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Talk Outline

Studies of Genome Wide Molecular Variation in Arabidopsis thaliana using Arrays Justin Borevitz Salk Institute naturalvariation.org. Talk Outline. Natural Variation in Light Response Transcriptional profiling for QTL candidate genes Single Feature Polymorphisms (SFPs) Potential deletions

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Talk Outline

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  1. Studies of Genome Wide Molecular Variation in Arabidopsis thaliana using ArraysJustin BorevitzSalk Institutenaturalvariation.org

  2. Talk Outline • Natural Variation in Light Response • Transcriptional profiling • for QTL candidate genes • Single Feature Polymorphisms (SFPs) • Potential deletions • Bulk Segregant Mapping • Extreme Array Mapping • Haplotype analysis

  3. Natural Mutation in PHYA photoreceptor Natural Mutation in PHYA photoreceptor

  4. Quantitative Trait Loci

  5. differences may be due to expression or hybridization

  6. Feature level model Gene Expression index that accounts for feature effect and polymorphisms FLC controls flowering time Difference detected it 3 day old seedlings

  7. PAG1 down regulated in Cvi PLALE GREEN1 knock out has long hypocotyl in red light

  8. Potential Deletions

  9. False Discovery and Sensitivity PM only GeneChip SAM threshold SFPs nonSFPs Cereon marker accuracy 5% FDR 3806 89118 100% Sequence 817 121 696 Sensitivity Polymorphic 340 117 223 34% Non - polymorphic 477 4 473 False Discovery rate: 3% Test for independence of all factors: value = 1.845e Chisq = 177.34, df = 1, p - - 40 real data Observed t statistics vs Null (permuted) t statistics 5% FDR Permuted data

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

  11. Potential Deletions 111 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

  12. FLOWERING1 QTL deletion of MAF1 MAF1 Flowering Time QTL caused by a natural deletion in MAF1 Potential Deletions Suggest Candidate Genes Chr1 (bp)

  13. Fast Neutron deletions FKF1 80kb deletion CHR1 cry2 10kb deletion CHR1

  14. 100 bibb mutant plants Map bibb 100 wt mutant plants

  15. bibb mapping Bulk segregant Mapping using Chip hybridization bibb maps to Chromosome2 near ASYMETRIC LEAVES1 AS1 ChipMap

  16. BIBB = ASYMETRIC LEAVES1 AS1 (ASYMMETRIC LEAVES1) = MYB closely related to PHANTASTICA located at 64cM as1 bibb Sequenced AS1 coding region from bib-1 …found g -> a change that would introduce a stop codon in the MYB domain bib-1 W49* as-101 Q107* bibb as1-101 MYB

  17. Chromosome 2 16 12 RED2 QTL LOD 8 4 0 0 20 40 60 80 100 cM RED2 QTL Composite Interval Mapping eXtreme Array Mapping LOD Chromosome 1 Chromosome 2 Chromosome 4 15 tallest RILs pooled vs 15 shortest RILs pooled QTL likelihood model using bulk segregant analysis with SFP genotyping Red light QTL RED2 from 100 Kas/ Col RILs

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

  19. Review • Transcriptional profiling to identify candidate genes and downstream responses that consider polymorphisms • Single Feature Polymorphisms (SFPs) can be used to identify recombination breakpoints, potential deletions, for bulk segregant mapping, and haplotyping

  20. Salk Jon Werner Todd Mockler Sarah Liljegren Joanne Chory Detlef Weigel Joseph Ecker UC Davis Julin Maloof UC San Diego Charles Berry Scripps Elizabeth Winzeler Salk Jon Werner Todd Mockler Sarah Liljegren Joanne Chory Detlef Weigel Joseph Ecker UC Davis Julin Maloof UC San Diego Charles Berry Scripps Elizabeth Winzeler NaturalVariation.org Syngenta Hur-Song Chang Tong Zhu Syngenta Hur-Song Chang Tong Zhu University of Guelph, Canada Dave Wolyn University of Guelph, Canada Dave Wolyn

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