monsanto 08-23-05a
TRANSCRIPT
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)
4
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
7
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
9
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
10
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
11
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
13
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%
14
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
15
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
16
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
17
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
18
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
19
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