Agi apr13 aylings
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Agi apr13 aylings

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Agi apr13 aylings Agi apr13 aylings Presentation Transcript

  • The Genome Analysis Centre Building Excellence in Genomics and Computational Bioscience
  • Sarah Ayling Computational Genomics Group Leader sarah.ayling@tgac.ac.uk Rice resequencing
  • The Genome Analysis Centre The Genome Analysis CentreThe Genome Analysis Centre The Genome Analysis Centre RiceResequencing Project Aim: To bring genomics capability to rice breeding in Vietnam in light of changing climates Approach: Sequence varieties with interesting phenotypes and provide training in bioinformatics View slide
  • The Genome Analysis Centre The Genome Analysis Centre Training at TGAC Two scientists from AGI visited TGAC in September 2012 for bioinformatics training Training topics:  NGS assembly and alignment tools  Phylogenetics  Browser training  Variant calling View slide
  • The Genome Analysis Centre The Genome Analysis Centre Varieties The Genome Analysis Centre The Genome Analysis Centre Stress Varieties: indica, japonica and javanica Bacterial Blight Resistance Hom rau; Khau dien lu; Nep meo nuong; Tep Thai Binh; Toc lun Blast Resistance Ble te lo; Khau mac Buoc; Chiem nho Bac Ninh 2; Nep lun; OM 6377 Brown Planthopper Resistance Chan thom; Coi ba dat; Khau giang; OM5629; Xuong ga Drought tolerance Ba cho K’te; Blao sinh sai; Tan ngan; Nang quot bien; Nep bo hong Hai Duong; Quality potential Nang thom cho Dao; Tam xoan Bac Ninh; Tam xoan Hai Hau; Te Nuong; OM 3536; Thom lai Salt tolerance Lua Ngoi; Mot bui do; Chiem do; Nang co do 2; Nep man Unclassified Nep ong tao; Khau Lien; Lua goc do; Chiem da; IS1.2
  • The Genome Analysis Centre The Genome Analysis Centre Sequencing The Genome Analysis Centre The Genome Analysis Centre Illumina HiSeq 2000 • DNA sheared into fragments 300-500 bp in length • 100bp sequenced from both ends of fragments • 18 lanes of sequencing (2.25 flowcells) • 1.3 Tb of sequence data
  • The Genome Analysis Centre The Genome Analysis Centre Chiemda Chiemdo ChiemnhoBacNinh2 IS1.2 Luagocdo Nangcodo2 NepbohongHaiDuong Neplun Nepman OM3536 OM6377 TepThaiBinh ThomLai Toclun Xuongga BachoK’te Blaosinhsai Bletelo Chanthom Coibadat Homrau Khaudienlu Khaugiang KhauLien Khaumacbuoc LuaNgoi Motbuido Nangthomchodao Nepmeonuong Nepongtao OM5629 TamxoanBacNinh TamxoanHaiHau Tanngan TeNuong Nangquotbien 0 10 20 30 40 50 60 70 Varieties Coverage(assuming430Mbgenomesize) Sequencing depth The Genome Analysis Centre The Genome Analysis Centre Average coverage Detect homozygous base p(0.9975) 30x Detect heterozygous base p(0.9975)
  • The Genome Analysis Centre The Genome Analysis Centre Reference genomes The Genome Analysis Centre The Genome Analysis Centre Indica: 93-11 Yu et al., Science 2002 Temperate japonica: Nipponbare Goff et al., Science 2002
  • The Genome Analysis Centre The Genome Analysis Centre Align reads to references (BWA) The Genome Analysis Centre The Genome Analysis Centre Chiemda Chiemdo ChiemnhoBacNinh2 IS1.2 Luagocdo Nangcodo2 NepbohongHaiDuong Neplun Nepman OM3536 OM6377 TepThaiBinh ThomLai Toclun Xuongga BachoK’te Blaosinhsai Bletelo Chanthom Coibadat Homrau Khaudienlu Khaugiang KhauLien Khaumacbuoc LuaNgoi Motbuido Nangthomchodao Nepmeonuong Nepongtao OM5629 TamxoanBacNinh TamxoanHaiHau Tanngan TeNuong Nangquotbien 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% unaligned Japonica-specific Indica-specific aligned to both Varieties Percentageofreads indicas japonicas javanica
  • The Genome Analysis Centre The Genome Analysis Centre SNP discovery The Genome Analysis Centre The Genome Analysis Centre Align reads to references using BWA v0.6.1 Detect variants using GATK v1.6 Insertion/deletion realignment SNP calling and filtering
  • The Genome Analysis Centre The Genome Analysis Centre SNPs by reference The Genome Analysis Centre The Genome Analysis Centre 0 200000 400000 600000 800000 1000000 1200000 1400000 1600000 1800000 0 200000 400000 600000 800000 1000000 1200000 1400000 1600000 NumberofSNPsonjaponicareference Number of SNPs on indica reference Indicas Japonicas javanica
  • The Genome Analysis Centre The Genome Analysis Centre Heterozygosity The Genome Analysis Centre The Genome Analysis Centre Average % heterozygous SNPs: 0.14% Range % heterozygous SNPs: 0.05-0.38% Average Ts/Tv: 2.39 Range Ts/Tv: 1.95-2.55
  • The Genome Analysis Centre The Genome Analysis Centre Grouped SNPs The Genome Analysis Centre The Genome Analysis Centre Trait Number of shared SNPs Unique to set Shared with 1 Shared with 2 Shared with 3 Shared with 4 Shared with 5 Shared with 6 Blast 43,755 - - - - 2 6 6 Blight 22,065 - - 1 20 9 15 32 Drought 27,109 - - - - 1 2 3 Planthopper 43,238 - - - 1 - 7 20 Quality 55,256 - - - 1 8 14 30 Salt 51,472 - - 3 9 18 56 149
  • The Genome Analysis Centre The Genome Analysis Centre tgac-browser.tgac.ac.uk Username: viet_rice Password: v1et_r1ce
  • The Genome Analysis Centre The Genome Analysis CentreThe Genome Analysis Centre The Genome Analysis Centre Acknowledgements Mario Caccamo Sarah Ayling Melanie Febrer Anil Thanki Xingdong Bian Prof Ham Khuat Huu Trung Khoa Nguyen Truong and colleagues Giles Oldroyd Christian Rogers
  • The Genome Analysis Centre The Genome Analysis Centre THANKS!