ARC Biotechnology Platform:
Sequencing for Game Genomics
Dr Jasper Rees
ReesJ@arc.agric.za
Vision
To create a world class
biotechnology platform to lead
research in agriculture in Africa
Genomic Selection
Genomics
Bioinformatics
Databases
DNA Isolation
High throughput
DNA Isolation
Annotation
Next Gen
Sequencing
Genotyping
Assembly
Informatics
Expression
Analysis
Genotyping
Genetic Mapping
Plant
Transformation
Tissue Culture
Mutation Breeding
Plant Phenotyping
High throughput
imaging and
sensing
Construct
development
GC MS/MS
Transformation
Informatics
Regeneration
Genome
Engineering
Reverse Genetics
Gene Silencing
Male Sterile
Technology
Targeted
Mutagenesis
Shift in Paradigm from Finding Animals/Plants to
Finding the right genes/genotypes
OLD PARADIGM
Finding the right Animals/Plants
NEW PARADIGM
Finding the right genotypes
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Platform Synergy for Agrigenomics Research
Discovery
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107
Focused Research/Validation
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105
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Whole Genome
Screening
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10
Single Marker
Interrogate
Validate/Screen
HiSeq 2000
iScan/HiScan SQ
BeadXpress
Applications
Platform
Discover
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►
De novo Genome
Sequencing
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Genome-wide marker /
phenotype association
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Genetic Purity Screening
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mRNA Sequencing &
Gene Expression
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Focused marker /
phenotype association
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Parentage / Lineage
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SNP Discovery
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Genetic Identity
Confirmation
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Marker Assisted
Selection
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DNA Methylation,
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Targeted Resequencing
QTL Mapping
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Disease Screening
The History of DNA Sequencing Technology
Next Generation Sequencing
July 2012 – 120 Gb/day
July 2011 – 150 Gb/10 days
March 2011 – 55 Gb/10 days
March 2008 – 300Mb/3 days
DNA Sequencing:
Costs and Throughput
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)
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
2 800 000 000 000 bases of DNA
sequence since 2011 – 1000 times the
size of the buffalo genome
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
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
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
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 !!!!
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
Can the Game Breeders get GS before
the cattle breeders?
“I gave blood…. Did you?”