3b. Biotechnolgies & Genomics - Jane Theaker

1. Workflow solutions for current
challenges in agricultural biotechnology
JaneTheaker, VP Science and Technology Development, LGC

2. Breeding program workflow
Sample
collection
DNA
extraction
Discovery,
breeding, and
association
studies
SNP validation,
QC, and routine
screening
Bio-
informatics
Challenges
Fit for purpose
collection tools
Automation for
sample collection
Sample tracking and
synchronizing
Single protocol for
PCR, sequencing,
array genotyping, etc.
Cost effective
extraction with DNA
quality sufficient for
storage
Robust scoring of
SSR markers
Lowering cost for
robust genotyping of
1000s of markers
Shortening trait to
market time
Time & throughput
pressure of the
breeding season.
Automating scoring
Analysis of large
datasets under time-
pressure
Finding robust methods
for de-novo assemblies
and imputation
Species
specific
challenges
Humidity, labour
costs, logistics
High phenols,
degradation,
contamination
Inbreeding, no
reference genome
Long breeding
cycles, other
Genome size, ploidy
LGC
solutions
Bespoke collection
tools and LGC plant
kit
Instruments,
chemistries, and
bespoke protocols
SSR to KASP
GBS and sequencing
solutions
KASP® and BHQ®
SNPline, IntelliQube®
and Nexar®
Genotyping services
KRAKEN and bespoke
algorithms
Intellics software
Case study
Orion Biosains
collection tool
AOCC training
courses for sample
collection and
extraction
SSR to KASP
conversion service
Bespoke customer
SNP screening
solution
Bespoke automated
data scoring algorithm
example
What is your challenge?

3. • Crop – 30 year lifespan, 6 years to
first fruit
• Ecosystem – late breeding
decisions can lead to unneccesary
deforestation
• Sampling environment – heat,
remote sites, humidity, logistics,
and lack of sampling expertise
3
Sample collection – Orion Oil palm challenge
Oil palm plantation

4. 4
“The test will bring a level of
scientific robustness into remote
geographic regions for an industry
which until now has largely relied
on pot luck.”
• LGC developed in-field
sampling / barcoding device
streamlining sample
collection and genotyping whilest
maintaining sample integrity
Sample collection – Bespoke LGC solution
Nathan Lakey, President and CEO, Orion Biosains

5. 5
Sample collection – So what?
Fit for
purpose
sample
collection
Reduced
logistics
and labor
costs
Improved
sample
tracking and
turnaround
time
Increased
throughput
and earlier
breeding
decisions
Faster “trait to
market”and
reduced land
usage
“Making breeding decisions earlier
reduces the amount of space
required for planting”

6. 6
• Goal: Improve the nutrition, productivity and climatic adaptability of 101 of
Africa’s most important “back garden” food crops
• Method: Sequence and annotate orphan crop genomes
• Challenge: Improve methods for collection and extraction
DNA extraction – AOCC challenge

7. 7
“LGC is a perfect partner for AOCC
and its extensive African
collaborators. This agreement
allows breeders to directly
incorporate the latest technologies
into their breeding programs”
• LGC training course at AOCC African
Plant Breeding Academy in Nairobi
and optimized LGC extraction
protocols for orphan crops.
DNA extraction – Bespoke LGC solution
LGC training course at AOCC in Nairobi

8. 8
DNA extraction – So what?
Sample collection
courses and
optimized DNA
extraction
protocols
Contributing to
AOCC efforts to
sequence 101
orphan genomes
Understanding
genomes and
training in
breeding
techniques
Improvement of
nutritional
value of orphan
crops and
prevention of
stunted growth
“Genome assemblies for 101 orphan
crops currently being released”
- Allen van Deynze, UC Davis, AOCC
Technical Leader, Feb 2017

9. • SSRs are extensively used in plant
breeding
• High costs per analysis
• Analysis times slow – not scalable
to high-throughput
• Robust and reproducible scoring
can be challenging
9
SNP discovery – General challenge
Microsatellites are extensively used

10. 10
“SNPs are more robust &
reproducible, faster in analysis &
scalable to higher throughput and
cost savings of over 44% per
sample can be achieved”
• LGC developed SSR
conversion service launched
in January 2017.
SNP discovery – Bespoke LGC solution
Extract
SSR
Amplify
Sequence
Discover
SNP
Design
KASP

11. 11
SNP discovery – So what?
Convert
SSRs to SNP
markers
Reduce
costs and
increase
throughput
Apply higher
throughput
breeding
strategies
(e.g. GS)
Faster
development
of markers
for targeted
traits
Competitive
advantages
“Bringing new tools and
advancements in analysis
techniques to the market helps our
customers face challenges and
gain competitive advantages”

12. Challenge
• Set up a high throughput
genotyping laboratory in Asia,
currently no genotyping performed
on site
• Genotype the first 80 million
datapoints within 6 months
12
Validation and screening – Challenge
Oil palm plantation

13. 13
LGC service laboratory
project for initial 80 million
datapoints in London
“The LGC service laboratory is the
largest commercial PCR
genotyping laboratory in the
world”
Validation and screening – LGC solution part 1

14. 14
• Simultaneously in Asia, SNPline
installed on site and Paul (Senior
LGC Technician) supported
customer on-site for 6 months
“LGC is the only genomics
company globally to offer
genotyping instruments as well as
reagents and services to fully
support customers in any situation”
Validation and screening – LGC solution part 2
Paul (Senior LGC Technician) supporting on site

15. 15
Validation and screening – So what?
Platforms,
reagents and
services for
validation and
screening
Robust and
reproducible
data in any
high demand
situation
Quick ramp up
time for new
sites, backup
solution for
peaks in
demand
Required
capacity
achieved –
time
exceeding
expectations
“62 million metric tonnes of edible
oil will be produced by oil palm
trees worldwide each year, a single
percent increase in yield is worth
as much as $1bn”

16. • Multiple fluorescence readers with
different settings used for
genotyping
• Comparing and overlaying data
from different projects over each
other, there was no way to score
the data
16
Bioinformatics – Challenge
LGC SNPline - Pherastar fluorescent readers

17. 17
“All data represented as a value
between 0 and 1 to allow
comparison”
• LGC scientific support team
developed algorithm for normalising
customer data
Bioinformatics – LGC solution
Normalized KASP data

18. 18
Bioinformatics – So what?
Data
normalisation
algorithm
Comparison
of data from
different
instruments
Larger
datasets and
increased
statistical
accuracy
Higher
throughput
and quality
“Much larger datasets can be
compared and analysed at the
same time”

19. Science for a safer world
1842 - 2017
175 years of experience helping our customers solve their challenges...
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