The Evolution of Pioneer’s Breeding Program: Marker Enhanced Pedigree

Selection

Geoff GrahamMarch 5, 2007

Illinois Corn Breeder School

Pioneer Confidential

0

20

40

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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

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120

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160

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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

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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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-2 -1 0 1 2

predicted

obse

rved

family 109

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-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