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

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

6. 6 Platform Synergy for Agrigenomics Research HiSeq 2000 iScan/HiScan SQ BeadXpress InterrogateValidate/ScreenDiscover ► De novo Genome Sequencing ► mRNA Sequencing & Gene Expression ► SNP Discovery ► DNA Methylation, Targeted Resequencing Applications Platform ► Genome-wide marker / phenotype association ► Focused marker / phenotype association ► Genetic Identity Confirmation ► QTL Mapping Disease Screening ► Marker Assisted Selection ► Parentage / Lineage ► Genetic Purity Screening ► 1 10 10 2 10 3 10 4 10 5 10 6 10 7 10 8 >10 9 Discovery Focused Research/Validation Screening Whole Genome Single Marker

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

8. DNA Sequencing: Costs and Throughput

9. Illumina HiScanSQ 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 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 SNP applications GWAS Association Genetics SNP validation Candidate Genes Diversity studies

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?”