

• Phytophthora, Pythium, Saprolegnia

H20

Hyphae, sporangia, and zoospores of Hyphae, sporangia, and zoospores of P. ramorumP. ramorum

Most of their lifecyclethey are 2n

Have cellulose in cellwall

Not fungi!!, but looklike them because of convergent evolution

Fungi do not photosynthesize

• Biotrophic: mycorrhyzae, rusts

• Endophites: clavicipetaceae, • Necrotrophic; most pathogens• Saprobes: primary (involved in litter decomposition)

DISEASE!!

• Symptoms vs. signs; e.g. chlorosis vs. fruit-body

• 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 Genetic resistance in host

Length of lesion (mm)

Proportion of stem girdled (%)

Nicasio\ 42.5a 0.71a

China Camp 40.5a 0.74a

San Diego 27.8b 0.41b

Ojai 25.0b 0.47b

Interior live oak (Maricopa)

14.1b 0.33b

Cankers byCankers by P. ramorum P. ramorum at 3 monthsat 3 monthsfrom time of inoculation on two coastfrom time of inoculation on two coastlive oakslive oaks

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

Chlamydospores of Chlamydospores of P. ramorumP. ramorum

Pr75 Qa MontereyPr75 Qa Monterey Pr87 Am MarinPr87 Am Marin Pr86b Am MarinPr86b Am Marin Pr86a Am MarinPr86a Am Marin Pr84 Soil MarinPr84 Soil Marin Pr82 Vo MarinPr82 Vo Marin Pr80 Vo MarinPr80 Vo Marin Pr72 Rh AlamedaPr72 Rh Alameda Pr65 Qp Santa CruzPr65 Qp Santa Cruz Pr58 Vo MarinPr58 Vo Marin Pr50 Qa SonomaPr50 Qa Sonoma Pr201b Rh Santa CruzPr201b Rh Santa Cruz Pr201a Rh Santa CruzPr201a Rh Santa Cruz Pr47b Qa SonomaPr47b Qa Sonoma Pr47a Qa SonomaPr47a Qa Sonoma Pr35 Qa SonomaPr35 Qa Sonoma Pr28 Ld SonomaPr28 Ld Sonoma Pr24 Qa SonomaPr24 Qa Sonoma Pr22 Qa SonomaPr22 Qa Sonoma Pr20 Qa SonomaPr20 Qa Sonoma Pr19 Qa NapaPr19 Qa Napa Pr16 Qa Santa CruzPr16 Qa Santa Cruz Pr13 Qa Santa CruzPr13 Qa Santa Cruz Pr11b Qa MontereyPr11b Qa Monterey Pr11a Qa MontereyPr11a Qa Monterey Pr10 Ld MontereyPr10 Ld Monterey Pr08 Qa NapaPr08 Qa Napa Pr06 Qa MarinPr06 Qa Marin Pr05 Ld MarinPr05 Ld Marin Pr04 Qk MarinPr04 Qk Marin Pr03 Ld MarinPr03 Ld Marin Pr88 Uc SonomaPr88 Uc Sonoma Pr89 Uc SonomaPr89 Uc Sonoma Pr90 Qa MarinPr90 Qa Marin Pr91 Uc SonomaPr91 Uc Sonoma Pr97 Qa NapaPr97 Qa Napa Pr102 Qa MarinPr102 Qa Marin Pr103 Ld MarinPr103 Ld Marin Pr104 Ld MarinPr104 Ld Marin Pr107 Uc SonomaPr107 Uc Sonoma Pr110 Uc MarinPr110 Uc Marin Pr112 Uc MarinPr112 Uc Marin Pr113 Uc MarinPr113 Uc Marin Pr114 Uc MarinPr114 Uc Marin Pr115 Uc MarinPr115 Uc Marin Pr116 Uc MarinPr116 Uc Marin Pr136 Uc MarinPr136 Uc Marin Pr156 Ld OregonPr156 Ld Oregon Pr157 Ld OregonPr157 Ld Oregon Pr158 Ld OregonPr158 Ld Oregon PrJL3.1 Ss SonomaPrJL3.1 Ss Sonoma PrSDC21.6 Ss SonomaPrSDC21.6 Ss Sonoma

Pr36 Qa SonomaPr36 Qa Sonoma Pr27 Qa MarinPr27 Qa Marin

Pr57 Ld Santa ClaraPr57 Ld Santa Clara Pr70 Vo MarinPr70 Vo Marin Pr159 Ld OregonPr159 Ld Oregon

Pr52a Rh Santa CruzPr52a Rh Santa Cruz Pr52b Rh Santa CruzPr52b Rh Santa Cruz PrCoen Rh Santa CruzPrCoen Rh Santa Cruz

PrJL3.5.3 Ss SonomaPrJL3.5.3 Ss Sonoma Pr106 Uc SonomaPr106 Uc Sonoma

Pr71 Qa SonomaPr71 Qa Sonoma Pr01 Qa MarinPr01 Qa Marin

PrE9/95 Rh GermanyPrE9/95 Rh Germany PrE16/99 Vb GermanyPrE16/99 Vb Germany

PrE12/98 Rh GermanyPrE12/98 Rh Germany PrE104 Water GermanyPrE104 Water Germany

PrE69082 Rh GermanyPrE69082 Rh Germany PrE9/3 Water GermanyPrE9/3 Water Germany

PrE14/98-a Rh GermanyPrE14/98-a Rh Germany Pl33 Cl Del Norte

Pl16 Soil Josephine Pl27 Tb Del Norte0.1

Clone groupClone group

European groupEuropean group

P. lateralisP. lateralis (outgroup)(outgroup)

100100

96969393

89896767

host-pathogen-environment

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

• Nutrient status

Colony diameter (mm) at 13 days

Colony diameter (mm) at 13 days

Presence of free water

Between 6 and 12 hours requiredBetween 6 and 12 hours requiredfor infection of bay leavesfor 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