1. A Maize Translational Research and Educational Collaborative
A presentation for the GEM program
5 December 2007
Chicago Illinois
Bill Beavis
GF Sprague Professor, ISU
Director, NCGR
Good morning,
Thanks for the introduction.
Generally these types of talks are largely technical – science centric. Initially, I was going to visit with you about the use of Bayesian inference to assign breeding value to allelic variants. Really cool stuff!
However, in the last 3 months, I’ve realized that public PB, in particular academic maize breeding, is in critical condition. Far worse than I thought when I contemplated moving from a non-profit research institute to academia.
So, what I’m going ask you to do is to think in another dimension, to integrate social concepts about relationships from the right side of your brain and consider whether or not there is going to be a role for the public maize breeder in the future.
Because if you think that there is a role for the academic maize breeder, it is going to take commitments from all of us to revive the patient.

2. Maize R & D Enterprise (circa 1980)
Basic:
Discovery
Modeling
Applied:
Translational:
Public
(Academic+ARS)
Geneticists
(Academic+ARS) Breeders
Commercial Breeders
Prepare
Next Gen QG
Models
Innovative
Methods
Develop
Germplasm
Develop &
Release Elite
Lines and Hybrids
Public Maize Breeders Provided Leadership in:
Developing Quantitative and Population Genetic Theory
Translating Theory to Innovative Breeding Methods
Releasing Useful Sources of Genetic Diversity
Preparing the Next Generation of Plant Breeders
Don Robertson, Pete Pederson, Reid Palmer
Moll and Stuber
Russell and Hallauer
There are some who still believe this model exists, In fact I did until recently. It is part of the reason that I was willing to work with Congress and ARS to assign ~$2M per year to the ARS Corn Insects and Crop Genetics unit in Ames.
But the fact is, since the emergence of expensive htp ‘omics’ technologies this model has been destroyed; particularly for maize R & D.

3. Maize R & D Enterprise (post genomics - 2007)
Basic:
Translational:
Applied:
Discovery
Modeling
Prepare
Next Gen QG
Models
Innovative
Breeding
Methods
Prepare
Next Gen
Develop
Germplasm
Develop &
Release Elite
Lines and Hybrids
Commercial XX XX XX XXX
USDA-ARS X X X X
Commercial –
Basic
Antoni Rafalski, Scott Tingey, Ceres,
Translational QG Models
Mark Cooper
Innov Breeding Methods
Mark Cooper, Sam Reddy, Sam Eathington
ARS –
Ed Buckler, Carolyn Lawrence
Jode Edwards, Ed Buckler
Jim Holland ?
Germplasm Development
GEM: Mike Blanco Candy Gardner
Acad –
Pat Schnable, Ron Phillips , Volker Brendel
Rex Bernardo, Martin Bohn?
Rex ?
Major Goodman
Preparing the next generation of PB?
To truly prepare we need both updated pedagogic information to transmit in the classroom and research experiences that actually use data from the same htp ‘omics’ tools that one will use in the workplace.
Academic XX XX x x x ?

4. Accelerated Recovery of Recurrent (Elite) Parent using MABC
Traditional
Backcross
% Recurrent
Parent
75.0
87.7
93.3
99.0 MA
Backcross
S. Kumpatla
Dow AgroSciences
% Recurrent
Parent
85.5
98.0
100
Donor
Genome
Recurrent
Genome
Cross-over
Region

5. htp genotyping
S. Eathington
Monsanto

6. Case 2: Genetic information and htp genotyping
Case 2: Genetic information and htp genotyping. Marker Assisted Recurrent Selection:
S. Eathington
Monsanto

7. Is There a Role for the Academic Maize Breeder in the R & D Enterprise ?
Basic:
Translational:
Applied:
Discovery
Modeling
Prepare
Next Gen QG
Models
Innovative
Breeding
Methods
Prepare
Next Gen
Develop
Germplasm
Develop &
Release Elite
Lines and Hybrids
Options:
Abandon Maize to the commercial sector
Abandon translational research to ARS and commercial sector
Redefine our role in translational research and education
Provide Plant Breeding training with other emerging crops, e.g., poplar, Miscanthus, Switchgrass…
Not really a solution
These other species have little or no basic research information to leverage.
Little or no translational $ for any species
Most academic plant breeders have already moved upstream closer to the funding, to ARS, or to the commercial sector. Jean-Luc Jannink
We will be abandoning the public trust and leaving the training of the next generation to the commercial sector.
Borrow pages from the commercial sector and create a new model of R&D:
coordination and collaboration among academic maize breeders
Develop sustainable funding models for translational research and education
Work with commercial sector to provide students with translational research experiences that involve access to data from htp technologies.

8. Redefine our role in translational research and education
While there is very little funding for translational research
There is some: USDA-NRI 52.1 Plant Genome (D):
Applied Plant Genomics Coordinated Agricultural Project (CAP)
Maize Translational Research and Education Collaborative
(Maize-TREC)
Principle Investigators:
Rex Bernardo
Martin Bohn
Natalia de Leon
Thomas Lubberstedt
Torbert Rocheford
Patrick Schnable
Margaret Smith

9. Maize-TREC
Reestablish leadership in development of quantitative genetic models, development of innovative breeding methods, release of useful germplasm resources, and educating the next generation of plant breeders.
Integrated research (40%), educational (40%) and extension (20%) projects that identify, validate, and exploit the genetic bases of adaptation in maize.
Goals of a Maize CAP

10. Maize-TREC: Specific Objectives
Identify functional alleles (haplotypes) responsible for adaptation of maize to production agricultural environments.
Assign breeding values to functional adaptation alleles (haplotypes) in multiple environmental and genetic backgrounds.
Develop and test methods to rapidly accumulate adaptation alleles in unadapted populations.
Integrate the use of ‘omics’ based information into plant breeding methods curricula.
Prepare the next generation of plant breeders for team-based research.
Diversify the educational base of plant breeding graduate students.
Develop a sustainable funding model for
translational research and education
in the plant sciences.

11. Hypothesis: Maize Adaptation Traits are Oligogenic
Evidence:
Limited number of adaptation traits
photoperiod, ear-height, grain quality, prolificacy, anthesis-silking interval, disease resistance, late season stalk strength
Population Genetic Theory +
Movement of maize from C.A. to N.A. in ~ 5,000 years.
Emergence of novel architecture (leaf angle) to high density planting in 5 cycles of recurrent selection of BSSS.
Adaptation of Suwan1 and Tuson to photoperiod in 5 & 10 generations of recurrent selection.
QTL and association genetic studies on adaptation traits

12. If adaptation traits are oligogenic,
What is the best breeding strategy to adapt landraces to MW production agriculture?
Case 1:
Absence of genetic information
Case 2:
Genetic information and htp genotyping
1-2 adaptation alleles per locus, 5-6 loci per trait, 9-10 traits = adaptation genes
=> ~0.1% of the functional genome.

13. Lose 75% of genetic variability to fix
Case 1: In the absence of genetic information. The GEM Allelic Diversity Breeding Method
Winter 1
ExPVP x Exotic Race
Make F1
Summer 1
ExPVP x (ExPVP x Exotic Race)
Make BC1
Summer 2
ExPVP x (ExPVP x Exotic Race) BC1F1
Self (or Make Double Haploid)
Winter 3
ExPVP x (ExPVP x Exotic Race) BC1F2
M. Blanco
USDA-ARS
Result:
Lose 75% of genetic variability to fix
0.1% of the loci

14. Marker Assisted Recurrent Selection (C0)
Fix 0.1% of the genome while
maintaining genetic variability in the remaining 99.9%
Chromosome 1
Chromosome 2
Chromosome 3
Chr 4
Chr 5
Chr 6
Chromosome 7
Chromosome 8
Chr 9
Chr 10
Markers
Markers
Markers
Markers
Markers
Markers
Markers
Markers
Markers
Mks
Lines
Donor
Recurrent Population
S. Kumpatla
Dow AgroSciences

15. Marker Assisted Recurrent Selection (C1)
Fix 0.1% of the genome while
maintaining genetic variability in the remaining 99.9%
Chromosome 1
Chromosome 2
Chromosome 3
Chr 4
Chr 5
Chr 6
Chromosome 7
Chromosome 8
Chr 9
Chr 10
Markers
Markers
Markers
Markers
Markers
Markers
Markers
Markers
Markers
Mks
Lines
Donor
Recurrent Population
S. Kumpatla
Dow AgroSciences

16. Marker Assisted Recurrent Selection (C2)
Fix 0.1% of the genome while
maintaining genetic variability in the remaining 99.9%
Chromosome 1
Chr 2
Chr 3
Chr 4
Chr 5
Chr 6
Chr 7
Chr 8
Chr 9
Chr 10
Markers
Markers
Markers
Markers
Markers
Markers
Markers
Markers
Markers
Mks
Lines
Donor
Recurrent Population
S. Kumpatla
Dow AgroSciences

17. If adaptation is oligogenic,
What is the best breeding strategy to adapt landraces to MW production agriculture…
even with genetic information and htp genotyping, Is MAB/MAS the most effective and efficient?
Evaluate DGt in a Cost/Benefit context
Simulation modeling
Operations Research
linear programming
control systems engineering

18. Maize-TREC: Specific Objectives
Identify functional alleles (haplotypes) responsible for adaptation of maize to production agricultural environments.
Assign breeding values to functional adaptation alleles (haplotypes) in multiple environmental and genetic backgrounds.
Develop and test methods to rapidly accumulate adaptation alleles in unadapted populations.
Integrate the use of ‘omics’ based information into plant breeding methods curricula.
Prepare the next generation of plant breeders for team-based research.
Diversify the educational base of plant breeding graduate students.
Develop a sustainable funding model for
translational research and education
in the plant sciences.

19. Acknowledgements Principle Investigators: Rex Bernardo Martin Bohn
Natalia de Leon
Thomas Lubberstedt
Torbert Rocheford
Patrick Schnable
Margaret Smith
Pioneer Hi-Bred:
Mark Cooper
David Bubeck
Geoff Graham
Bill Niebur
Monsanto
Sam Eathington
Ted Crosbie
Dow AgroSciences
Siva Kumpatla
Sam Reddy
USDA-ARS Ames
Jode Edwards
Candy Gardner
Mike Blanco
Mark Millard
USDA-ARS Ithaca
Ed Buckler
USDA-ARS, Raleigh
Jim Holland
Iowa State University
Chuck Hurburgh
Kendall Lamkey
Uschi Frei
Lizhi Wang