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Talk Outline

Light response QTL in Arabidopsis thaliana : LIGHT1 cloning Justin Borevitz Ecology & Evolution University of Chicago naturalvariation.org. Talk Outline. Natural Variation in Light Response QTL Mapping/ fine mapping Gene Expression candidates KO candidates Aquilegia : new model organism.

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Talk Outline

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  1. Light response QTL in Arabidopsis thaliana: LIGHT1 cloning Justin BorevitzEcology & EvolutionUniversity of Chicagonaturalvariation.org

  2. Talk Outline • Natural Variation in Light Response • QTL Mapping/ fine mapping • Gene Expression candidates • KO candidates • Aquilegia: new model organism • Natural Variation in Light Response • QTL Mapping/ fine mapping • Gene Expression candidates • KO candidates • Aquilegia: new model organism

  3. Light Affects the Entire Plant Life Cycle Light response variation can be seen under constant conditions in the lab Natural Variation under selection? Test in field

  4. Quantitative Trait Loci

  5. Marker Mb SM184 5.50 SM50 5.87 SM35 6.34 SM106 7.01 G2395 7.30 SNP377 7.44 CER45 7.60 MAT7787 7.79 MSAT7964 7.96 TH1 8.13 8.29 SEQ8298 8.65 SM40 SNP65 9.32 mm Near-Isogenic Lines for LIGHT1 Ler / Cvi RVE7 GI Ler 81N-J 17A-A/J 114 124 189 Line 194 6 2 4 3 3 3 Plants 3 5.8 5.8 5.1 5.9 5.7 5.8 Phenotype 5.0

  6. LIGHT1 Fine-mapping (Ler / Cvi) NIL189 NIL114 Mb 7.440 NIL194 7.460 7.480 7.500 7.520 7.540 Mb 7.540 7.560 7.580 Candidate Interval: 135 Kb 34 predicted genes Original Marker 7.600 7.620 7.640 7.660 7.680 7.675 Mb 7.700 7.720 7.740 7.760 7.780

  7. Ler 189 194 114 Ler 189 194 114 Ler 189 194 114 LIGHT1 (Ler / Cvi) in different light environments

  8. Gene Expression polymorphism between Ler and NIL189 50 genes down regulated in NIL189 compared to Ler 5 genes up regulated in NIL189 compared to Ler

  9. At1g21600 only gene in the LIGHT1 interval that is misexpressed

  10. At1g21600 is circadian-regulated

  11. TDNA lines in the LIGHT1 region No quantitative hypocotyl differences in 22 lines

  12. LIGHT1: At1g21600

  13. At1g21600 an allelic series of artificial mutations Tilling: splice junction TDNA: Salk_024431 Ler: F29L Tilling: A30= Tilling: D103N Tilling Intron; C to T

  14. At1g21600 is a single copy gene in multiple plant species

  15. 5’ end of At1g21600 is not well conserved LF At1g21600 The candidate QTN has mutated several times independantly

  16. Natural Varition in At1g216003 nt and 1 AA change between Ler and Cvi Sequenced 96 accessions for At1g21600, LIGHT1 candidate gene Magnus Nordborg 10 accessions sequenced for 5’ end of At1g21600 Mt-0 (North Africa) shares AA change with Ler (Poland)

  17. At1g21600 AA change is associated with Hypocotyl length and Flowering time Hypocotyl data: P-value Red light + PhyB 2 0.01828 Red light + PhyB 7 0.01627 White light + PhyB 7 0.04189 Blue light + PhyB 1 0.03489 Flowering time data: LD True Leaf Number + FRI 0.01482 LD Days to Flowering + FRI 0.004912

  18. LIGHT1 (Ler / Cvi) : future projects Further fine-mapping: Screen 4000 NIL189 Het plants Phenotype KO mutants (25 of the 34 candidate genes)Sequence some candidate SNPs across accessionsTransgenics (complementation / functional analysis)

  19. Seasons in the Growth Chamber • Changing Day length • Cycle Light Intensity • Cycle Light Colors • Cycle Temperature

  20. Aquilegia (Columbines) Recent adaptive radiation, 350Mb genome

  21. Plant lineage: crop plant coverage > 20k dbEST 11/14/2003 Animal lineage: good coverage

  22. NSF Genome Complexity • 35,000 ESTs 5’ and 3’ • 350 arrays, RNA and genotyping • High density SFP Genetic Map • Physical Map (BAC tiling path) • Physical assignment of ESTs • QTL for pollinator preference • ~400 RILs, map abiotic stress • QTL fine mapping/ LD mapping • Develop transformation techniques Scott Hodges (UCSB) Elena Kramer (Harvard) Magnus Nordborg (USC) Justin Borevitz (U Chicago) Jeff Tompkins (Clemson)

  23. NaturalVariation.org NaturalVariation.org Salk Todd Michael Olivier Loudet Joanne Chory Detlef Weigel Joseph Ecker Scripps Sam Hazen Salk Todd Michael Olivier Loudet Joanne Chory Detlef Weigel Joseph Ecker Scripps Sam Hazen University of Chicago Xu Zhang Evadne Smith UC Davis Julin Maloof University of Chicago Xu Zhang Evadne Smith UC Davis Julin Maloof

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