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Utilization of Genomic Information to Accelerate Soybean Breeding and Product Development
through Marker Assisted Selection
Rico Caldo ,Vergel Concibido, Susannah Cooper, Yan Fu, Mike Gerau, Karen Grote, Ivan Husic, Jennifer Yates
Paul Chomet, Tom Osborn
Presented by: Ruth Wagner August 5, 2014
SOY2014
Copyright 2014 Monsanto Company
Presentation Overview
Molecular Breeding in the Ag Industry
Technology Application for Accelerating Trait Mapping
Marker Deployment in Commercial Product Development
Molecular Breeding in the Ag Industry
Copyright 2014 Monsanto Company
The Application of Science and Technology in Agriculture has Helped Deliver Increased Productivity and Resource-Use Efficiency
0
1
2
3
4
5
6
1960 1970 1980 1990 2000 2010
Yie
ld (
Mt/
Ha)
World Yields of Staple Food Crops
Source: FAOSTAT
Maize
Wheat
Rice
Soybeans
0
1
2
3
1948 1958 1968 1978 1988 1998 2008
U.S. agricultural output, inputs and productivity
Output
Inputs
Productivity
Index, 1948=1 Source: USDA-ERS data product, Agricultural Productivity in the U.S. (2010)
3 Copyright 2014 Monsanto Company
To Further Improve Performance, We Must Identify and Create Better Genetic Combinations
4
Existing Genetic Variation
Yield, Stress Tolerance, etc.
Transgenic Genetic Variation
Disease Resistance, etc.
Tolerance to Herbicides, Insects, etc.
Yield, Quality Traits, etc.
Copyright 2014 Monsanto Company
The Evolution of the Use of Molecular Markers Increased Capacity and Decreased Cost Enables Large Scale Plant Breeding
Applications
Key growth drivers Automation
Technological Advances
In era of gene-based
breeding, the amount of
data explodes,
accelerating the ability to
realize step-change
improvements
Cost/Data Point
Total Data Points
5
Soy
Corn
Cotton Melon
Wheat Copyright 2014 Monsanto Company
Effective Markers for MAS breeding require multiple components
Penetrant QTL
Genetic marker(s)
tightly linked to the trait
Informative marker(s) in
relevant germplasm
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Alignment of Technology Platforms Enables Cross-Talk
High Coverage Re-sequence
Reference Sequence
Capture Re-sequence
Infinium Fingerprinting
TaqMan Genotyping
Discovery Production
Copyright 2014 Monsanto Company
Efficiency is Achieved by Aligning Technologies with Desired Outcomes R
ela
tive
co
st/s
amp
le
Density of information/sample
Few
SNPs
Complete
sequence
Genome
chunks
High density
SNPs
High density
High cost
Low sample volume
Low density
Low cost
V. high sample volume
Circle size represents
relative sample capacity
Parents 1 2 Progeny
Progenitors A B C
MAS
MABC GWS
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Resistant
Susceptible
Marker Screening
Marker-Assisted Selection (MAS) For Simple Traits in Soy Expands Breeding Pipeline and Decreases Cost
No
. o
f so
yb
ean
MA
S d
ata
po
ints
Disease Screening
9
Year
Copyright 2014 Monsanto Company
Integrated Data Analysis and Decision Making System Is Needed
Field System:
Phenotypic data collection
and analysis
Genotyping System:
Genotypic data collection
and analysis
Analysis System: Integrate
and analyze phenotypic and
genotypic data
Data Data Decisions
10 Copyright 2014 Monsanto Company
Presentation Overview
Molecular Breeding in the Ag Industry
Technology Application for Accelerating Trait Mapping
Marker Deployment in Commercial Product Development
Copyright 2014 Monsanto Company
1. Classic QTL Mapping
Leveraging Available Public Data Accelerates Trait Marker Development
2.Leverage available data (public literature)
Validate QTL in breeding
germplasm
(joint linkage mapping,
association mapping)
map trait with background markers
Validate QTL
validate markers
(Reduce QTL size)
Deploy markers
Breeding Pipeline
Discovery
Screening/Testing
Seed Production
Product
Copyright 2014 Monsanto Company
M1 100 cM
M2 105
M3 107
M4 110
M5 115
M6 120
M7 123
M8 125 cM
Phenotype
RP 0 0 0 0 0 0 0 0 S
Grp1 2 0 0 0 0 0 0 0 S
Grp2 2 2 2 2 0 0 0 0 S
Grp3 2 2 2 2 2 2 2 0 R
Grp4 0 0 0 0 0 0 0 2 S
Grp5 0 0 0 0 0 2 2 2 S
Grp6 0 0 0 0 2 2 2 2 R
Grp7 0 2 2 2 2 2 2 2 R
Donor 2 2 2 2 2 2 2 2 R
TM4 TM5 2 0 0 0 0 0 0 0 0
2 2 0 0 0 0 0 0 0
2 2 2 0 0 0 0 0 0
2 2 2 2 0 0 0 0 0
2 2 2 2 2 0 0 0 0
2 2 2 2 2 2 0 0 0
2 2 2 2 2 2 2 0 0
2 2 2 2 2 2 2 2 0
0 0 0 0 0 0 0 0 2
0 0 0 0 0 0 0 2 2
0 0 0 0 0 0 2 2 2
0 0 0 0 0 2 2 2 2
0 0 0 0 2 2 2 2 2
0 0 0 2 2 2 2 2 2
0 0 2 2 2 2 2 2 2
0 2 2 2 2 2 2 2 2
Leveraging Technology: Higher marker density improves resolution
• QTL TM1-TM8 • New markers between • 7 recombinant groups by TM • Refine QTL to TM4 and TM6 (25 cM 10 CM) • If more markers are needed, repeat the process
Recombination break point, Red: donor allele, Blue: RP allele, S: susceptible, R: resistant, TM: Taqman marker
TM1 TM8
QTL
25 cM
Recombinant group 2
Recombinant group 6
Recombinant #1
Recombinant #2
Recombinant #3
Recombinant #4
Recombinant #5
Recombinant #6
Recombinant #7
Recombinant #8
Recombinant #9
Recombinant #10
Recombinant #11
Recombinant #12
Recombinant #13
Recombinant #14
Recombinant #15
Recombinant #16
Soy
Chip and genotype with M4, M5
Apply hi res markers only selected seed QTL
Copyright 2014 Monsanto Company
Leveraging Technology: Sequence Capture Southern Stem Canker (SSC)
Pathogen Facts • Causative agent: Diaporthe phaseolorum f. sp. Meridionalis • Soybean losses from SSC totaled approximately $67.1 million
in 2003 (Wrather, 2004) • SSC infects the plant early in its vegetative growth, but
symptoms don’t appear until reproductive stages (Ploetz and Shokes, 1985)
• Because of the long asymptomatic latent period, genetic
resistance is the best option
• Six independent dominant resistance factors have been reported: Rdc1, Rdc2, Rdc3, Rdc4, and two unnamed loci
• (Tyler, 1995)
• Phenotyping is tedious, time-consuming, and often unreliable and has hampered the use of markers for marker-assisted selection (MAS).
• A highly effective 5 week greenhouse assay was implemented in 2006.
Malvick, 2002
Copyright 2014 Monsanto Company
Experimental workflow for SSC
F2:F3 family phenotyping
Pool Creation and Sequence Capture
-F4 derived DNA mixed in in equimolar amounts
Quantitative Sequencing and Mapping
-Single lane per sample on GAIIx
SSC Susceptible
Copyright 2014 Monsanto Company
Sequence Capture Allows Even, High-definition Interrogation of the Entire Genome
Over 330,000 unique probes completely cover the soybean genome
Copyright 2014 Monsanto Company
Comparing Allele Frequency in Resistant vs. Susceptible Pools Efficiently Identifies the Trait Region
Trait Target Region
Copyright 2014 Monsanto Company
Even Great Technology Isn’t Perfect! In-Gene Marker Performance Varies Across Maturity Groups for Flower Color
99% (P) 64% (W)
~98% (P) 100% (W)
~99% (P) 69% (W)
~35%
~99% (P) 74% (W)
~98% (P) 97% (W)
~99% (P) 98% (W)
~99% (P) 91% (W)
~100% (P) 95% (W)
Copyright 2014 Monsanto Company
Presentation Overview
Molecular Breeding in the Ag Industry
Technology Application for Accelerating Trait Mapping
Marker Deployment in Commercial Product Development
Copyright 2014 Monsanto Company
7%
Tens of Millions Genotyping Data Points Were Collected for Soy Traits in 2013
16%
27% 44%
3% 2%
Copyright 2014 Monsanto Company
Technology Pipeline
Copyright 2014 Monsanto Company
Key Message
Combining genome wide selection with marker-assisted
breeding…
Using multiple technologies and new technologies…
While increasing capacity and reducing costs…
Thereby Increasing Our Speed to Product Development
Allows us to map traits efficiently and track them in our germplasm…
Copyright 2014 Monsanto Company
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