agricultural research council biotechnology platform
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Agricultural Research Council Biotechnology Platform
Purpose of the Biotechnology Platform
Vision Statement
To create a world class biotechnology platform to lead research in agriculture
in Africa
Service and Research Facilities Model
Core Services
Development group
Research teams within
platform
Unit
Research teams at Institutes
Technology Focus of Unit
Key technologies being performed with the sub-platform as services to research groups and pipelines with the ARC and to outside clients
Each sub-platform to have a development group responsible for introducing new technology and applications into the core services
Internal Research teams, lead by SR, SpR, PR level scientists. With MSc, PhD and PD level students as the major part of each team. Primarily externally funded with competitive grants
External Research teams, led by SR, SpR, PR level scientists. MSc, PhD and PD level students are the major part of each team. Primarily externally funded with competitive grants
DNA Isolation
Next Gen Sequencing
Genotyping
Genetic Mapping
Quantitative Genetics
Genomics
Databases
Annotation
Assembly
Expression Analysis
Molecular Modeling and Docking
Bioinformatics
Tissue Culture
Construct development
Transformation
Regeneration
Plant Transformation
Reverse Genetics
Gene Silencing
Male Sterile Technology
Targeted Mutagenesis
Genome Engineering
High throughput DNA Isolation
Genotyping
Informatics
Mutation Breeding
Double Haploids
Genomic Selection
High throughput imaging and
sensing
GC MS/MS
Informatics
Plant Phenotyping
NEW PARADIGM
Finding the right
genotypes
OLD PARADIGMFinding the right Animals/Plants
Shift in Paradigm from Finding Animals/Plants to Finding the right
genes/genotypes
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• Cultivar and Breed ID• Genomic Selection• SNP validation• Candidate Genes• Diversity studies• Methylation
Illumina HiScanSQ Platform (Feb 2011)
• 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)
Focused Genotyping
• BovineSNP50 BeadChip• BovineSNPHD Beadchip• CanineSNP20 BeadChip• CanineHD BeadChip• EquineSNP50 BeadChip• OvineSNP50 BeadChip• PorcineSNP60 BeadChip• CaprineSNP50 BeadChip• ChickenSNP60 BeadChip• ChickenSNPHD BeadChip• iSelect Custom Panel
Infinium BeadChip
s
SNP genotyping projects since February 2011
• 816 Bovine SNP50
• 48 Bovine HD
• 336 Caprine SNP50
• 192 Ovine SNP50
• 432 Chicken iselect SNP50
Illumina MiSeq Platform (August 2012)
• Next Generation Sequencing• Initial Specification (2012) was 1.5Gb per
run• Now: 15 Gb of DNA sequence per run
(25Gb in 2014)• Paired end sequencing• 40 M filtered clusters per flow cell• 1 lane per flow cell• Sample Multiplexing up to 96 samples per
lane• Third indexing will provide thousands of
samples at very low cost (R100 per sample).
• Sequencing costs higher then that HiSeq2500
Illumina HiSeq2500 Platform (Feb 2014)• Dual function system
• Rapid mode and standard mode sequencing• Rapid Mode
• 150 Gb of DNA sequence in 27 hours (current)• 1000 Gb of DNA sequence in 6 days (new chemistry)
• Standard Mode• 600 Gb DNA sequence in 11 days• Paired end sequencing• 1800 M filtered clusters per flow cell• 8 lanes per flow cell• Sample Multiplexing up to 96 samples per lane• Up to 384 samples per flow cell (up to 10 000 samples next year)
Illumina HiSeq2500 Platform (Feb 2014)
• Biggest DNA sequencer in Africa• Data for 10 human genomes every 6 days• Or Cow, Sheep, Chicken, Sunflower, wheat, maize
• jasper
Liquid Handling Roboticsfor “1000 samples a day”
Laser Capture Micro-dissection
What to cut…. Laser capture of samples
• Automated sample collection and object recognition
• Cutting: Manual, interactive and automated image object recognition(AxioVision)
09/11/2011 CZ South Africa Grant Martin 16
Livestock Genomics
• Genomic Selection– Livestock Genomics Consortium
• Population diversity studies - SNPs– Cattle, goats, chickens
• Diversity studies – genome sequencing– Nguni Cattle, buffalo
• Genetic studies– Swakara sheep; pig disease
Livestock Pathogens
• Many projects at OVI now using Illumina sequencing
• BTP genomics work on Anthrax, TB, E. coli• BTP molecular modeling on FMD• Tick genomics
New applications for Sequencing
• Meat Species ID – new DAFF project• Metagenomics of bacterial communities• Pathogen discovery and testing• Genotype-by-sequencing for mapping and
Marker Assisted Breeding
How much will it cost you???
March 2011 – 55 Gb/10 days
DNA Sequencing – now even faster and cheaper
March 2008 – 300Mb/3 days
July 2012 – 120 Gb/day
July 2011 – 150 Gb/10 days
Jan 2014 – 1000 Gb/6 days
Cost of sequencing
• MiSeqR1500 sample prepR2500/GB data generated
~ R2000 to generate data for a complete mitochondrial genome of 1 animal @ X30 coverageSample multiplexing options
Cost of sequencing
• HSeq2500R1100 sample prepR1100/GB data generated
~ R95 000 to generate data for a complete genome of 1 bull @ X30 coverage
Cost of genotyping
• 50-60K SNP chips R1100-R1300 landing cost of chips/animal genotyped
• 10% processing cost• ~ R1200-R1500 for genotyping an animal
Cost expected to go down with increased genotyping
Biotech Platform Jan 2013
Contacts
Dr. Jasper Rees: ReesJ@arc.agric.za
Dr. Farai Muchadeyi: MuchadeyiF@arc.agric.za
Mr. Jonathan Featherston: FeatherstonJ@arc.agric.za
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