Transcript sources_of_variabili..

Sources of Variability
Soybean
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Diseases of Soybean
Fungal diseases
Alternaria leaf spotAlternaria spp.AnthracnoseColletotrichum truncatum
Colletotrichum dematium f. truncatum
Glomerella glycines
Colletotrichum destructivum [anamorph]Black leaf blightArkoola nigraBlack root rotThielaviopsis basicola
Chalara elegans [synanamorph]Brown spotSeptoria glycines
Mycosphaerella usoenskajae [teleomorph]Brown stem rotPhialophora gregata
= Cephalosporium gregatumCharcoal rotMacrophomina phaseolinaChoanephora leaf blightChoanephora infundibulifera
Choanephora trisporaDamping-offRhizoctonia solani
Thanatephorus cucumeris [teleomorph]
Pythium aphanidermatum
Pythium debaryanum
Pythium irregulare
Pythium myriotylum
Pythium ultimumDowny mildewPeronospora manshuricaDrechslera blightDrechslera glycinesFrogeye leaf spotCercospora sojinaFusarium root
rotFusarium spp.Leptosphaerulina leaf spotLeptosphaerulina trifoliiMycoleptodiscus root rotMycoleptodiscus terrestrisNeocosmospora stem
rotNeocosmospora vasinfecta
Acremonium spp. [anamorph]Phomopsis seed decayPhomopsis spp.Phytophthora root and stem rotPhytophthora sojaePhyllosticta leaf spotPhyllosticta
sojaecolaPhymatotrichum root rot = cotton root rotPhymatotrichopsis omnivora
= Phymatotrichum omnivorumPod and stem blightDiaporthe phaseolorum
Phomopsis sojae [anamorph]Powdery mildewMicrosphaera diffusaPurple seed stainCercospora kikuchiiPyrenochaeta leaf spotPyrenochaeta
glycinesPythium rotPythium aphanidermatum
Pythium debaryanum
Pythium irregulare
Pythium myriotylum
Pythium ultimumRed crown rotCylindrocladium crotalariae
Calonectria crotalariae [teleomorph]Red leaf blotch = Dactuliophora leaf spotDactuliochaeta glycines
= Pyrenochaeta glycines
Dactuliophora glycines [synanamorph]Rhizoctonia aerial blightRhizoctonia solani
Thanatephorus cucumeris [teleomorph]Rhizoctonia root and stem rotRhizoctonia solaniRustPhakopsora pachyrhiziScabSpaceloma glycinesSclerotinia
stem rotSclerotinia sclerotiorumSouthern blight (damping-off and stem rot) = Sclerotium blightSclerotium rolfsii
Athelia rolfsii [teleomorph]Stem cankerDiaporthe phaseolorum
Diaporthe phaseolorum var. caulivora
Phomopsis phaseoli [anamorph]Stemphylium leaf blightStemphylium botryosum
Pleospora tarda [teleomorph]Sudden death syndromeFusarium solani f.sp. glycinesTarget spotCorynespora cassiicolaYeast spotNematospora coryli
Taken from Wikipedia
Nematodes, parasitic
Lance nematodeHoplolaimus columbus
Hoplolaimus galeatus
Hoplolaimus magnistylusLesion nematodePratylenchus spp.Pin nematodeParatylenchus projectus
Paratylenchus tenuicaudatusReniform nematodeRotylenchulus reniformisRing nematodeCriconemella ornataRootknot nematodeMeloidogyne arenaria
Meloidogyne hapla
Meloidogyne incognita
Meloidogyne javanicaSheath nematodeHemicycliophora spp.Soybean cyst nematodeHeterodera glycinesSpiral
nematodeHelicotylenchus spp.Sting nematodeBelonolainus gracilis
Belonolainus longicaudatusStubby root nematodeParatrichodorus minorStunt nematodeQuinisulcius acutus
Tylenchorhynchus spp.
Viral diseases
Alfalfa mosaicgenus Alfamovirus, Alfalfa mosaic virus (AMV)Bean pod mottlegenus Comovirus, Bean pod mottle
virus (BPMV)Bean yellow mosaicgenus Potyvirus, Bean yellow mosaic virus (BYMV)Brazilian bud blightgenus
Ilarvirus, Tobacco streak virus (TSV)Cowpea chlorotic mottlegenus Bromovirus, Cowpea chlorotic mottle virus
(CCMV)Mung bean yellow mosaicgenus Begomovirus, Mung bean yellow mosaic virus (MYMV)Peanut
mottlegenus Potyvirus, Peanut mottle virus (PeMoV)Peanut stripegenus Potyvirus, Peanut stripe virus
(PStV)Peanut stuntgenus Cucumovirus, Peanut stunt virus (PSV)Soybean chlorotic mottlegenus Caulimovirus,
Soybean chlorotic mottle virus (SbCMV)Soybean crinkle leafgenus Begomovirus, Soybean crinkle leaf virus
(SCLV)Soybean dwarfgenus Luteovirus, Soybean dwarf virus (SbDV)Soybean mosaicgenus Potyvirus, Soybean
mosaic virus (SMV)Soybean severe stuntgenus Nepovirus, Soybean severe stunt virus (SSSV)Tobacco ringspot =
bud blightgenus Nepovirus, Tobacco ringspot virus (TRSV)
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Taken from wikipedia
Resistance to Disease
• Design an experiment
Biological Samples
• Resistant variety vs Susceptible variety
• Resistant variety, following infection.
• Resistant soybean, infective/non infective
pathogen
Plant selection
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From where would the plants come?
Lighting conditions
Plant varieties
Temperature
Cy3/Cy5
• Channel variability?
• Depends on what sort of experiment we
do. Time courses will be single colour.
Infective Process
• Different amounts of infection
• Different strains of pathogen
With array variability
• Printing Defects
• Hybridisation defects
• Probe strengths
Between arrays
• Different conditions for hybridisation
• Different detection machines