Genomics-Enabled Genetic Improvement Kay Simmons National Program Leader

1. Genomics-Enabled Genetic Improvement Kay Simmons National Program Leader Plant Genetic Resources, Genomics & Genetic Improvement USDA, Agricultural Research Service Aug. 2, 2006

2. Evolution of maize from wild ancestor, teosinte maize teosinte Source: Sarah Hake, USDA-ARS, Albany, CA

3. Most crops have evolved from human selection during breeding We have selected crops for food, why not select crops for fuel? Source: Sarah Hake, USDA-ARS, Albany, CA

4. Biomass crops have not been subjected to selection - yet Average European forest yield Average Indiana corn yield Source: European Forest Institute (www.efi.fi)

5. Renewable Energy from Cell Walls Determine genetic characteristics that maximize energy value (corn cell wall gene mutants (> 1000) Identify all cell wall synthesis genes in grasses (grains) Use results to develop new energy crop varieties Cell Walls (Lignocellulosic Feedstocks Cellulose (glucose polymer) Hemicellulose (pentose-hexose polymer) Lignin (phenol polymer) Glucose Cellulose Xylose Lignins Fuels Fibers Polymers, Resins, Solvents Emulsifiers, Binders, Adhesives

6. Select for plants with increased mass and walls with more accessible polysaccharides • Transgenes that break down lignin in the right cell types Source: Sarah Hake, USDA-ARS, Albany, CA

7. CORN: Using maize mutants to find genes that affect plant architecture and cell wall composition Sarah Hake USDA-ARS Plant Gene Expression Center Albany, CA Annu. Rev. Cell Dev. Biol. 20:125-151, 2004 The role of knox genes in plant development. Hake et al.

8. Expression of KNOX (knotted-1 like homeobox) genes in leaves alters plant morphology Wild-type tomato 35S:KN1 in tomato (Lifschytz) Kn1-mum1 in maize 35S:KN1 in Arabidopsis 35S:KN1 in tobacco Hooded (Salomini) also 35S:KN1 in barley) Source: Sarah Hake, USDA-ARS, Albany, CA

9. KNOX mutant, brevipedicellus (bp1) affects cell wall synthesis by regulating (negative) the lignin pathway bp mutants have short pedicels and short internodes Source: Sarah Hake

10. Can we manipulate transcription factors like KNOX1 in biomass plants to have less lignin and thus more available cellulose? Source: Sarah Hake

11. Recessive knox mutants have increased lignin. Plants overexpressing knox have decreased lignin Source: Sarah Hake

12. Brachypodium distachyon, a model temperate grass • Physical attributes suitable for high-throughput molecular genetic approaches (small size, small genome, short generation time, self fertile etc.) • A model grass to understand where dicot and monocot biology diverge (e.g. cell wall composition) Source: Olin Anderson, USDA-ARS, Albany, CA

13. Development of Brachypodium resourcesOlin Anderson, Yong Gu, and John Vogel, USDA, ARS, Western Regional Research Center, Albany, CA control transformed • Developed a high efficiency Agrobacterium-mediated transformation method. • Submitted 20,440 ESTs to genbank, the first significant genomic resources for Brachypodium. • Constructed three BAC libraries and are currently sequencing >50,000 BAC ends. • Are creating a physical map by fingerprinting 70,000 BAC clones. • Are creating EMS and insertional mutant collections that will be screened for alterations in cell wall composition. • Serve as one of three PIs guiding the whole genome sequencing project at DOE’s JGI. Phylogeny based on EST data

14. Switchgrass Acceleration of switchgrass domestication through the application of genomics, biotechnology, and genetics. Switchgrass Brachypodium Source: Olin Anderson, USDA-ARS, Albany, CA

15. controls transgenic lines C4H expression Switchgrass improvement • Decrease lignin content by down-regulating lignin biosynthetic genes (4CL, C4H, CAD) Source: Olin Anderson, USDA-ARS, Albany, CA

16. Switchgrass genomics • EST sequencing • pilot project sequenced 11,990 ESTs, the first significant genomic resources for switchgrass • DOE funded project to sequence 500,000 ESTs at JGI is just starting (Tobias PI). • Mapping to facilitate breeding • generating molecular markers from EST sequences • genotyping a cross to make a genetic map based on easy to use molecular markers • >100 markers have been identified and scored on the mapping cross Source: Olin Anderson, USDA-ARS, Albany, CA

17. Genetic Improvement –Switchgrass, Alfalfa, and Sorghum Keneth Vogel, Jeff Pedersen, Lincoln, NE Michael Casler, Dairy Forage Unit, Madison, WI Bruce Dien, Fernmentation Biotech Research Unit, Peoria, IL J. Lamb, H-JG Jung, Plant Science Unit, St. Paul, MN

18. Figure 1. Half-sib families in the EY x FF C4 High IVDMD (low lignin) Progeny Test Nursery, Mead, NE.Note: Some families have excellent survival –others do not. Source: Ken Vogel, USDA-ARS, Lincoln, NE

19. Genomics-Enabled Genetic Improvement Acquisition, Conservation Germplasm Collections Trait Screening and DNA Profiling of Domesticated and Wild Germplasm Genetic Resources DNA Markers, DNA Sequences, Bioinformatics, Genome Databases Genomic Tools Marker-Assisted Breeding Genetic Engineering, Intragenics Technologies Classical Breeding Biotechnology Plants with Increasd Biomass Accessible Polysaccharides and Transgenes that break down Lignin New Varieties for Biofuels

20. Current Variety Other Variety #1 Other Variety #2 Genomics-Enabled Genetic Improvement- More efficient breeding made possible by comprehensive trait and DNA profiling of the national germplasm collections Yield Disease Resistance Flavor Available Germplasm Optimal Result Good Allele* Neutral Allele Bad Allele *alternate forms of a gene affecting a trait Adapted from Ed Buckler, USDA-ARS, Ithaca, NY