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Sources of Variability. Soybean

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Presentation on theme: "Sources of Variability. Soybean"— Presentation transcript:

1 Sources of Variability

2 Soybean

3 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 coryliAlternariaColletotrichum truncatum Colletotrichum dematium f. truncatum Glomerella glycines Colletotrichum destructivumArkoola nigraThielaviopsis basicola Chalara elegansSeptoria glycines Mycosphaerella usoenskajaePhialophora gregataCephalosporium gregatumMacrophomina phaseolinaChoanephora infundibulifera Choanephora trisporaRhizoctonia solani Thanatephorus cucumeris Pythium aphanidermatum Pythium debaryanum Pythium irregulare Pythium myriotylum Pythium ultimumPeronospora manshuricaDrechslera glycinesCercospora sojinaFusariumLeptosphaerulina trifoliiMycoleptodiscus terrestrisNeocosmospora vasinfecta AcremoniumPhomopsisPhytophthora sojaePhyllosticta sojaecolaPhymatotrichopsis omnivoraPhymatotrichum omnivorumDiaporthe phaseolorum Phomopsis sojaeMicrosphaera diffusaCercospora kikuchiiPyrenochaeta glycinesPythium aphanidermatum Pythium debaryanum Pythium irregulare Pythium myriotylum Pythium ultimumCylindrocladium crotalariae Calonectria crotalariaeDactuliochaeta glycinesPyrenochaeta glycines Dactuliophora glycinesRhizoctonia solani Thanatephorus cucumerisRhizoctonia solaniPhakopsora pachyrhiziSpaceloma glycinesSclerotinia sclerotiorumSclerotium rolfsii Athelia rolfsiiDiaporthe phaseolorum Diaporthe phaseolorum var. caulivora Phomopsis phaseoliStemphylium botryosum Pleospora tardaFusarium solani f.sp. glycinesCorynespora cassiicolaNematospora coryli Taken from Wikipedia

4 Nematodes, parasitic Lance nematodeHoplolaimus columbus Hoplolaimus galeatus Hoplolaimus magnistylusLesion nematodePratylenchus spp.Pin nematodeParatylenchus projectus Paratylenchus tenuicaudatusReniform nematodeRotylenchulus reniformisRing nematodeCriconemella ornataRoot- knot 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.Hoplolaimus columbus Hoplolaimus galeatus Hoplolaimus magnistylusPratylenchusParatylenchus projectus Paratylenchus tenuicaudatusRotylenchulus reniformisCriconemella ornataMeloidogyne arenaria Meloidogyne hapla Meloidogyne incognita Meloidogyne javanicaHemicycliophoraHeterodera glycinesHelicotylenchusBelonolainus gracilis Belonolainus longicaudatusParatrichodorus minorQuinisulcius acutus Tylenchorhynchus 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)AlfamovirusAlfalfa mosaic virus (AMV)ComovirusBean pod mottle virusPotyvirusBean yellow mosaic virus IlarvirusTobacco streak virusBromovirusCowpea chlorotic mottle virusBegomovirusMung bean yellow mosaic virusPotyvirusPeanut mottle virusPotyvirusPeanut stripe virusCucumovirusPeanut stunt virusCaulimovirus Soybean chlorotic mottle virusBegomovirusSoybean crinkle leaf virusLuteovirusSoybean dwarf virusPotyvirusSoybean mosaic virusNepovirusSoybean severe stunt virusNepovirusTobacco ringspot virus 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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