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

2. Linkage mapping (quantitative) intoleranttolerant

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

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

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

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

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

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

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

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

17. Two loci, incomplete dominance

18. or BA Two loci, incomplete dominance

19. or BA Two loci, incomplete dominance

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

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

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

23. 00.51.01.5 Phenotype Two loci, incomplete dominance

24. 00.51.01.5 Phenotype * What is the genotype? A.AA/AA B.AB/AA C.BB/AA D.AA/AB Two loci, incomplete dominance

25. 00.51.01.5 Phenotype * What is the genotype? A.AA/AB B.BB/AB C.AB/AB D.AA/BB Two loci, incomplete dominance

26. 00.51.01.5 Phenotype * How many F2’s have this genotype? A.1/16 B.2/16 C.3/16 D.4/16 Two loci, incomplete dominance

27. Fig. 3.17 Notation is different, trait is qualitative; math is the same.

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

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

30. 2-locus interaction

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

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

39. A model quantitative trait

40. Lab parent

41. A model quantitative trait Lab parentPathogenic parent

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

43. NO progeny as extreme as diploid hybrid

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

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

47. Did the fine-mapping…

48. Which gene is causative?

49. Tested in hybrid diploids Lab Pathogenic Lab Pathogenic

50. Tested in hybrid diploids Lab Pathogenic Lab Pathogenic

51. Tested in hybrid diploids Lab Pathogenic Lab Pathogenic

52. Tested in hybrid diploids Different in sequence Lab Pathogenic Lab Pathogenic

53. One mutant gene… From pathogenic strain

54. One mutant gene… From pathogenic strain From lab strain

55. One mutant gene… From pathogenic strain From lab strain So diploid with this gene from the pathogenic strain grows BETTER at high T.

56. Two mutant genes… From pathogenic strain From lab strain

57. Two mutant genes… From pathogenic strain From lab strain Again, diploid with this gene from the pathogenic strain grows BETTER at high T.

58. Three mutant genes From lab strain Diploid with this gene from the pathogenic strain grows WORSE at high T! From pathogenic strain

59. Three mutant genes From pathogenic strain

60. Three mutant genes From pathogenic strain

61. Three mutant genes From pathogenic strain Alleles from the same strain at different genes/loci can have different effects.

62. No common coding alleles across strains

63. And no expression differences of >3-fold…

64. Three mutant genes in same “locus”

66. Three mutant genes So why did 0/900 haploid progeny have a phenotype as extreme as the diploid hybrid?

67. Lab parentPathogenic parent NO progeny as extreme as diploid hybrid Diploid hybrid

68. Lab parentPathogenic parent NO progeny as extreme as diploid hybrid Diploid hybrid

69. Linked mutations of opposite effect Path

70. Linked mutations of opposite effect Path Lab

71. Linked mutations of opposite effect Path Lab Very unlikely

72. “Multiple linked loci”