1 / 20

Genome-Wide Analysis of Transposon Insertion Polymorphisms (TIPs) Reveals Intraspecific Variation in Cultivated Rice

Genome-Wide Analysis of Transposon Insertion Polymorphisms (TIPs) Reveals Intraspecific Variation in Cultivated Rice. The TE insertion in the Pigment Gene affect the Synthesis of the Purple Pigment .

malini
Download Presentation

Genome-Wide Analysis of Transposon Insertion Polymorphisms (TIPs) Reveals Intraspecific Variation in Cultivated Rice

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. Genome-Wide Analysis of Transposon Insertion Polymorphisms (TIPs) Reveals Intraspecific Variation in Cultivated Rice

  2. The TE insertion in the Pigment Gene affect the Synthesis of the Purple Pigment . Sixty Years Ago: A high degree of intraspecific variation in maize caused by “Controlling Element” Feschotte et al, Nat. Rev. Genet. 3 (5):329-341 (2002)

  3. Natural Genetic Variation caused by Transposable Elements in cultivated Rice • Case studies on TE-Induced variation • Abundance of TE insertion polymorphisms in rice • Affect Individual Genes • Affect Genome Size • Retrotransposon polymorphisms in evolutionary analysis • Conclusions

  4. Binding to xylanases is necessary for inhibition activity May function in plant defense against secreted fungal pathogen xylanases Wheat Xylanase Inhibitor Protein I (XIP-I) XIP-I Xylanase Payan et al, J. Biol. Chem. 279 (34):36029-36037 (2004)

  5. The Rice Ortholog of Wheat XIP-I Tokunaga et al 2007 Goesaert et al 2005 Durand et al 2005 Park et al 2002

  6. The XIP-I gene split by a LTR retrotransposon in Japonica

  7. Detection of the insertion in the XIP-I gene by PCR assays

  8. Confirmation of the variation via microarray data analysis

  9. Types of TE-Induced Genetic Variation Generation of Alternative Splicing Shift of Transcription Initiation Site Expansion of Intron Size Rearrangement of Promoter Regions

  10. Identifying Transposon Insertion Polymorphisms between subspecies Step 1: Align Each Indica Contig (or BAC) to Japonica Genome Comparative genomic method Step 2: Find Cadidate Insertions and deletions between the two Genomes Homology-based method Step 3: Detect Transposon Insertions from Cadidate Insertions Structure-based method Step 4: Remove all artifacts via TSD Detection and Manual Checking

  11. 2041 between Nipponbare and 93-11 691 between Nipponbare and Guangluai 4 The Abundance of Transposon Insertion Polymorphisms in cultivated rice

  12. SNP, TIP and Introgression Feltus et al, Genome Res. 14:1812-1819 (2004)

  13. The Role on Intra-Variation in rice

  14. A Global View of Transposon Insertion Polymorphisms in a collinear region

  15. In Number In Size Majority of divergence between the two subspecies is due to TE insertions

  16. Generating ~14% (53.5 Mb) of the genomic DNA sequence different between indica and japonica The smaller size of indica genome: Deletions of TEs occur more frequently

  17. PCR-based Assays Stable Polymorphisms In a class by oneself Ancestral State is known Retrotransposon Polymorphisms in Evolutionary Analysis ? SSR ? SNP ? DNA transposon polymorphism

  18. —— Insertion Event in Different Conditions The Expected Pattern of Absence/Presence of Retrotransposon Insertion

  19. Distinct Evolutionary Route With Limited Introgression In Silico Analysis in ~23Mb Nip/GLA4 Collinear Region

  20. Conclusions • Using an integrated approach, 2041 TIPs between Nip/93-11 and 691 TIPs between Nip/GLA4 were identified; • We estimated that there’re ~11517 Transposon Insertion Polymorphisms between indica and japonica; • They also generated ~14% of the genomic DNA (53.5 Mb) sequence different between subspecies; • > 10% of TE insertions affect more than 1000 genes via various ways; • Among them, the retrotransposon polymorphisms can be used in a wide range, like genetic diversity, evolutionary route and introgression of rice varieties.

More Related