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