Variation in submergence toleranceLinkage mapping (quantitative)Fine-mappingFinding the causative variantTransgenic testSlide 6Coding variantsSingle-locus:1 locus, incomplete dominanceTwo lociSlide 11Slide 12Slide 13Slide 14Slide 15Slide 16Two loci, incomplete dominanceSlide 18Slide 19Slide 20Slide 21Slide 22Slide 23Slide 24Slide 25Slide 26Slide 272-locus interactionSlide 29Slide 30Slide 31Slide 32Slide 33Slide 34PowerPoint PresentationOther foibles in QTL mappingPathogenic yeastSlide 38A model quantitative traitSlide 40Slide 41Slide 42NO progeny as extreme as diploid hybridSlide 44Slide 45Did the mapping…Did the fine-mapping…Slide 48Tested in hybrid diploidsSlide 50Slide 51Slide 52One mutant gene…Slide 54Slide 55Two mutant genes…Slide 57Three mutant genesSlide 59Slide 60Slide 61No common coding alleles across strainsSlide 63Three mutant genes in same “locus”Slide 65Slide 66Slide 67Slide 68Linked mutations of opposite effectSlide 70Slide 71“Multiple linked loci”Variation in submergence toleranceQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.http://www.a2mediagroup.com/data/images/news/categories/riceplant.jpgLinkage mapping (quantitative)QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.intolerant tolerantFine-mappingFinding the causative variantTransgenic testQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.http://www.plantsci.cam.ac.uk/Haseloff/SITEGRAPHICS/Agrotrans.GIFTransgenic testQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.Coding variantshttp://homepages.strath.ac.uk/~dfs99109/BB310/CFTRgene.jpgFig. 2BSingle-locus:AA x BBAB(F1)AB x ABAAABBABB(F2)25%50% 25%AAABBABBAAABBABB“Effect of having a B”1 locus, incomplete dominanceTwo locilong chromshort chromlocus 1locus 2Two lociA AA Along chromshort chromlocus 1locus 2Parent ATwo lociA AA Along chromshort chromlocus 1locus 2Parent AB BB Blong chromshort chromlocus 1locus 2Parent BTwo lociAA/AA x BB/BBA AA Along chromshort chromlocus 1locus 2Parent AB BB Blong chromshort chromlocus 1locus 2Parent BTwo lociAA/AA x BB/BBAB/AB(F1)A AA Along chromshort chromlocus 1locus 2Parent AB BB Blong chromshort chromlocus 1locus 2Parent BTwo lociAA/AA x BB/BBAB/AB(F1)A AA Along chromshort chromlocus 1locus 2Parent AB BB Blong chromshort chromlocus 1locus 2Parent BLocus1/Locus 2Two lociAA/AA x BB/BBAB/AB(F1)A AA Along chromshort chromlocus 1locus 2Parent AB BB Blong chromshort chromlocus 1locus 2Parent BLocus1/Locus 2AB/AB x AB/AB(F2)16 possibilitiesTwo loci, incomplete dominanceQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.or BATwo loci, incomplete dominanceQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.or BAor BATwo loci, incomplete dominanceQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.or BAor BATwo loci, incomplete dominanceHow many squares of the Punnett square are represented here?QuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.Effect of B at locus 2Two loci, incomplete dominanceQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.Effect of B at locus 2Two loci, incomplete dominanceQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.0 0.5 1.0 1.5PhenotypeTwo loci, incomplete dominanceQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.0 0.5 1.0 1.5Phenotype*What is the genotype?A. AA/AAB. AB/AAC. BB/AAD. AA/ABTwo loci, incomplete dominanceQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.0 0.5 1.0 1.5Phenotype*What is the genotype?A. AA/ABB. BB/ABC. AB/ABD. AA/BBTwo loci, incomplete dominanceQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.0 0.5 1.0 1.5Phenotype*How many F2’s have this genotype?A. 1/16B. 2/16C. 3/16D. 4/16Two loci, incomplete dominanceTwo loci, incomplete dominanceFig. 3.17Notation is different, trait is qualitative; math is the same.2-locus interactionQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.http://www.projects.roslin.ac.uk/chickmap/organism.htmlQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.LeghornJunglefowlTwo lociJJ/JJ x LL/LLJL/JL(F1)J JJ Jlong chromshort chromlocus 1locus 2Parent JL LL Llong chromshort chromlocus 1locus 2Parent LLocus1/Locus 2JL/JL x JL/JL(F2)16 possibilities2-locus interactionQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.2-locus interactionQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.Effect of J at locus 22-locus interactionQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.Effect of J at locus 22-locus interactionQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.Effect of J at locus 2Effect of variation at locus 2 depends on genotype at locus 1: non-additive2-locus interactionQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.Effect of J at locus 2Effect of variation at locus 2 depends on genotype at locus 1: non-additiveFor example: locus 1 is polymorphism in a transcription factor gene that affects protein binding affinity, locus 2 is in a binding site2-locus interactionQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.Effect of J at locus 2Locus 2 is epistatic to locus 1: effects of locus 1 are masked in individuals with JJ or JL,LJ at locus 2Locus 2 follows a dominance model: JJ and JL,LJ have the same phenotype, LL differs“The dominant allele of locus 2 does the masking”Other foibles in QTL mappingPathogenic yeastQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.Pathogenic yeastQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.How did YJM145 gain the ability to grow at body temperature?A model quantitative traitA model quantitative traitLab parentA model quantitative traitLab parent Pathogenic parentA model quantitative traitLab parent Pathogenic parent100 progeny ≥ pathogenic parentNO progeny as extreme as diploid hybridQuickTime™ and aTIFF (Uncompressed) decompressorare needed to see this picture.NO progeny as extreme as diploid
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