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

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.