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Variation in submergence tolerance

Variation in submergence tolerance. http://www.a2mediagroup.com/data/images/news/categories/riceplant.jpg. Linkage mapping (quantitative). intolerant. tolerant. Fine-mapping. Finding the causative variant. Transgenic test. http://www.plantsci.cam.ac.uk/Haseloff/SITEGRAPHICS/Agrotrans.GIF.

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Variation in submergence tolerance

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  1. Variation in submergence tolerance http://www.a2mediagroup.com/data/images/news/categories/riceplant.jpg

  2. Linkage mapping (quantitative) intolerant tolerant

  3. Fine-mapping

  4. Finding the causative variant

  5. Transgenic test http://www.plantsci.cam.ac.uk/Haseloff/SITEGRAPHICS/Agrotrans.GIF

  6. Transgenic test

  7. Coding variants http://homepages.strath.ac.uk/~dfs99109/BB310/CFTRgene.jpg Fig. 2B

  8. Single-locus: AA x BB AB (F1) AB x AB AA AB BA BB (F2)

  9. 1 locus, incomplete dominance AB BA AA BB “Effect of having a B” 25% 50% 25% AB BA AA BB

  10. Two loci long chrom short chrom locus 2 locus 1

  11. Two loci long chrom short chrom Parent A A A A A locus 2 locus 1

  12. Two loci long chrom long chrom short chrom short chrom Parent A Parent B A A B B A A B B locus 2 locus 2 locus 1 locus 1

  13. Two loci long chrom long chrom short chrom short chrom Parent A AA/AA x BB/BB Parent B A A B B A A B B locus 2 locus 2 locus 1 locus 1

  14. Two loci long chrom long chrom short chrom short chrom Parent A AA/AA x BB/BB Parent B A A B B A A B B locus 2 locus 2 locus 1 locus 1 AB/AB (F1)

  15. Two loci long chrom long chrom short chrom short chrom Parent A AA/AA x BB/BB Parent B A A B B A A B B locus 2 locus 2 locus 1 locus 1 AB/AB (F1) Locus1/Locus 2

  16. Two loci long chrom long chrom short chrom short chrom Parent A AA/AA x BB/BB Parent B A A B B A A B B locus 2 locus 2 locus 1 locus 1 AB/AB (F1) Locus1/Locus 2 AB/AB x AB/AB 16 possibilities (F2)

  17. Two loci, incomplete dominance

  18. Two loci, incomplete dominance or BA

  19. Two loci, incomplete dominance or BA or BA

  20. Two loci, incomplete dominance How many squares of the Punnett square are represented here? or BA or BA

  21. Two loci, incomplete dominance Effect of B at locus 2

  22. Two loci, incomplete dominance Effect of B at locus 2

  23. 0 0.5 1.0 1.5 Phenotype Two loci, incomplete dominance

  24. 0 0.5 1.0 1.5 Phenotype Two loci, incomplete dominance * What is the genotype? AA/AA AB/AA BB/AA AA/AB

  25. 0 0.5 1.0 1.5 Phenotype Two loci, incomplete dominance * What is the genotype? AA/AB BB/AB AB/AB AA/BB

  26. 0 0.5 1.0 1.5 Phenotype Two loci, incomplete dominance * How many F2’s have this genotype? 1/16 2/16 3/16 4/16

  27. Two loci, incomplete dominance Notation is different, trait is qualitative; math is the same. Fig. 3.17

  28. 2-locus interaction Junglefowl Leghorn http://www.projects.roslin.ac.uk/chickmap/organism.html

  29. Two loci long chrom long chrom short chrom short chrom Parent J JJ/JJ x LL/LL Parent L J J L L J J L L locus 2 locus 2 locus 1 locus 1 JL/JL (F1) Locus1/Locus 2 JL/JL x JL/JL 16 possibilities (F2)

  30. 2-locus interaction

  31. 2-locus interaction Effect of J at locus 2

  32. 2-locus interaction Effect of J at locus 2

  33. 2-locus interaction Effect of J at locus 2 Effect of variation at locus 2 depends on genotype at locus 1: non-additive

  34. 2-locus interaction For example: locus 1 is polymorphism in a transcription factor gene that affects protein binding affinity, locus 2 is in a binding site Effect of J at locus 2 Effect of variation at locus 2 depends on genotype at locus 1: non-additive

  35. 2-locus interaction Effect of J at locus 2 Locus 2 is epistatic to locus 1: effects of locus 1 are masked in individuals with JJ or JL,LJ at locus 2 Locus 2 follows a dominance model: JJ and JL,LJ have the same phenotype, LL differs “The dominant allele of locus 2 does the masking”

  36. Other foibles in QTL mapping

  37. Pathogenic yeast

  38. Pathogenic yeast How did YJM145 gain the ability to grow at body temperature?

  39. A model quantitative trait

  40. A model quantitative trait Lab parent

  41. A model quantitative trait Lab parent Pathogenic parent

  42. A model quantitative trait 100 progeny ≥ pathogenic parent Lab parent Pathogenic parent

  43. NO progeny as extreme as diploid hybrid

  44. NO progeny as extreme as diploid hybrid

  45. NO progeny as extreme as diploid hybrid Diploid hybrid Lab parent Pathogenic parent

  46. Did the mapping… Significant linkage to yeast chrom XIV and chrom XVI.

  47. Did the fine-mapping…

  48. Did the fine-mapping… Which gene is causative?

  49. Tested in hybrid diploids Pathogenic Pathogenic Lab Lab

  50. Tested in hybrid diploids Pathogenic Pathogenic Lab Lab

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