10/10/2017. Presentation Outline

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1 The status of corn breeding in the United States: The beginning of the end, the end of the beginning, or somewhere in-between? Agron 338 Stephen Smith Affiliate Professor Dept. of Agronomy, Iowa State University, Ames, Iowa Visiting Scientist Seed Science Center, Ames, Iowa October 10 th 9.30am Presentation Outline Where Yield comes from Corn Innovation and Events slide: What are the concerning issues here? From whence comes yield? Genetic Gain Input from traditional breeding and use of transgenic; potential for gene editing Push Pull concepts in breeding Major gene effects, multigenic effects So what about the diversity of the US corn genetic base? The picture in 1992 What happened on the germplasm front among breeding programs What are the trends? Current state? Some imperatives for consideration Rebuild adapted germplasm base Pull breeding isn t going away Push breeding may be more feasible with innovative breeding methods? Critically important roles for public sector Part the First Where Yield comes from Corn Innovation and Events slide: What are the concerning issues here? From whence comes yield? Genetic Gain Input from traditional breeding and use of transgenic; potential for gene editing Push Pull concepts in breeding Major gene effects, multigenic effects 5 6 1

2 Proportions of national yield increase due to plant breeding 1 Winter barley: UK 88%, Germany 73% 2 Winter wheat: UK 111%, Germany 74%, USA 50-75% 3 Spring barley: UK 88%, Germany 81% 4 Maize grain: Germany 102%; USA 75% 5 Oilseed rape: Germany 98% References: UK (McKay et al TAG 2010) Germany Laidig et al TAG 2014) USA maize (Smith et al Crop Sci 2014) USA soybean Fox et al Crop Sci 2013) USA wheat ( 6 Sugar Beet: Germany 41% 7 Soybean: USA 85% The concepts of Intrinsic and Operational yield Intrinsic yield, the highest that can be achieved, is obtained when crops are grown under ideal conditions; it may also be thought of as potential yield. Operational yield is obtained under field conditions, when environmental factors such as pests and stress result in yields that are considerably less than ideal. Gurian-Sherman, 2009 Failure to Yield: Evaluating the Performance of Genetically Engineered Crops Union of Concerned Scientists Is this categorisation helpful or even meaningful? For example, does it make sense to criticize single gene effects contributed via GMOs because while they helped improve operational yield they did not increase intrinsic or potential yield? Intrinsic yield, the highest that can be achieved, is obtained when crops are grown under ideal conditions; it may also be thought of as potential yield. NCGA Competition winning yield gains are akin to Potential Yield BUT how much of this yield is economically and/or environmentally sustainable? Effect of Cry1Ab GMO protecting yield contributes to operational yield NOT Intrinsic Yield (Nonetheless, mean % of genetic gain is economically significant!) Intrinsic yields 12 2

3 Is the European Corn Borer an endangered species? Non GMO and organic farmers are also beneficiaries THE CONTRIBUTION OF BREEDING TO YIELD ADVANCES IN MAIZE (ZEA MAYS L.) Donald N. Duvick 2005 Advances in Agronomy, Volume 86: Most genetic contributions to yield gain in US maize have been via increase stress resistance due to increased planting densities more effective mining of sunlight, water and nutrients. Thus, all of the genetic basis of yield gain in US maize could be classified as Operational yield-is this genetic contribution any the less because it is not Intrinsic: yield? Operational yield is obtained under field conditions, when environmental factors such as pests and stress result in yields that are considerably less than ideal. Drought Resistance: traditional breeding Optimum AQUAmax TM (DuPont Pioneer, Johnston, IA, USA) Operational yields Actually, US Corn Breeding is contributing via BOTH intrinsic and operational. The balance of which it is depends upon the agronomic environment and management Artesian corn hybrids contain multiple genes for season-long drought protection, responding to water stress with multiple modes of action at virtually any stage of growth. a unique scientific process to select, validate and deploy multiple natural corn genes that protect the corn plant from water stress in several different ways. Drought breeding: Monsanto s Genuity TM DroughtGard TM, traditional plant breeding and a transgenic trait. Monsanto with BASF, developed the first biotechnology-derived drought-tolerant maize (MON 87460) by expressing bacterial cold shock protein B (CspB) in maize. Drought-Tolerant Corn Hybrids Yield More in Drought-Stressed Environments with No Penalty in Non-stressed Environments Adee et al October 2016 Frontiers Plant Sci. Physiological responses related to increased grain yield under drought in the first biotechnology-derived drought-tolerant maize NEMA et al 2015 Plant Cell and envt 38:

4 Comparison of the ARGOS8 expression in genome-edited variants and wild-type maize plants. Another way to look at plant breeding ARGOS8 variants generated by CRISPR- Cas9 improve maize grain yield under field drought stress conditions Shi et al 2017 Plant Biotech. Jour. 15: PULL breeding (e.g. select for multigenc factors eg yield, or drought, and then let the plant determine the traits and genetics, made more efficient by (e.g.) improved genomic selection using markers, performance prediction, precision phenotyping PUSH breeding Breeder selects the trait component or a gene and selects on that component PULL breeding (e.g. select for yield, or drought, let the plant determine the traits) more efficient by (e.g.) improved genomic selection using markers, performance prediction, precision phenotyping Examples of Trait PUSH breeding: You identify the gene, find or make alleles and select directly on those alleles, allelic effects Backcrossing Making a GMO Gene Editing Examples of recent single gene breeding approaches Japan rice: changing the plants' hormonal balance, the number of husks in each ear of rice increases, as does the size of the rice grains themselves. China rice: Scientists identified a mutant gene (sdt) causing semi-dwarf and hightillering, which when cloned onto super rice, resulting in increased yield of over 20 per cent China rice: Genes NPT1 and DEP1 (Os09g γ subunit of G protein affecting Plant height Erect panicle Grain size) that enhances grain yield. Expression of barley SUSIBA2 transcription factor yields high-starch low-methane rice Su et al 2015 doi: /nature14673 Expression of trehalose-6-phosphate phosphatase in maize ears improves yield in wellwatered and drought conditions Nuccio et al 2015 VOLUME 33 NUMBER 8 AUGUST 2015 nature biotechnology Have we been here before? The ideotype model (Donald 1968, reviewed Rasmusson 1987 Crop Sci ) -a method to augment traditional breeding not as a coequal nor as a substitute for yield breeding -The largest challenge is to decide which traits to include -To date, only one trait in barley, long awns, has been demonstrated to increase yields -Other traits have been hypothesized-short stature, harvest index, biomass, and several other traits hypothesized to increase yields but the evidence has been inconsistent or in conflict a breeder who desires to do ideotype breeding will need to gamble on a trait just as a traditional breeder gambles when selecting parents for crossing. Progress in ideotype breeding in the future may be proportional to the amount of information that is available about how yield is achieved Improved phenotyping is especially important so that breeders can consider a larger array of traits of both aerial and root portions of the plant 4

5 Multigenic traits: Lots of loci-alleles to chose from!!!!!!!!!!!!!!! NUE Maize High N Qtl left, Low H Qtl right Gallia's A and Hirel B An approach to the genetics of nitrogen use efficiency in maize. J. Exp. Bot. 55: Identification of candidate genes for drought tolerance by whole-genome resequencing in maize Xu et al 2014 BMC Plant Biol.14:83. Distribution of nssnps and associated genes on maize chromosomes. Concentric circles showed aspects of the genome. Density of common nssnps identified in drought-tolerant maize inbreds (A) and in drought-sensitive maize inbreds (B). Genome mapping of candidate nssnps identified by common variants method (C). The fold change of expression level for candidate genes in ovaries (D), leaves (E) and roots (F) under water-stressed conditions compared with well-watered conditions Annals of the Missouri Botanical Garden. 35: (1948) THE SOUTHERN DENT CORNS: WILLIAM L. BROWN, Pioneer Hi-Bred Corn. Company, Johnston, Iowa EDGAR ANDERSON, Missouri Botanical Garden Anticipated impact of improvements in agronomics, breeding, and biotechnology on average corn yields in the United States. IS THIS PREDICTION BIOLOGICALLY/GENETICALLY REALISTIC? HOW MANY SINGLE-GENE/REGULATORY EXPRESSION INTERVENTIONS WILL APPLY TO ECONOMICALLY IMPORTANT TRAITS? From the viewpoint either of the practical breeder or of general evolutionary theory, the genes which control multiple-factor differences are of far greater importance than the single genes ordinarily employed in genetic experiments. Yet in spite of their over-all importance we know little about them, and experiments designed to tell us more have been so discouragingly difficult that little real advance has been made since East's preliminary investigations. HOW MUCH OF THESE STATEMENTS REMAINS TRUE TODAY? Need to know a lot more about physiology and genetics by American Society of Plant Biologists Michael D. Edgerton Plant Physiol. 2009;149: Part the Second So what about the diversity of the US corn genetic base? The picture in 1992 What happened on the germplasm front among breeding programs What are the trends? Current state? 1985 United States Farm Maize Germplasm Base and Commercial Breeding Strategies L. L. Darrah and M. S. Zuber 1986 Crop Sci Post 1979 HUGE decline in use of publicly developed inbred lines as parents of hybrids 5

6 1985 United States Farm Maize Germplasm Base and Commercial Breeding Strategies L. L. Darrah and M. S. Zuber 1986 Crop Sci Use of inbreds for further breeding-post 1984 primarily not publicly bred inbred lines, use proprietary instead, but what does other mean in terms of germplasm? Diversity of U.S. Hybrid Maize Germplasm As Revealed by Restriction Fragment Length Polymorphisms Smith et al., Crop Sci. 32: (1992). Some Brand name hybrids associated with each other-see >95 similarity groupings ALSO Some Brand name hybrids that appear more unique from other germplasm. Some Brand name hybrids associated with each other ALSO Some Brand name hybrids that appear more unique from other germplasm. Restriction Fragment Length Polymorphisms Can Differentiate among U.S. Maize Hybrids J. S. C. Smith and O.S Smith Crop Sci. 31: (1991): Some Brand name hybrids associated with each other and public or licensed lines ALSO Some Brand name hybrids that appear more unique from other germplasm. From these (1992) and recorded pedigree data 1. Most, if not all proprietary programs had developed inbreds and commercial hybrids with public lines in their pedigrees 2. Some proprietary programs had developed unique germplasm including from early in the history of US hybrid corn by sourcing OPVs 3. Some previously purely foundation seed increase programs went beyond backcrossing in publicly available disease resistance genes (e.g. Ht) and began to breed e.g. Holden Foundation seeds, Illinois Foundation Seeds 4. Some proprietary programs licensed inbred lines from foundation seed companies Developments during 1980s 2000s STIFF STALK Evolution of North American Dent Corn from Public to Proprietary Germplasm Mark A. Mikel* and John W. Dudley Crop Sci. 46: (2006) 6

7 Developments during 1980s 2000s NON STIFF STALK Evolution of North American Dent Corn from Public to Proprietary Germplasm Mark A. Mikel* and John W. Dudley Crop Sci. 46: (2006) Developments during 1980s 2000s IODENT Evolution of North American Dent Corn from Public to Proprietary Germplasm Mark A. Mikel* and John W. Dudley Crop Sci. 46: (2006) Access to Competitor US maize germplasm for further breeding and commercialization Under PVP Commercial hybrid seed Y Not sold, Parental inbred lines? 1991 Pioneer vs Holden, inbred lines represent trade secrets Parental lines placed into the public domain by USDA upon expiration of protection Y Under Utility Patent Commercial hybrid seed: Not without license period of protection Parental inbreds: Not without license during period of protection Seed available via the public domain upon expiration of patent protection Important to know breadth of germplasm carried through to other breeding programs to help monitor trends in genetic diversity usage-this relates to 1) inbreds and or 2) hybrids accessed. Access via F2 seed from hybrid harvest provides more germplasm diversity, may be difficult to implement depending on heterotic pool alignments There are more differences in the genomes of two unrelated corn plants than between the genomes of a human and a chimpanzee (two species separated by 3.5 million years of evolution). James and the giant corn Genetics: Studying the Source Code of Nature (2010) The maize genome exhibits rather variable levels of naturally occurring genetic diversity depending on the lines involved in the comparison [49, 61]. On average, the frequency of single nucleotide polymorphism between two maize inbreds is approximately 1 substitution per 100 bases [62, 63]. Interestingly, this level of intraspecies polymorphism is striking when compared to mammals; this average rate of polymorphism is 10 times higher than that observed between humans and also higher than that observed between human and chimpanzees [64]. The complex corn genome coming in at a hearty two billion base pairs (compared with the human genome's 2.9 billion base pairs) The corn genome actually has 12,000 more genes than humans Any two maize varieties are as diverse from each other as humans are from chimpanzees," REFS [61] A. Rafalski and M. Morgante, Corn and humans: recombination and linkage disequilibrium in two genomes of similar size, Trends in Genetics, vol. 20, no. 2, pp , [62] M. I. Tenaillon, M. C. Sawkins, A. D. Long, R. L. Gaut, J. F. Doebley, and B. S. Gaut, Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.), Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 16, pp , [63] A. Ching, K. S. Caldwell, M. Jung et al., SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines, BMC Genetics, vol. 3, article no. 19, [64] E. S. Buckler, B. S. Gaut, and M. D. McMullen, Molecular and functional diversity of maize, Current Opinion in Plant Biology, vol. 9, no. 2, pp ,

8 Genetic Composition of Contemporary U.S. Commercial Dent Corn Germplasm Mark A. Mikel Crop Sci. 51: (2011) What happened to germplasm developed by? What about available useful genetic diversity? Average number of differences between ancestral haplotypes between individual maize inbred lines. (van Heerwaarden et al (2012) Proc. Natl. Acad. Sci.) Rate of loss Zero by Stiff Stalk 160/yr 2127 Non Stiff-Stalk 100/yr 2240 Iodent 450/yr 2037 What about available useful genetic diversity? Average number of direct ancestors within individual maize heterotic groups. (van Heerwaarden et al (2012) Proc. Natl. Acad. Sci.) Rate of loss Zero by Stiff Stalk /yr Non Stiff-Stalk 1/yr 1998 Iodent /yr ERAs 1=1950s 2=1970s 3= 1990s From Van Heerwaarden et al 2012 Historical genomics of north American maize PNAS 109: ERAs 1=1950s 2=1970s 3= 1990s From Van Heerwaarden et al 2012 Historical genomics of north American maize PNAS 109: Part the Third US Corn Belt Dents, a large amount of adapted and useful genetic diversity: A KEY advantage for maize breeders. Compare to where wheat breeders find themselves: A Revolution in Plant Breeding Tina Barsby FARMING FIT FOR FOOD Thursday, 8th June Some imperatives for consideration Rebuild adapted germplasm base Pull breeding isn t going away Push breeding may be more feasible with innovative breeding methods? Critically important roles for public sector 8

9 Genetic signals of origin, spread, and introgression in a large sample of maize landraces Joost van Heerwaardena,1, John Doebleyb, William H. Briggsc, Jeffrey C. Glaubitzd, Major M. Goodmane, Jose de Jesus Sanchez Gonzalezf, and Jeffrey Ross-Ibarra PNAS January 18, 2011 vol. 108 no. 3 There is no shortage of genetic diversity in maize and teosinte The challenge is to find USEFUL genetic diversity from amongst this vast repository of diversity! Maize breeding just got tougher! Requiring more knowledge and application of research. 49 Evolution in breeding technologies facilitates access to genetic resources Create a molecular atlas to source new genetic diversity 51 9

10 Results from Corn Breeder Questionnaire 2016 Availability of a relatively limited array of diversity in welladapted U.S. corn germplasm could limit further progress especially with increasing biotic and abiotic challenges requiring additional useful diversity. Off-PVP and off-patent corn inbred lines could not provide required new diversity to the U.S. breeding base as a whole. Maize landrace accessions collected from outside the U.S. were seen as potentially useful sources of new germplasm with CRW teosinte and Tripsacum being potential, but last resort, sources of new specific diversity, possibly informing the application of gene-editing methods. 55 Results from Corn Breeder Questionnaire 2016 The ability to find marker-trait associations facilitates access to exotic germplasm yet ii) this ability is dependent upon the genetic complexity of the trait and requires large investments in research. Gene-editing methods likely increase the utility of conserving a broad germplasm base as a source of gene-trait discovery and allele enquiry. Application of gene-editing at least in maize may be limited due to the complexity of gene networks. There is a need for a day-length conversion program similar to that undertaken for sorghum. 56 ASTA: Strong support for the NPGS and Genetic Enhancement programs (GEM) What have we learned and where does that take us? The critical importance of more effective use and stewardship of PGRFA A broader diversity of PGRFA even more potentially useful as new breeding methods, phenotyping, association studies, gene-editing, MAS progress Is the trend in US corn germplasm usage since the late 1970s sustainable? What will breeders do about it? When? What are the levels of diversity, trends on US farms? Crucial importance of excellence in education and public research Need to re-instill long term thinking/funding Much basic physiology-genetics research required Breeding and variety deployment required beyond that which private sector supports More integration of plant breeding /agriculture as ecosystem services Challenge current opinions and the status quo with sound science What have we learned and where does that take us? The status of corn breeding in the United States: The beginning of the end, the end of the beginning, or somewhere in-between. What have we learned from 35 years of single-gene traits, primarily GMOs Corn hybrids MUST have excellent insect resistance and herbicide resistance to be marketable BUT SINGLE GENE RESISTANCES ARE VULNERABLE TO BREAKDOWN AND THEY ALONE DO NOT INCREASE YIELD POTENTIAL Imperative to learn more about physiology and genetics of agronomically important traits Need to earlier and better determine traits needed and research and development costs (biological complexities) for 1) single gene approach and 2) if must take regulatory approval path Can improved breeding methods e.g. editing, use of more diverse PGRFA provide native gene insect resistance that does not require regulatory approval? Pull breeding works well! Always, perhaps inevitably place too much focus and hype on latest scientific discoveries! 10

11 Questions - Discussion 11