Toward the genetic basis of adaptation: Arrays/Association Mapping Justin Borevitz Ecology & Evolution University o

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

2. Arabidopsis thaliana • Genome Sequence 2000 (120Mb), • 20 strains by Perlegen, Weigel, Nordborg, Ecker • ~1% sequence variation, LD extends 50-250kb • ~3000 collected “inbred” lines, >50 RIL sets • A. lyrata, Capsella rubella sister species JGI 2006 • >5300 Research Labs (17th annual conference) • Fields study data to come, Annie Schmidt et al • 340k Sequence Indexed collection of KO lines • Gene Expression Atlas >300 tissues, time points • 15,000 full length cDNAs in recombination clones

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

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

5. Local Population Variation Ivan Baxter Scott Hodges

6. Seasonal Variation Matt Horton Megan Dunning

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

9. 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

10. 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

15. Quantitative Trait Loci

17. 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

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

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

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

21. 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

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

23. Potential Deletions

24. 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%

25. 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

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

27. 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

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

29. 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

30. 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)

31. Natural Variation on Tiling Arrays

32. 100 bibb mutant plants Map bibb 100 wt mutant plants

33. Array Mapping Hazen et al Plant Physiology 2005

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

35. 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 Drosophila, Chao-Qiang Lai -Tufts University Allele frequencies determined by SFP genotyping. Thresholds set by simulations Red light QTL RED2 from 100 Kas/ Col RILs

36. 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)

37. 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

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

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

40. Chromosome Wide Diversity

41. Diversity 50kb windows

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

43. R genes vs bHLH

44. 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

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

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

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

48. Genetics of Speciationalong a Hybrid Zone

49. 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)

50. 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