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Sources of Variability

Sources of Variability. Soybean. http://en.wikipedia.org/wiki/Image:Soy_sauce.jpg. http://en.wikipedia.org/wiki/Image:Soybean.USDA.jpg. http://en.wikipedia.org/wiki/Image:Tofu-beijingchina.jpg. Diseases of Soybean.

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Sources of Variability

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  1. Sources of Variability

  2. Soybean http://en.wikipedia.org/wiki/Image:Soy_sauce.jpg http://en.wikipedia.org/wiki/Image:Soybean.USDA.jpg http://en.wikipedia.org/wiki/Image:Tofu-beijingchina.jpg

  3. Diseases of Soybean Fungal diseasesAlternaria leaf spotAlternaria spp.AnthracnoseColletotrichum truncatumColletotrichum dematium f. truncatumGlomerella glycinesColletotrichum destructivum [anamorph]Black leaf blightArkoola nigraBlack root rotThielaviopsis basicolaChalara elegans [synanamorph]Brown spotSeptoria glycinesMycosphaerella usoenskajae [teleomorph]Brown stem rotPhialophora gregata= Cephalosporium gregatumCharcoal rotMacrophomina phaseolinaChoanephora leaf blightChoanephora infundibuliferaChoanephora trisporaDamping-offRhizoctonia solaniThanatephorus cucumeris [teleomorph]Pythium aphanidermatumPythium debaryanumPythium irregularePythium myriotylumPythium ultimumDowny mildewPeronospora manshuricaDrechslera blightDrechslera glycinesFrogeye leaf spotCercospora sojinaFusarium root rotFusarium spp.Leptosphaerulina leaf spotLeptosphaerulina trifoliiMycoleptodiscus root rotMycoleptodiscus terrestrisNeocosmospora stem rotNeocosmospora vasinfectaAcremonium 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 phaseolorumPhomopsis sojae [anamorph]Powdery mildewMicrosphaera diffusaPurple seed stainCercospora kikuchiiPyrenochaeta leaf spotPyrenochaeta glycinesPythium rotPythium aphanidermatumPythium debaryanumPythium irregularePythium myriotylumPythium ultimumRed crown rotCylindrocladium crotalariaeCalonectria crotalariae [teleomorph]Red leaf blotch = Dactuliophora leaf spotDactuliochaeta glycines= Pyrenochaeta glycinesDactuliophora glycines [synanamorph]Rhizoctonia aerial blightRhizoctonia solaniThanatephorus cucumeris [teleomorph]Rhizoctonia root and stem rotRhizoctonia solaniRustPhakopsora pachyrhiziScabSpaceloma glycinesSclerotinia stem rotSclerotinia sclerotiorumSouthern blight (damping-off and stem rot) = Sclerotium blightSclerotium rolfsiiAthelia rolfsii [teleomorph]Stem cankerDiaporthe phaseolorumDiaporthe phaseolorum var. caulivoraPhomopsis phaseoli [anamorph]Stemphylium leaf blightStemphylium botryosumPleospora tarda [teleomorph]Sudden death syndromeFusarium solani f.sp. glycinesTarget spotCorynespora cassiicolaYeast spotNematospora coryli Taken from Wikipedia

  4. Nematodes, parasiticLance nematodeHoplolaimus columbusHoplolaimus galeatusHoplolaimus magnistylusLesion nematodePratylenchus spp.Pin nematodeParatylenchus projectusParatylenchus tenuicaudatusReniform nematodeRotylenchulus reniformisRing nematodeCriconemella ornataRoot-knot nematodeMeloidogyne arenariaMeloidogyne haplaMeloidogyne incognitaMeloidogyne javanicaSheath nematodeHemicycliophora spp.Soybean cyst nematodeHeterodera glycinesSpiral nematodeHelicotylenchus spp.Sting nematodeBelonolainus gracilisBelonolainus longicaudatusStubby root nematodeParatrichodorus minorStunt nematodeQuinisulcius acutusTylenchorhynchus spp. Viral diseasesAlfalfa 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) • Taken from wikipedia

  5. Resistance to Disease • Design an experiment

  6. Biological Samples • Resistant variety vs Susceptible variety • Resistant variety, following infection. • Resistant soybean, infective/non infective pathogen

  7. Plant selection • From where would the plants come? • Lighting conditions • Plant varieties • Temperature

  8. Cy3/Cy5 • Channel variability? • Depends on what sort of experiment we do. Time courses will be single colour.

  9. Infective Process • Different amounts of infection • Different strains of pathogen

  10. With array variability • Printing Defects • Hybridisation defects • Probe strengths

  11. Between arrays • Different conditions for hybridisation • Different detection machines

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