The Evolution of Pioneer’s Breeding Program: Marker Enhanced Pedigree
Selection
Geoff GrahamMarch 5, 2007
Illinois Corn Breeder School
Pioneer Confidential
0
20
40
60
80
100
120
140
160
180
1920 1925 1930 1935 1940 1945 1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 2000 2005
Yiel
d in
bua
cr
b=1.52
b = 2.85
b = -0.67b = 1.17
198819831970 1974
1993
193619
1947
2004
Year
160
Single Cross Hybrids
Double Cross Hybrids
Open Pollinated
U.S. Average Corn Yields 1920 - 2005
Pioneer Hi-Bred History
1926: Hi-Bred Corn Company Formed
1928: First Corn Breeder hired: Raymond Baker
1935: Became Pioneer Hi-Bred Corn Company
1940’s: Two research centers added, Testing expanded to 14 States
1950’s: Expansion into Nebraska and Tennessee
1960’s: First Overseas division established. Winter Nursery Sites Developed. 3369A—First Single Cross Hybrid
1970’s: Corn Research Centers in Europe, Argentina, and Brazil
1980’s: Biotechnology Group started. First Experience with molecular markers
1990’s: Transformation, Gene Cloning, GMO’s, equipment, computers, large marker projects
2000’s: Stacked GMO’s, Technology enables MAS
Pioneer Confidential
Breeding has been extremely successful!
Male Heterotic GroupFemale Heterotic Group
0
20
40
60
80
100
120
140
160
180
1920 1925 1930 1935 1940 1945 1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 2000 2005
Yiel
d in
bua
cr
b=1.52
b = 2.85
b = -0.67b = 1.17
198819831970 1974
1993
193619
1947
2004
Year
160
Single Cross Hybrids
Double Cross Hybrids
Open Pollinated
U.S. Average Corn Yields 1920 - 2004
Time1930’s1940’s1950’s1960’s1970’s1980’s1990’s2000’s
Pioneer Confidential
Pioneer Historical Pedigree Information
1920’s
2000’s
Pioneer Diversity Project: Sequence over 600 key lines with 10,000 sequences to understand the history of genes during Pioneer breeding history
Pioneer Confidential
Allele frequencies for SNPs under selection
Pioneer Confidential
Allele frequencies differences between SSS and NSS under divergent selection
SSSX
NSS
X
Pioneer Confidential
ERA to Elite Genetics Mapping
Component 1 (45%)-15 -10 -5 0 5 10 15
Com
ponent 2 (14%)
-6
-4
-2
0
2
4
6
8
10
12
Α25 ΔΦΓΔ
ΣΔΦΣ
ΓΗϑΨ9
ΔΣΦΣ
Α33ΓΠ2ΔΦΓΗ
ΣΔΦΔΣ
Α63
Α99
ϑΓΗϑ8
ΑΔ38
ΑΕ1
ΔΦΓΦΔ79
ΔΦΓΔ1
Ας6ΜΝ
ΣΔΦΣ
ΣΔΦΔΣΣΔΦ1
ΑΣΔΦΣ
Χϑ13
Χϑ61
ΧΣΔΦ7
ΕΒ34
ΕΒ38ΕΒ90
ΣΔΦ3
ΕΧ24
ΕΧ77
ΕΔ25Τ
ΕΔ44
ΕΓΗϑ4ΡΦ
ΓΗΔ4ΡΓ ΕΔ705
ΕΔΑΔΑ
ΕΔΑΔΠΕΔΧΑ5ΕΔΧΕΡΕΔΕ4Ν
ΕΔΓΗϑ
ΕΕ26ΕΕ3ΔΤΕΕ4ΡΔ
ΕΕ5ΩΑ
ΓϑΓΓ
ΕΕΑΡ1
ΕΕΧ77
ΕΕΧΠΡ
ΕΕΔΤΔ
ΓΗϑΓ
ΕΦ5Ω4ΕΦ6ΩΧ
ΓΗϑΓΔ
Φ2
Φ3
ΣΔΦ5
ΦΓΗΦ
ΦΔ
ΔΣΦ
ΣΔΦ1
ΣΔΦ6
ΔΦΔΣ
Γ3ΗΓ7
ΑΣΣΔ
ΣΔΦΣ
ΣΔΦ6
Γ5
ΓΓ14
ΓΜ12
ΓΝ2ΧΜ2
ΓΝ2Ψ
ΓΠ24
ΓΠΧ8ΗΓΡ1Β5
ΓΡ2ΜΩ
ΓΡ3ΚΠ
ΓΡ3ΚΠΒ3
ΓΡ3ΚΠΒ6
ΓΡ581Β1
ΣΔΦΔ4
ΓΡ8ϑΡΓΡΑϑΕΓΡΒ1ς
ΓΡΧ8Π
ΓΡΧϑΜ
ΓΡΧϑΝ
ΓΡΧϑΠ
ΓΡΧΝΔ
ΣΔΦΣ
Η43
ΗΧ29
ΗΧ69
ΗΔ22
ΗΔ93
ΣΔΦΔΣ6
ΣΔΦ1
ΗΓ11
ΗΜΧΑΚ
ΔΦΣ
ΗΝ16ΗΝ1ΒΧ
ΗΝ2Ν0
ΗΝ3ΑΓ
ΗΝ4Χς
ΣΔΦΩ
ΣΔΦΣ
ΗΝ8ΧΩΗΝ8ΧΩΒ1ΗΝ8ΔΒ
ΗΝ8ΤΝΗΝΑΧΕ
ΣΔΦΔ8
ΗΝΔΩΑΗΝΕΒΑ
Κ77Ψ
Κ78ΨΣΔΦ3
ΣΣΔΦΔ
ΣΔΦΔΣ
ΜΨ1ΜΨ1ΣΒ88
Σ3Σ
ΣΚ2
ΣΝ1
ΣΤ1
ΣΔΦ
ΣΤ5ΩΛ
ΣΔΦΣΑ
ΣΤ6
ΣΔΦΣΣΔΦΔDX
NSS
SS
Heterotic Groups
Germplasm Knowledge
Time
Pioneer Confidential
Pioneer Historical Pedigree InformationIdentity by State (IBS)
1920’s
2000’s
Pioneer Confidential
Pioneer Historical Pedigree InformationIdentity by Descent (IBD)
1920’s
2000’s
Pioneer Confidential
Breeding Diversity-Allele View
Inbred LinesGenetic Position
Pioneer Confidential
Breeding Diversity--IBD View
Inbred LinesGenetic Position
Pioneer Confidential
Breeding History
Year of Release
Pioneer Confidential
Breeding History
Genetic Similarity
Pioneer Confidential
Breeding Populations
MEPS Molecular Enhanced Pedigree Selection
The goal of MEPS is to develop and use marker trait associations in our elite breeding populations using multiple segregating populations and understanding the history of alleles in our germplasm
Instead of using 1 large populations we use many smaller populations already in our breeding program.
Pioneer Confidential
Ability to Detect Marker-Trait Associations
Breeding Populations
Pioneer Confidential
Understanding the past…and establishing the effect of each region…
Genetic DB
Pioneer Confidential
Application of Molecular Breeding
Germplasm StewardshipLesion RepairGenetic Prediction
Population SelectionAugmented Phenotypic SelectionHybrid Prediction
SS NSS
Crosses
HybridTesting
Populations
Testers
Pioneer Confidential
0
20
40
60
80
100
120
140
160
180
1920 1925 1930 1935 1940 1945 1950 1955 1960 1965 1970 1975 1980 1985 1990 1995 2000 2005
Yiel
d in
bua
cr
b=1.52
b = 2.85
b = -0.67b = 1.17
19881983
1970 1974
1993
193619
1947
2004
Year
160
Single Cross Hybrids
Double Cross Hybrids
Open Pollinated
U.S. Average Corn Yields 1920 - 2004
Germplasm Stewardship
Pioneer Elite Germplasm80 yrs of breeding.
Access New GermplasmAccess to Elite “Old” Breeding MaterialTropical GermplasmExotic GermplasmWorldwide Germplasm Stewardship
Mexico BrazilArgentina
EuropeUnited States
Male Heterotic GroupFemale Heterotic Group
Time1930’s1940’s1950’s1960’s1970’s1980’s1990’s2000’s
Pioneer Confidential
By selecting on regions with known effects we can fix perceived lesions.
Flowering Time
Late Early
Lesion Repair
Pioneer Confidential
Genetic Prediction: Choosing breeding crossesInbreds
Potential crosses
Inbreds
Predicted MST (var)0.0 0.5 1.0 1.5 2.0 2.5
Pred
icte
d M
ST (m
ean)
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Low
High
DesirableBreeding candidates
Desirable Breeding/QTL mapping
candidates
Mea
n
Traits
Envi
ronm
ents
Mea
nM
ean
Var Var Var
Augment with other sources of information
Prediction
Pioneer Confidential
Genetic information can tell us what population will show significant genetic variation.
Family % Similarity Cross-corr. Prediction Ability108 78% 0 Poor109 55% 0.5 Good106 33% 0.7 Excellent
family 108
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23
24
25
-2 -1 0 1 2
predicted
obse
rved
family 109
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25
-2 -1 0 1 2
predicted
obse
rved
family 106
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-2 -1 0 1 2
predictedob
serv
ed
Genetic Prediction: Choosing breeding crosses
Predicted Predicted Predicted
Obs
erve
d
Pioneer Confidential
Genetic PredictionChoosing best individuals within specific crosses
Favorable Allele Be careful—You get what you select for!!!
Progeny within population
Pioneer Confidential
MST20 21 22 23 24 25 26 27
Yiel
d
140150160170180190200210
Predicted MST
Yiel
d
140150160170180190200210
Not selected based on MST performance (phenotype)
Potentially selected based on predicted MST performance (MAS)
SS NSS
Crosses
HybridTesting
Populations
Testers
Genetic Prediction: Marker-assisted selection
Pioneer Confidential
We can use the genetic information to predict the hybrid performance and position products in the right environments
NSS InbredsSS Inbreds
Potential Hybrids
SS NSS
Crosses
HybridTesting
Populations
Testers
Genetic Prediction: Hybrid Prediction
Observed
Pred
icte
dGDDNGD
SFDGSF
SDFSD
GDHDFDASDFSA
DSFGDSFSDFSDFS
SDFSDG
FGHJH
FGHJF
JYYYFJ
DFGHD
DFGFH
HJGGH
JFHGFJFGHFG
FGJGFJ
TYITJT
JRTRT
RTJRT
RYJYT
RJRRT
RTHJR
YUIYYU
YUIYUIYDFGDFG
SDGSDGFGHFGH
RTYRTY
GFJHG
FDGHJFG
RTRTY
FGHFGH
FJGFGHRDFHJFG
HJGFHJCVNBCVB DFGDFXCVXVF
TYUTYUGHJGJG
TYUTYTYUTUGHJGHJ
TYUTYU
RTYRTEDFHDFHD
DGHJFDH
RTYRT
DFHWSHSHSHHDF
SFDGSDF
GHDFHGD
VBCVCV
DFGDFASDFGS
TARRRERSYGERT
XCGVFX
EERTEWFGHSFHG
ERTERTRTYRTYR
RTYRYY
ERTYERT
HJKJKH
FGHGFG
BGFGFG
KJGFGF HJFGHJSERTSE
DFGDFGDGHDFGH
DFHGDF
DGHFDG
SDFGS
DFGSDFG
DFGDFFG
SDFGSDFRETERT
SDFSDF
SDFSDF
SDFSDF
TYRTYRTUYTYUT
TUIUYIYUTYUTYTYERERTEE
ETYHRTY
XCBVFF
DFDFGG
XBXCVXHGFHFD
DFGFD
CVBCVCF
SFGSG
DFGDFGSFDGSG
DFGDFG
ADFASFD
ASDSAFD
ASDASDAFSGFE
FGDFGDF
YTDHJTR
HGDFGD
DRYGRG
DGDFDFGSDFSDFSFHFDGDF
DSFDDFGD
Low
Highr=0.74
Pioneer Confidential
ConclusionsThe development of our molecular breeding efforts includepedigree, phenotypic, and genetic characterization of our breedinggermplasm.We have the ability to detect MTA as a routine part of our breeding program based on pedigree and marker information.The ability to phenotype the trait is the most important part of identifying the MTAGiven good genetic information we can predict performance of individuals, populations, and hybrids.Molecular Information increases the potential for genetic diversity.But…you need to know what you are selecting for!!!!
Pioneer Confidential
“As the joy of artistic creation begins to assert itself we may expect many interesting developments in the newer methods of corn breeding. … In brief, the new method of corn breeding gives us such definite control over our material that we can go in almost any direction which we think desirable. The costs in money and time may be great but the possibilities of accomplishment are commensurate.”
H. A. Wallace, 1930 Manuscript