Widely Distributed

1. Tiling arrays for genetic, epigentic, and environmental variation in Arabidopsis thalianaJustin BorevitzEcology & EvolutionUniversity of Chicagohttp://naturalvariation.org/

2. Widely Distributed Olivier Loudet http://www.inra.fr/qtlat/NaturalVar/NewCollection.htm

3. Local Population Variation Ivan Baxter Scott Hodges

4. Seasonal Variation Matt Horton Megan Dunning

5. Seasons in the Growth Chamber Seasons in the Growth Chamber Developmental Plasticity == Behavior Developmental Plasticity == Behavior Sweden Spain • Changing Day length • Cycle Light Intensity • Cycle Light Colors • Cycle Temperature • Changing Day length • Cycle Light Intensity • Cycle Light Colors • Cycle Temperature

6. Which arrays should be used? BAC array cDNA array Long oligo array

7. Which 25mer arrays should be used? Gene array Exon array Tiling array 35bp tile, 25mers 10bp gaps

8. Which 25mer arrays should be used? SNP array Ressequencing array Tiling/SNP array

9. Universal Whole Genome Array DNA RNA Gene/Exon Discovery Gene model correction Non-coding/ micro-RNA Chromatin Immunoprecipitation ChIP chip Alternative Splicing Methylation Antisense transcription Polymorphism SFPs Discovery/Genotyping Transcriptome Atlas Expression levels Tissues specificity Comparative Genome Hybridization (CGH) Insertion/Deletions Copy Number Polymorphisms RNA Immunoprecipitation RIP chip Allele Specific Expression Control for hybridization/genetic polymorphisms to understand true EXPRESSION polymorphisms

10. Improved Genome Annotation ORFa Transcriptome Atlas ORFb start AAAAA deletion M M M M M M M M M M M M SFP SNP SNP SFP SFP conservation Chromosome (bp)

11. Talk Outline • Whole Genome Tiling Arrays • Spatial Correction, grid alignment • Alternative splicing • Methylation • Single Feature Polymorphisms (SFPs) • Genetic Mapping • Potential deletions/ Copy Number Variants • Allele Specific Expression • Resequencing/ Haplotypes • Variation Scanning • Whole Genome Tiling Arrays • Spatial Correction, grid alignment • Alternative splicing • Methylation • Single Feature Polymorphisms (SFPs) • Genetic Mapping • Potential deletions/ Copy Number Variants • Allele Specific Expression • Resequencing/ Haplotypes • Variation Scanning

12. Tiling Array Re annotation • 6.25Million probes • 3.125Million PM probes • 1.67Million unique PM probes 17bp (blast) • 736k PM features in TUs (exon array) • 130k TUs • 28k genes

13. Spatial Correction, grid Alignment Background correction for RNA, ! For DNA

14. Transcription subUnits (TUs) Intron1 Exon1 Exon2 Tu1 Tu2 Tu3

15. Alternative Splicing Van Col V V V C C C Xu Zhang

16. Gene/Tu model for alternative splicing

17. ChIP chip treatment effect! Experimental Design same protocol/antibody dynamic binding model treatment effect Actual biological signal

18. Potential Deletions

19. Methods for labeling • Extract genomic 100ng DNA (single leaf) • Digest with either msp1 or hpa2 CCGG • Label with biotin random primers • Hybridize to array • Fit model Y = m + E * G + e

20. SFP detection on tiling arrays Delta p0 FALSE Called FDR 1.00 0.95 18865 160145 11.2% 1.25 0.95 10477 132390 7.5% 1.50 0.95 6545 115042 5.4% 1.75 0.95 4484 102385 4.2% 2.00 0.95 3298 92027 3.4%

21. methylated features and mSFPs Enzyme effect, on CCGG features GxE mQTL? >10,000 of 100,000 at 5% FDR 276 at 15% FDR

22. Chip genotyping of a Recombinant Inbred Line 29kb interval

23. 100bibb mutant plants Mapbibb 100wt mutant plants

24. Array Mapping Hazen et al Plant Physiology 2005

25. Potential Deletions (wild lines) >500 potential deletions 45 confirmed by Ler sequence 23 (of 114) transposons Disease Resistance (R) gene clusters Single R gene deletions Genes involved in Secondary metabolism Unknown genes

26. Het Fast Neutron deletions FKF1 80kb deletion CHR1 cry2 10kb deletion CHR1

27. Natural Variation on Tiling Arrays

28. FLM natural deletion FLM Potential Deletions Suggest Candidate Genes FLOWERING1 QTL Chr1 (bp) Flowering Time QTL caused by a natural deletion in FLM (Werner et al PNAS 2005)

29. Allele specific expression

30. Col Female imprint Col allele expressed cis regulatory variation Col/Col Col/Van Van allele expressed Van/Col Van/Van

31. Allele specific expressionbetween Col and Van

32. Array Haplotyping • What about Diversity/selection across the genome? • A genome wide estimate of population genetics parameters, θw, π, Tajima’D, ρ • LD decay, Haplotype block size • Deep population structure? • Col, Lz, Bur, Ler, Bay, Shah, Cvi, Kas, C24, Est, Kin, Mt, Nd, Sorbo, Van, Ws2 Fl-1, Ita-0, Mr-0, St-0, Sah-0

33. Chromosome1 ~500kb Col Ler Cvi Kas Bay Shah Lz Nd Array Haplotyping Inbred lines Low effective recombination due to partial selfing Extensive LD blocks

34. SFPs for reverse genetics 14 Accessions 30,950 SFPs` http://naturalvariation.org/sfp

35. Chromosome Wide Diversity

36. Diversity 50kb windows

37. Tajima’s D like 50kb windows RPS4 unknown

38. R genes vs bHLH

39. NaturalVariation.org NaturalVariation.org University of Chicago Xu Zhang Evadne Smith Ken Okamoto Yan Li Michigan State Shinhan Shui Purdue Ivan Baxter Sainsbury Laboratory Jonathan Jones University of Chicago Xu Zhang Evadne Smith Ken Okamoto Yan Li Michigan State Shinhan Shui Purdue Ivan Baxter Sainsbury Laboratory Jonathan Jones USC Magnus Nordborg Paul Marjoram Max Planck Detlef Weigel Scripps Sam Hazen University of Michigan Sebastian Zollner USC Magnus Nordborg Paul Marjoram Max Planck Detlef Weigel Scripps Sam Hazen University of Michigan Sebastian Zollner