Revolution in Plant Breeding

Dr. Sam EathingtonBreeding Applications Lead

2

Outline

• DNA markers and genotyping• Integrated IT systems• Application of markers in plant breeding

– Biotech trait integration– Selection for simply inherited traits– Increasing the rate of genetic gain– Predictive breeding

3

DNA MARKERS: Where Do They Come From?

Plant Tissue Plant Cell

DNA

Chromosome

...ATGTTTAGCCCAGTGACG...

...ATGTTTGGCCCAGTGACG...

Plant 1:

Plant 2:DNA markers can be thought of as differences in DNA sequence. These differences are easily identified in the laboratory.

Single Nucleotide Polymorphism (SNP)

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Monsanto’s Maize Genetic Map with Thousands of SNPs

5

0

5

10

15

20

25

1998 2000 2002 2004

Ank

eny

Dat

a P

oint

Vol

ume

(Mill

ions

)

New Facility Additional StaffTECAN reaction assembly

Introduction of SNPsIT enhancements

SNPs using TaqMan systemFully automated reaction assembly

Key Factors AffectingVolume and Cost

Genotyping Improvements Continue to Increase Capacity and Decrease Cost

Data Point Cost

6

0

500,000

1,000,000

1,500,000

2,000,000

2,500,000

3,000,000

3,500,000

Phenotypicdata

Genotypicdata

QC tests Analysis

Monsanto Breeder"Typical" PhD Project

A lot of Data must be Processed in a Short Period of Time

Dat

a po

ints

(mill

ions

)

Large Increase After Graduate School

Breeder’s have 1-2 weeks to process and make decisions on millions of dps

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MIDAS: Phenotypic data collection, quality screening and analysis

MolBreed: Genotypic data collection, scoring, and quality analysis

RUBICON: Integrate and Analyze Field and Marker data

DataData Decisions

Built and Connected Decision Systems to our Transactional IT Systems

Application of markers in plant breeding

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Marker Selection Accelerates the Integration of Biotech Traits into Elite Germplasm

66

Over 500 projectsOver 500 projects

6060

7070

8080

9090

100100

11 22 33 44 55

Traditional*Traditional*

Percent recovery Percent recovery of elite inbredof elite inbred

Number of backcrossesNumber of backcrosses

RP DP 1 2 3 4 5 6 8 9 107Marker A

Marker B

Marker C

Marker D

Marker E

Backcross Progeny

Classical Process; 2 generations/yrClassical Process; 2 generations/yrIntegration Timeline = 54 monthsIntegration Timeline = 54 months

Accelerated Process; 4 generations/yrAccelerated Process; 4 generations/yrIntegration Timeline = 30 monthsIntegration Timeline = 30 months

Marker Assisted Backcrossing Multi-Generation Nurseries

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Traits are Rapidly Incorporated into a Wide Range of Elite Varieties to meet Customer Needs

80-day corn

120-day corn

New TraitReleased From Chesterfield

New TraitReleased From Chesterfield

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AA AA

aa aa

AA

a

A

aa a

A

a

AAParent 1 Parent 2 Progeny

aa

Gene responsible for plant height

(AA vs. aa)

Genetic Mapping is the Core Process for Marker Assisted Breeding Applications

• Location of Genes in the genome

• Parentalcontribution

• Magnitude of the genetic effect

Marker Information Improves the Efficiency and Scale of Screening for Resistance to Soybean Cyst Nematode (SCN)

Prior MethodMarker

selected

Automated Sampling

Resistant

Susceptible

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Integration of Breeding, Molecular Breeding, and Genomic Technologies Enable Rapid Development of New Selection Tools

Breeding Molecular Breeding GenomicsMay Low Linolenic soybean concept

Assembled germplasmDefined resources Identified

candidate genes

June Resequenced candidate genes in germplasm

July Identified SNPs for selection

Oct Developed SNP assays

Nov Segregating breeding popsSent LL lines to Chile

Marker assisted selection on thousands of lines

May Yield trials on LL lines

• In one year: Concept MAS Yield testing• Improved selection gain for grain yield by 38%

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Marker Associations Combined with New Technology Enabled Large Scale Implementation of Marker Assisted Selection

0100200300400500600700800900

1000

Dat

a po

ints

(100

0s)

1997 1998 1999 2000 2001 2002 2003

Automated Sampling

Conversion to SNPs

Over 70 Fold Increase

0100200300400500600700800900

1000

Dat

a po

ints

(100

0s)

1997 1998 1999 2000 2001 2002 2003

Automated Sampling

Conversion to SNPs

Over 70 Fold Increase

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Complex Traits (like Yield) are Controlled by Many Genes

Mapping genes which control key traits

Yield from Parent 2Yield from Parent 1

1 2 5 6 7 8 9 103 4Corn has tens of thousands of genes, hundreds of which probably affect yield

Over 3 billion different genotypes result from just 2 forms of each of 20 genes

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Marker Assisted BreedingRapidly Increases the Frequency of Favorable Genes

TissueSampling

DNA extraction

Generate Marker Fingerprint

Data Analysis

Selection and Recombination

GenotypingLab

Breeder Multiple cycles of MAB increases the frequency of favorable marker alleles associated with agronomic traits

Multiplecycles

0.4

0.5

0.6

0.7

0.8

0.9

1.0

Freq

uenc

y of

Fav

orab

le G

ene

C0 C1 C2 C3

Cycle Freq. of Best Genotype0 2 per trillion1 5 per billion2 1 per 5,0003 0.96

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Marker Assisted Breeding Drives Increased Genetic Gain

MTI = Multiple Trait Index that combines multiple traits like grain yield, grain moisture, standability, and test weight.

0.00.20.40.60.81.01.21.41.61.8

MTI

val

ue (P

aren

t = 0

)

2002 2003 2004 All Years

Conventional Markers

2x Improvement

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We Continue to Expand our Knowledge

0

200,000

400,000

600,000

800,000

1,000,000

1,200,000

~No.

of M

arke

r-Ph

enot

ype

Ass

ocia

tions

1999 2000 2001 2002 2003 2004 est-2005

Continue to add to this information each year

Over 40 Fold Increase

0

200,000

400,000

600,000

800,000

1,000,000

1,200,000

~No.

of M

arke

r-Ph

enot

ype

Ass

ocia

tions

1999 2000 2001 2002 2003 2004 est-2005

Continue to add to this information each year

Over 40 Fold Increase

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Selection Based on Predictive Associations Improves Gain as Much as does MAB in Breeding Projects, with NO Prior Field Data

Selection for Grain Moisture at Harvest

Parent 2 bestParent 1 best

1 2 5 6 7 8 9 103 4

12 QTL identified in a breeding population

2.5% Change 3.9% Change-2.5

-1.5

-0.5

0.5

1.5

2.5

3.5

Cha

nge

in G

rain

Moi

stur

e (%

)

Hybrid Inbred

FavorableUnfavorable

Revolution in Plant Breeding

Thank you