1. Toward the genetic basis of adaptation: Arrays/Association Mapping Justin Borevitz Ecology & Evolution University of Chicago http://naturalvariation.org/

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

3. Aranzana, et al PLOS genetics (2005), Sung Kim, Keyan Zhao 17k SNPs 96 lines

4. Local Population Variation Scott Hodges Ivan Baxter

5. Seasonal Variation Matt Horton Megan Dunning

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

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

9. Talk Outline Arabidopsis Light Response –PHYA, QTL mapping Whole Genome Tiling Arrays –Alternative splicing/Methylation –Single Feature Polymorphisms (SFPs) –Potential deletions/ Copy Number Variants –Genetic Mapping Resequencing/ Haplotypes –Variation Scanning Aquilegia for Genetics of Adaptive Radiations Arabidopsis Light Response –PHYA, QTL mapping Whole Genome Tiling Arrays –Alternative splicing/Methylation –Single Feature Polymorphisms (SFPs) –Potential deletions/ Copy Number Variants –Genetic Mapping Resequencing/ Haplotypes –Variation Scanning Aquilegia for Genetics of Adaptive Radiations

14. Quantitative Trait Loci

16. Tiling Arrays vs Resequencing Arrays AtTILE1, universal whole genome array 25mer every ~35bp, > 6.5 Million features single array, many individuals. Re-sequencing array 120Mbp*8features ~1 Billion features, 8 wafers 20 Accessions available mid year Perlegen, Max Planck (Weigel), USC (Nordborg), Salk (Ecker) GeneChip

17. Which arrays should be used? cDNA array Long oligo array

18. Which 25mer arrays should be used? Gene array Exon array Tiling array

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

20. RNADNA Universal Whole Genome Array Transcriptome Atlas Expression levels Tissues specificity Transcriptome Atlas Expression levels Tissues specificity Gene Discovery Gene model correction Non-coding/ micro-RNA Antisense transcription Gene Discovery Gene model correction Non-coding/ micro-RNA Antisense transcription Alternative Splicing Comparative Genome Hybridization (CGH) Insertion/Deletions Comparative Genome Hybridization (CGH) Insertion/Deletions Methylation Chromatin Immunoprecipitation ChIP chip Chromatin Immunoprecipitation ChIP chip Polymorphism SFPs Discovery/Genotyping Polymorphism SFPs Discovery/Genotyping Control for hybridization/genetic polymorphisms to understand true EXPRESSION polymorphisms True cis variation == Allele Specific Expression

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

22. Potential Deletions

23. Deltap0FALSECalledFDR 1.000.951886516014511.2% 1.250.95104771323907.5% 1.500.9565451150425.4% 1.750.9544841023854.2% 2.000.953298920273.4% SFP detection on tiling arrays IntergenicExonintron SFPs607702351917216 total685575665524301648 %8.86%3.53%5.71% SFPs/gene0>=1>=2>=3>=4>=5 genes1632291464304249516871121

24. 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

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

26. SFP Resequencing Advantages –Discovery and typing tool –Indels, rare variants, HMM tool –Quantitative score –Good for low polymorphism < 1% Caveats –No SNP knowledge, synonymous? –Bad for high polymorphism > 1% Rearrangements, Reference sequence

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

28. Potential Deletions >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

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

30. Natural Variation on Tiling Arrays

31. Map bibb 100 bibb mutant plants 100 wt mutant plants

32. Array Mapping Hazen et al Plant Physiology 2005

33. eXtreme Array Mapping 15 tallest RILs pooled vs 15 shortest RILs pooled

34. LOD eXtreme Array Mapping Allele frequencies determined by SFP genotyping. Thresholds set by simulations 0 4 8 12 16 020406080100 cM LOD Composite Interval Mapping RED2 QTL Chromosome 2 RED2 QTL 12cM Red light QTL RED2 from 100 Kas/ Col RILs Drosophila, Chao-Qiang Lai -Tufts University

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

36. Array Haplotyping What about Diversity/selection across the genome? A genome wide estimate of population genetics parameters, θ w, 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

37. Array Haplotyping Inbred lines Low effective recombination due to partial selfing Extensive LD blocks ColLerCviKasBayShahLzNd Chromosome1 ~500kb

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

39. Chromosome Wide Diversity

40. Diversity 50kb windows

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

42. R genes vs bHLH

43. Experimental Design of Association Study Sample > 3000 wild strains, ~100 SNPs Select 500 less structured reference fine mapping set for SFP resequencing Scan Genome for variation/selection Measure phenotype in Seasonal Chambers Haplotype map/ LD recombination blocks Associate Quantitative phenotypes with HapMap

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

45. Species with > 20k ESTs 11/14/2003 Animal lineage: good coverage Plant lineage: crop plant coverage

46. 300 F3 RILs growing (Evadne Smith) TIGR gene index 85,000 ESTs >16,00 SNPs Complete BAC physical map Clemson Nimblegen arrays Aquilegia (Columbines)

47. Genetics of Speciation along a Hybrid Zone

48. NSF Genome Complexity Microarray development –QTL candidates 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 –VIGS Whole Genome Sequencing (JGI?) Scott Hodges (UCSB) Elena Kramer (Harvard) Magnus Nordborg (USC) Justin Borevitz (U Chicago) Jeff Tompkins (Clemson)

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