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Breeding To Plan Using Marker

TechnologyMichael Thompson, Ph.D.

May, 2014

2

Focus Areas For Today’s Presentation

Genomic

Selection

[ GS ]

The Vision & Mission

Tools

Impact

3

Information Is PowerWinning the genetic lottery – Luck or Skill?

Luck

Genomics

Information

4

Genomics: A Powerful Tool In The Tool BoxAdvancing our understanding & harnessing of complex traits

5

Tools Are Driving Paradigm ChangeGenomics enables understanding and harnessing of complex traits

Timeline

Paradigm DiscoveryAssisted

Discovery

Predictive

Discovery

Predictive

Breeding

6

Unlocking the power of the genome to

Improve human health through agriculture

Our VisionInnovating for the Future of Human Health

7

Our ProductsComplete Solutions for Unlocking the Power of the Genome

Apps

Complete Workflows for Genetic Analysis Applications

Consumables InstrumentsSoftware &

Informatics

8

ARRAYSBeadArray, Infinium, GoldenGate, DASL

SEQUENCINGSequencing by Synthesis (SBS) Powered by TruSeq Chemistry

Our PlatformsAdvancing the Understanding of Genetics

POPULATIONPOWER

$1,000 human genome and extreme

throughput for population-scale

sequencing

PRODUCTIONPOWER

Power and efficiency for large-

scale genomics

FLEXIBLEPOWER

Speed and simplicity for whole-

genome, exome, and transcriptome

sequencing

FOCUSED DxPOWER

The first and only FDA-cleared in vitro diagnostic next-generation

sequencing

FOCUSEDPOWER

Speed and simplicity for

targeted and small-genome

sequencing

FROM GENOME-WIDE DISCOVERY TO TARGETING VALIDATION AND SCREENING

POWERFUL ARRAY

SCANNER

Optimized for high-density HumanOmniBeadChips

* The HiSeq X™ Ten is a set of ten sequencers.

CUTTING-EDGE ARRAY

SCANNER

Process up to 96

multi-sample BeadChips

per day

HiSeq® 2500HiSeq X™ Ten* NextSeq™ 500 MiSeqDx™ MiSeq® HiScan® iScan

9

Species Identification Classification Provider Consortium # SNPs

Potato Potato Public Illumina SolCAP 8,303

Tomato Tomato Public Illumina SolCAP 7,720

Apple Apple Public Illumina RosBREED 8,788

Peach Peach Public Illumina RosBREED 8,144

Cherry Cherry Public Illumina RosBREED 5,696

Maize MaizeSNP50 Commercial Illumina Commercial 56,110

Chicken Chicken Private: Public Sale Illumina Cobb Vantress-Hendrix-USDA 57,636

Cat Feline Private: Public Sale Illumina Morris Animal Foundation 62,897

Horse Equine Private: Public Sale Illumina Neogen(GeneSeek) 65,157

Sheep Ovine Private: Public Sale Illumina AgResearch 5,409

Cattle BovineHD Commercial Illumina Various 777,962

Cattle BovineSNP50v2 Commercial Illumina Various 54,609

Sheep OvineSNP50 Commercial Illumina Various 52,241

Cattle BovineLD Commercial Illumina Various 6,909

Pig PorcineSNP60 Commercial Illumina Various 62,163

Dog CanineHD Commercial Illumina Various 173,662

Wheat Wheat 9k Public Illumina Australia/USWheat Consortium 8,632

Brassica Brassica 50k Public Illumina Intl Brassica SNP Consortium In manufacturing

Pu

blic

Co

ns

ort

ia-D

eve

lop

ed

Ag

ric

ult

ure

Arr

ays

10

Variant

Discovery

Genomic

Selection

Marker

Assisted

Selection

[ MAS ]

Marker

Assisted

Backcrossing

QTL

Mapping

GMO

Testing

Genetic

Purity

Transformation

& Event Purity

Parentage

Verification

Plants

Both

Animals

Fingerprinting

KEY

Genetic

Merit

Genotyping

Technology

Discover. Develop. Deploy.Access to multiple applications

Pathogen

Detection

11

Genomics: Accelerating The Rate Of Genetic Progress

(Falconer, 1989)

Selection Intensity(population size and proportion selected)

Accuracy(reference population size)

Genetic Variation(within population)

Generation IntervalShorter

generation

interval

Larger

reference

populations

Larger

breeding

populations

More robust

quantification

of variationGi r σA

=L

12

Genomics-Based Breeding – An Example From

Syngenta

Breeding for improved yield stability through drought

protection

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Drought tolerance is one of the most challenging areas of research in agriculture, says

Monsanto drought and water utilization lead Mark Edge. In recent years, technologies that

allow more rapid screening for promising raw genetic material have

helped advance both traditional breeding and genetic modification

programs in this area

http://www.technologyreview.com/news/429100/drought-

puts-modified-corn-seed-to-the-test/

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No Drought Of Headlines (2012)

15

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Nature 469, 144 (2011) | doi:10.1038/469144a

News

Drought-tolerant maize gets US debut

Seed companies race to tap multibillion-dollar market.

Jeff Tollefson

When the planting season arrives later this year, farmers in the United States

will have a new way to safeguard their crops from drought. Last week, DuPont

subsidiary Pioneer Hi-Bred International, headquartered in Johnston, Iowa,

announced plans to release a series of hybrid maize (corn) strains that can

flourish with less water. The seeds will compete with another maize strain

unveiled last July by Swiss agribusiness Syngenta. Both companies

used conventional breeding rather than genetic

engineering to produce their seeds.Pioneer says that field studies show its new hybrids will increase maize yields

by 5% in water-limited environments, such as the western states of the

intensively agricultural Corn Belt region. That compares with the 15% yield

gain promised by Syngenta for its maize. Both companies, as well as seed

firm Monsanto, based in St Louis, Missouri, are also working on transgenic

maize varieties, hoping to tap into a multibillion-dollar market (see Nature 466,

548–551; 2010).

http://www.nature.com/news/author/Jeff+Tollefson/index.htmlhttp://www.nature.com/uidfinder/10.1038/466548a

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Breeding Goal

Higher Yield Potential through drought tolerance– Sub-optimal water

– Optimal water

– Variable water

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All-In Candidate Gene ApproachGenomics for hypothesis-based lead selection

Sequence lines to characterize extensive germplasm diversity & ID

variants

Scan genome to identify trait-associated genomic regions

ID & rank candidate genes

– Known (previously characterized) biological function

– Positional candidate: Located in LD with QTL-identified chromosomal

segment

– Comparative structural & functional genomics

Test candidate genes in as many combinations as resources allow

Picture courtesy of Joe Clarke, Syngenta

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Syngenta Has Confidence In It’s Drought-Tolerant

Hybrids

Confidence in drought-tolerant corn performance

Rich Keller, Editor, Ag Professional | August 6, 2012

Syngenta has confidence in its drought-tolerant hybrids with

Agrisure Artesian technology outperforming standard hybrids and

other drought-tolerant hybrids on the market, according to Wayne

Fithian, Syngenta technical product lead for Agrisure Artesian

technology.

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PUBLISHED SAT, SEP 08, 2012

Drought-resistant corn developed in RTP shows

promise

Cyrulik, who grows corn and beans on his nearly 5,000-acre farm about 20 miles south of

Bloomington, Ill., wasn’t anticipating abnormally dry weather. He just wanted to see how

Syngenta’s new Agrisure Artesian corn would stack up in a typical year. That plan was

thwarted by the record-setting drought that has plagued the Midwest this summer.

But the parched conditions didn’t ruin the 220 acres that Cyrulik planted with Agrisure

Artesian. Although it won’t be harvested until later this month, he estimates Agrisure

Artesian will end up producing between 30 and 50 bushels more per

acre than the other hybrid corn he planted.

Read more here: http://www.newsobserver.com/2012/09/08/2326723/drought-resistant-

corn-developed.html#storylink=cpy

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Record drought puts Agrisure Artesian corn technology

from Syngenta to the test – trials show yield advantage of

16.8%12.04.12

Drought-resistant hybrid corn seed outperforms trial averages by 16.8%, or an additional 10.9 bushels/acre, in severe and extreme drought conditions, as observed in

1,100 field trials in 2012

Increases crop yields during water-stressed growing conditions all season long

Effective risk management tool that helps growers stabilize yield and grow more corn

Minnetonka, Minn., U.S.A. - Syngenta announced today that results from extensive field

trials during 2012 confirmed that under severe and extreme drought conditions, hybrids with

Agrisure ArtesianTM technology produced 16.8% higher yields compared to the plot average.

The trial database included competitor hybrids with and without drought tolerance technology.

In a widespread drought like the one experienced in the 2012 season, one quarter of the corn

crop could have conceivably been affected by at least severe and extreme level drought. A

16.8% yield increase on these acres would translate to enough corn to fill a train of railcars

more than 1,315 miles long, or long enough to span the entire Corn Belt – from Ohio to

Colorado.

http://www.syngenta.com/

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Agrisure Artesian™: strong performance in

drought conditions

PR NewswirePress Release: Syngenta – Tue, Dec 4, 2012 1:00 AM EST

BASEL, Switzerland, Dec. 4, 2012 /PRNewswire/ -- Syngenta announced

today that results from expanded US field trials in 2012 have confirmed that

corn hybrids with the Agrisure Artesian™ native trait outperform comparable

hybrids. An average yield advantage of around 17 percent was observed

across severe and extreme drought conditions.

In areas of severe drought stress, Agrisure Artesian hybrids increased yields

by 12 percent. The yield gain in extreme drought

conditions reached 48 percent.

23

Agrisure Artesian™ Technology – Performance Summary1

Classification: Public

1 Data is based on 2010-13 Syngenta on-farm strip trials

Slide courtesy of Syngenta

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Gene Modes of Action:

Improve water and nutrient

uptake

Maintain normal growth

and development longer

into the stress event

Control how resources are

allocated in the plant

Optimize health of

developing shoot and floral

tissues

Agrisure Artesian Increases Yield Under Stress

159 bu/A

56.3 Test Weight130 bu/A

56.0 Test Weight

Seward, NE Dryland Hybrid Advancement Trial, September 14, 2010

Isoline hybrid without

Artesian trait

Classification: Public Slide courtesy of Syngenta

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Genomic SelectionRepeated cycles of recombining & selecting favorable alleles using genome-wide markers in linkage disequilibrium with every QTL

Genomic

Selection

[ GS ]

Achieve more genetic gain faster with genomic selection

Field performance

Selection

RecombinationBREEDER

Sample

Extract DNA

Marker analysis

Data analysis

GENOTYPING

LAB

MODEL

Reference

population

Phenotype

Genotype

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Enabling an AgriGenomics Revolution

http://www.technologyreview.com/news/429100/drought-

puts-modified-corn-seed-to-the-test/