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

Widely Distributed Olivier Loudet

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

Local Population Variation Scott Hodges Ivan Baxter

Seasonal Variation Matt Horton Megan Dunning

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

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

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

Quantitative Trait Loci

Which arrays should be used? cDNA array Long oligo array

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

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

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

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

Potential Deletions

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

Deltap0FALSECalledFDR % % % % % SFP detection on tiling arrays IntergenicExonintron SFPs total %8.86%3.53%5.71% SFPs/gene0>=1>=2>=3>=4>=5 genes

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

Chip genotyping of a Recombinant Inbred Line 29kb interval

Map bibb 100 bibb mutant plants 100 wt mutant plants

Array Mapping Hazen et al Plant Physiology 2005

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

LOD eXtreme Array Mapping Allele frequencies determined by SFP genotyping. Thresholds set by simulations cM LOD Composite Interval Mapping RED2 QTL Chromosome 2 RED2 QTL 12cM Red light QTL RED2 from 100 Kas/ Col RILs

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

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)

Natural Variation on Tiling Arrays

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

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

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

SFPs for reverse genetics 14 Accessions 30,950 SFPs`

Chromosome Wide Diversity

Diversity 50kb windows

Tajima’s D like 50kb windows RPS4 unknown

R genes vs bHLH

Aquilegia (Columbines) Recent adaptive radiation, 350Mb genome

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

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

Genetics of Speciation along a Hybrid Zone

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)

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