Widely Distributed

1. Toward the genetic basis of adaptation: Arrays/Association MappingJustin BorevitzEcology & EvolutionUniversity of Chicagohttp://naturalvariation.org/

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

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

4. Local Population Variation Ivan Baxter Scott Hodges

5. Seasonal Variation Matt Horton Megan Dunning

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

8. 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

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

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

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

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

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

21. Potential Deletions

22. 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

23. 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%

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

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

26. 100 bibb mutant plants Map bibb 100 wt mutant plants

27. Array Mapping Hazen et al Plant Physiology 2005

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

29. Chromosome 2 16 12 RED2 QTL LOD 8 4 0 0 20 40 60 80 100 cM RED2 QTL 12cM Composite Interval Mapping eXtreme Array Mapping LOD Allele frequencies determined by SFP genotyping. Thresholds set by simulations Red light QTL RED2 from 100 Kas/ Col RILs

30. 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

31. 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)

32. Natural Variation on Tiling Arrays

33. 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)

34. 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

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

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

37. Chromosome Wide Diversity

38. Diversity 50kb windows

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

40. R genes vs bHLH

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

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

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

44. Genetics of Speciationalong a Hybrid Zone

45. 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)

46. NaturalVariation.org NaturalVariation.org 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 USC Magnus Nordborg Paul Marjoram Max Planck Detlef Weigel Scripps Sam Hazen University of Michigan Sebastian Zollner