1 / 43

Talk Outline

Natural Variation in Arabidopsis thaliana Light Response: Genomic Approaches Justin Borevitz Salk Institute naturalvariation.org. Talk Outline. Survey of light response in Arabidopsis thaliana accessions QTL mapping of light response in Ler/Cvi Recombinant Inbred Lines

leena
Download Presentation

Talk Outline

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Natural Variation in Arabidopsis thalianaLight Response:Genomic ApproachesJustin BorevitzSalk Institutenaturalvariation.org

  2. Talk Outline • Survey of light response in Arabidopsis thaliana accessions • QTL mapping of light response in Ler/Cvi Recombinant Inbred Lines • Transcriptional profiling for QTL candidate genes • Analysis of Single Feature Polymorphisms (SFPs)

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

  4. My only collection

  5. Quantitative Trait Loci

  6. Epistasis scan BQTL http://hacuna.ucsd.edu/bqtl 43,956 pair-wise tests 163 markers and 133 intervals Permutation threshold p < 0.05 (5000 permutations) Chr1 Chr2 Chr3 Chr4 Chr5 Chr1 Chr2 Chr3 Chr4 Chr5

  7. 8 58 23 62 Ka Ks McDonald-Kreitman p = 0.027 replacement synonymous = 0.23 Within Species = Between Species =

  8. Review Natural Variation • Light response variation is correlated with latitude • Functional variation in Photoreceptors PHYA, PHYB, CRY2 (El-Din El-Assal et al 2001) • New QTL identified in common and unique photoreceptor pathways • QTL may be under selection?

  9. differences may be due to expression or hybridization

  10. Potential Deletions

  11. False Discovery and Sensitivity • Cereon • may be a • sequencing • Error • TIGR • match is • a match 90% 80% 70% 41% 53% 85% 90% 80% 70% 67% 85% 100% 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 GeneChip SAM threshold SFPs nonSFPs Cereon marker accuracy 18% FDR 10627 82297 100% Sequence 817 223 594 Sensitivity Polymorphic 340 195 145 57% Non - polymorphic 477 28 449 False Discovery rate: 13% Test for indep endence of all factors: Chisq = 265.13, df = 1, p - value = 1.309e - 59

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

  13. bibb mutant phenotypes • three independent recessive alleles • medial sepals remain attached • “cabbage-like” rosette leaves • flowers open prematurely • fruit appear more slender 23 days Col bib-1 det2-1 Ler bib-3 bib-3 bib-3

  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=AS1 • 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. 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

  18. Gene expression revisited Gene Expression index that accounts for feature effect and polymorphisms ~100 genes @ 20% FDR FLC controls flowering time Difference detected at 3 day old seedling stage

  19. Gene expression revisited PAG1 down regulated in Cvi PLALE GREEN1 knock out

  20. pag1 KO is light insensitive pag1 KO has long hypocotyl in red light

  21. Review • Transcriptional profiling to identify candidate genes and downstream responses • Single Feature Polymorphisms (SFPs) can be used for identifying recombination breakpoints, bulk segregant mapping, and haplotyping • Consider polymorphisms for expression analysis

  22. Complete Genome Tiling Chip 1st Set 25 bp 25 bp 8 bp 25 bp 25 bp 2nd Set 16 bp 25 bp 25 bp 3rd Set Extra Chips: 9 Whole-Genome Expression Chips 2 Splicing Chips 2 5’ Mapping Chips New Gene Discovery Improve Annotation Alternative Splicing Micro RNAs ChIP – Chip (DNA binding sites) Polymorphisms (re-sequencing) Global methylation (Methylome) Comparative Genomics (Brassica) Validate features

  23. ChipViewer: Mapping of transcriptional units of ORFeome From 2000v At1g09750 (MIPS) to the latest AGI At1g09750 2000 v Annotation (MIPS) The latest AGI Annotation

  24. 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

More Related