ARC Biotechnology Platform: Sequencing for Game Genomics

1. ARC Biotechnology Platform:Sequencing for Game Genomics Dr Jasper Rees ReesJ@arc.agric.za

2. Vision To create a world class biotechnology platform to lead research in agriculture in Africa

4. Bioinformatics Genomic Selection Genomics Databases Annotation Assembly Expression Analysis High throughput DNA Isolation Genotyping Informatics Mutation Breeding DNA Isolation Next Gen Sequencing Genotyping Genetic Mapping Genome Engineering Plant Phenotyping Plant Transformation Reverse Genetics Gene Silencing Male Sterile Technology Targeted Mutagenesis High throughput imaging and sensing GC MS/MS Informatics Tissue Culture Construct development Transformation Regeneration

5. Shift in Paradigm from Finding Animals/Plants to Finding the right genes/genotypes OLD PARADIGM Finding the right Animals/Plants NEW PARADIGMFinding the right genotypes

6. Platform Synergy for Agrigenomics Research Screening Discovery Focused Research/Validation >109 108 107 106 105 104 103 102 1 10 Single Marker Whole Genome Discover Interrogate Validate/Screen Platform HiSeq 2000 iScan/HiScan SQ BeadXpress ► Genetic Purity Screening ► Parentage / Lineage Applications ► Marker Assisted Selection ► Disease Screening

7. Next Generation Sequencing The History of DNA Sequencing Technology July 2012 – 120 Gb/day July 2011 – 150 Gb/10 days March 2011 – 55 Gb/10 days March 2008 – 300Mb/3 days

8. DNA Sequencing: Costs and Throughput

9. IlluminaHiScanSQ Platform • Dual function system • SNPs and Sequencing • High throughput SNPs • Infinium and GoldenGate technology • 1k to 2.5M SNP chips • Next Generation Sequencing • 150 Gb of DNA sequence per run • Paired end sequencing • 800 M filtered clusters per flow cell • 8 lanes per flow cell • Sample Multiplexing up to 48 samples per lane • Up to 384 samples per flow cell (up to 10 000 samples next year)

10. Genomics Applications Sequencing applications SNP applications GWAS Association Genetics SNP validation Candidate Genes Diversity studies • Genomes, • De novo and re-sequencing • SNPs and CNV calling • Transcriptomes, • De novo and re-sequencing • SNPs and splicing variation • Expression profiling • Small RNA • discovery and expression analysis

11. 2 800 000 000 000 bases of DNA sequence since 2011 – 1000 times the size of the buffalo genome

12. Livestock Genomics Consortium • ARC-BTP, ARC-API, UP, US, companies, TIA • Developing funding plan for full value chain to achieve genomic selection in cattle and other livestock • Genotyping – Holsteins, Ngunis– diversity analysis and start of genomic selection data • 1000 Bull Genomes Project – sequencing 10 genomes at 10x coverage to going and access full 1000 genomes dataset – 70% of data acquired

13. 1000 Bull Genomes Project • International program for bovine genome diversity analysis • Aim to sequence 1000 bull genomes from a range of breeds • Will allow the development of comprehensive genomics tools for all breeds • Will encourage collaboration and data sharing • 150 genomes sequenced to date

14. Nguni Genomes Project • To provide data to allow SA to access the 1000 bull genomes data • To generate a basic understanding of the Nguni genome variation • To provide the first resources to facilitate the understanding of the genetic value of Nguni cattle • Target: 10 genomes at 10x coverage • Progress: 9 genomes at 10-12x coverage

15. Game genomics?Getting into the genomics game… • Development of genome sequences for key species – does not need finished genomes • Sequencing a diverse range of animals to explore genetic diversity • Build of new SNP chips which cover a wide range of genetic diversity • Genotyping of wide range of animals for association genetics • PHENOTYPING !!!!

16. How are we going to Fund this? • Mixed strategies and shared funding • This is your project; so you must decide on the value to the game breeder and industry • ARC will provide some internal funds and postgraduate students • ARC will continue to invest in infrastructure to increase throughput and reduce costs (R50m and rising) • All industry funds can be increased through THRIP • R&D Tax incentive – 150% tax reclaims against R&D expenditure • Livestock Genomics Initiative and TIA

17. Can the Game Breeders get GS before the cattle breeders?

18. “I gave blood…. Did you?”