1. The Genome Analysis Centre Building Excellence in Genomics and Computational Bioscience

2. Sarah Ayling Computational Genomics Group Leader sarah.ayling@tgac.ac.uk Rice resequencing

3. The Genome Analysis Centre Rice Resequencing 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

4. 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 Training topics:  NGS assembly and alignment tools  Phylogenetics  Browser training  Variant calling

5. The Genome Analysis Centre Varieties The Genome Analysis Centre StressVarieties: 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

6. The Genome Analysis Centre Sequencing 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

7. The Genome Analysis Centre Sequencing depth The Genome Analysis Centre Average coverage Detect homozygous base p(0.9975) 30x Detect heterozygous base p(0.9975)

8. The Genome Analysis Centre Reference genomes The Genome Analysis Centre Indica: 93-11 Yu et al., Science 2002 Temperate japonica: Nipponbare Goff et al., Science 2002

9. The Genome Analysis Centre Align reads to references (BWA) The Genome Analysis Centre indicas japonicas javanica

10. The Genome Analysis Centre SNP discovery 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 Detect variants using GATK v1.6 Insertion/deletion realignment SNP calling and filtering

11. The Genome Analysis Centre SNPs by reference The Genome Analysis Centre

12. Heterozygosity The Genome Analysis Centre Average % heterozygous SNPs: 0.14% Range % heterozygous SNPs: 0.05-0.38% Average % heterozygous SNPs: 0.14% Range % heterozygous SNPs: 0.05-0.38% Average Ts/Tv: 2.39 Range Ts/Tv: 1.95-2.55 Average Ts/Tv: 2.39 Range Ts/Tv: 1.95-2.55

13. The Genome Analysis Centre Grouped SNPs The Genome Analysis Centre TraitNumber of shared SNPs Unique to set Shared with 1 Shared with 2 Shared with 3 Shared with 4 Shared with 5 Shared with 6 Blast43,755----266 Blight22,065--12091532 Drought27,109----123 Planthopper43,238---1-720 Quality55,256---181430 Salt51,472--391856149

14. The Genome Analysis Centre tgac-browser.tgac.ac.uk Username: viet_rice Password: v1et_r1ce

15. 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

16. The Genome Analysis Centre THANKS!