A Maize Translational Research and Educational Collaborative

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

2. Maize R & D Enterprise(circa 1980) Applied: • 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 Basic: Translational: Discovery Modeling Prepare Next Gen Innovative Methods Prepare Next Gen QG Models Develop Germplasm Develop & Release Elite Lines and Hybrids Public (Academic+ARS) Geneticists Public (Academic+ARS) Breeders Commercial Breeders

3. Maize R & D Enterprise(post genomics - 2007) Basic: Applied: Translational: Discovery Modeling Prepare Next Gen Innovative Breeding Methods Prepare Next Gen QG Models Develop Germplasm Develop & Release Elite Lines and Hybrids Commercial XX - XX XX - - XXX USDA-ARS X - X X - X -- Academic XX XX xxx ? --

4. Accelerated Recovery of Recurrent (Elite) Parent using MABC BC1 BC2 BC3 BC6 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.Marker Assisted Recurrent Selection: S. Eathington Monsanto

7. Is There a Role for the Academic Maize Breeder in the R & D Enterprise ? Basic: Applied: Translational: Discovery Modeling Prepare Next Gen Innovative Breeding Methods Prepare Next Gen QG Models 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

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.

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

13. Winter 1 ExPVP x Exotic Race Case 1: In the absence of genetic information.The GEM Allelic Diversity Breeding Method 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. Donor Recurrent Population 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 S. Kumpatla Dow AgroSciences

15. Donor Recurrent Population 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 S. Kumpatla Dow AgroSciences

16. Donor Recurrent Population 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 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