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Talk Outline

High Resolution Patterns of Variation in the Arabidopsis Genome Justin Borevitz University of Chicago naturalvariation.org. Talk Outline. Natural Variation in Light Response Single Feature Polymorphisms (SFPs) Potential deletions Haplotype analysis Patterns in gene Families New Arrays

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Talk Outline

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  1. High Resolution Patterns of Variationin the Arabidopsis GenomeJustin BorevitzUniversity of Chicagonaturalvariation.org

  2. Talk Outline • Natural Variation in Light Response • Single Feature Polymorphisms (SFPs) • Potential deletions • Haplotype analysis • Patterns in gene Families • New Arrays • Aquilegia • Natural Variation in Light Response • Single Feature Polymorphisms (SFPs) • Potential deletions • Haplotype analysis • Patterns in gene Families • New Arrays • Aquilegia

  3. Light Affects the Entire Plant Life Cycle Light response variation can be seen under constant conditions in the lab Natural Variation under selection? Test in field

  4. What is Array Genotyping? • Affymetrix expression GeneChips contain 202,806 unique 25bp oligo nucleotides. • 11 features per probset for 21546 genes • New array’s have even more • Genomic DNA is randomly labeled with biotin, product ~50bp. • 3 independent biological replicates compared to the reference strain Col GeneChip

  5. Potential Deletions

  6. 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

  7. 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

  8. Pairwise Correlation between and within replicates

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

  10. Distribution of T-stats 208,729 null (permutation) actual 32,427 Calls Not Col NA Col NA duplications 12,250 SFPs

  11. Sequence confirmation of SFPs

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

  13. Chromosome Wide Diversity

  14. Diversity 50kb windows

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

  16. RPS4 R genes vs bHLH Theta W

  17. RPS4 Rgenes vs bHLH Tajimas’ D

  18. R genes vs bHLH

  19. Review • Single Feature Polymorphisms (SFPs) can be used to • Potential deletions (candidate genes) • Identify recombination breakpoints • eXtreme Array Mapping • Haplotyping • Diversity/Selection • Association Mapping

  20. 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 ~35 bp tile, non-repetitive regions, “good” binding oligos, evenly spaced

  21. 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)

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

  23. NSF Genome Complexity • 35,000 ESTs 5’ and 3’ • 350 arrays, RNA and genotyping • High density SFP Genetic Map • Physical Map (BAC tiling path) • Physical assignment of ESTs • QTL for pollinator preference • and abiotic stress • QTL fine mapping/ LD mapping • Develop transformation techniques Scott Hodges (UCSB) Elena Kramer (Harvard) Magnus Nordborg (USC) Justin Borevitz (U Chicago) Jeff Tompkins (Clemson)

  24. Future work with Natural Variation • VanC advanced intercross RIL population • Backcross collections

  25. NaturalVariation.org NaturalVariation.org Salk Jon Werner Sarah Liljegren Huaming Chen Joanne Chory Detlef Weigel Joseph Ecker UC San Diego Charles Berry Scripps Sam Hazen Elizabeth Winzeler University of Chicago Xu Zhang Evadne Smith Syngenta Hur-Song Chang Tong Zhu UC Davis Julin Maloof University of Guelph, Canada Dave Wolyn Sainsbury Laboratory Jonathan Jones Salk Jon Werner Sarah Liljegren Huaming Chen Joanne Chory Detlef Weigel Joseph Ecker UC San Diego Charles Berry Scripps Sam Hazen Elizabeth Winzeler University of Chicago Xu Zhang Evadne Smith Syngenta Hur-Song Chang Tong Zhu UC Davis Julin Maloof University of Guelph, Canada Dave Wolyn Sainsbury Laboratory Jonathan Jones

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