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Talk Outline

Natural Variation in Arabidopsis thaliana Light Response Justin Borevitz Salk Institute naturalvariation.org. Talk Outline. Survey of light response in Arabidopsis thaliana accessions QTL mapping of light response in Ler/Cvi Recombinant Inbred Lines

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Talk Outline

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  1. Natural Variation in Arabidopsis thaliana Light ResponseJustin BorevitzSalk Institutenaturalvariation.org

  2. Talk Outline • Survey of light response in Arabidopsis thaliana accessions • QTL mapping of light response in Ler/Cvi Recombinant Inbred Lines • Sequence variation at a PHYTOCHROME B • Extent of Linkage Disequilibrium and Association Mapping

  3. Light Affects the Entire Plant Life Cycle de-etiolation } hypocotyl

  4. Light Affects the Entire Plant Life Cycle Light response variation can be seen under constant conditions in the lab Natural Variation != Natural Selection

  5. My only collection

  6. Natural Variation in Light Sensitivity

  7. M548T alters PHYB Red Light Sensitivity

  8. PHYTOCHROME A variation • Met 548 is conserved in all plant phytochromes. Lm-2 is the only accession with The 548 • Lm-2 bulk descent lines all have M548T • Lm-2, Single amino acid change and 2 synonymous changes, relative to Col-0 • Col and Ler PHYA sequence is the same. • Kas1 PHYA has 3 new synonymous changes in 6kb

  9. Quantitative Trait Loci

  10. Epistasis scan Chr1 Chr2 Chr3 Chr4 Chr5 Chr1 Chr2 Chr3 Chr4 Chr5

  11. 8 58 23 62 Ka Ks McDonald-Kreitman p = 0.027 replacement synonymous = 0.23 Within Species = Between Species =

  12. Review Light response variation is correlated with latitude Functional variation in Photoreceptors PHYA, PHYB, CRY2 New loci identified in common and unique photoreceptor pathways QTL may be under selection?

  13. Linkage Disequilibrium Mapping • What is the extent of LD in Arabidopsis? locus and genome wide • Can this be used to fine map QTL? • Genome wide association scans?

  14. The extent of LD is highly variable 100kb, 250kb, 50kb Tian et. al. 2002 RPS5 LD < 10kb

  15. A star phylogeny 163 markers 73 accessions ~ 750kb/marker

  16. Test for association with light response

  17. Association mapping at LIGHT1 LIGHT1 QTL interval SNP108 Test statistic Decay of LD with distance Chromosome 1 (7.1Mb – 7.5Mb) White light

  18. SNP108 Chromosome 1 (6.5Mb – 8Mb) Association mapping at LIGHT1 SNP108 Test statistic Chromosome 1 (7.1Mb – 7.5Mb) Red light

  19. LD mapping at LIGHT2 (PHYB) Test statistic PHYB Chromosome 2 (8Mb – 8.25Mb)

  20. Future work with Natural Variation • VanC advanced intercross RIL population • Backcross collections

  21. NaturalVariation.org • Salk • Joanne Chory • Detlef Weigel • Joseph Ecker • UC Davis • Julin Maloof • UC San Diego • Charles Berry • USC • Magnus Nordborg • Jenny Hagenblad • Stanford • Tina Noyes • Sujatha Krishnakumar • Peter Oefner • Salk • Joanne Chory • Detlef Weigel • Joseph Ecker • UC Davis • Julin Maloof • UC San Diego • Charles Berry • USC • Magnus Nordborg • Jenny Hagenblad • Stanford • Tina Noyes • Sujatha Krishnakumar • Peter Oefner • UChicago • Eli Stahl • Joy Bergelson • Martin Kreitman • UChicago • Eli Stahl • Joy Bergelson • Martin Kreitman

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