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.

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.

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 ? --

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

htp genotyping S. Eathington Monsanto

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

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.

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

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

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.

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

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 = 50-100 adaptation genes => ~0.1% of the functional genome.

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

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

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

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

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

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.

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