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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 10th 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 1980-2002 • 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

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Proportions of national yield increase due to plant breeding

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Winter barley: UK 88%, Germany 73%

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Winter wheat: UK 111%, Germany 74%, USA 50-75%

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Spring barley: UK 88%, Germany 81%

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Maize grain: Germany 102%; USA 75%

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Oilseed rape: Germany 98%

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Sugar Beet: Germany 41%

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Soybean: USA 85%

References: UK 1982-2007 (McKay et al TAG 2010) Germany 1983-2012 Laidig et al TAG 2014) USA maize 1963-2011 (Smith et al Crop Sci 2014) USA soybean Fox et al Crop Sci 2013) USA wheat (https://www.ers.usda.gov/webdocs/publications/42517/13599_aib786d_1_.pdf?v=41055)

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

http://www.ucsusa.org/sites/default/files/legacy/assets/documents/food_and_agriculture/failure-to-yield.pdf

• 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?

Intrinsic yields

Effect of Cry1Ab GMO protecting yield –contributes to operational yield NOT Intrinsic Yield

(Nonetheless, mean 2000-2007 5.3% of genetic gain is economically significant!)

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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 86:83-145

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?

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“Operational yield is obtained under field conditions, when environmental factors such as pests and stress result in yields that are considerably less than ideal.“

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.

Drought Resistance: “traditional breeding” Optimum AQUAmaxTM (DuPont Pioneer, Johnston, IA, USA)

http://www.syngenta-us.com/corn/agrisure/agrisure-artesian http://www3.syngenta.com/country/us/en/agriculture/seeds/agrisure-traits/documents/Artesian_Compare_sheet_HR.pdf

“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 GenuityTM DroughtGardTM , “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 2016 3 October 2016 Frontiers Plant Sci. https://doi.org/10.3389/fpls.2016.01534 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: 1866-1880

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Comparison of the ARGOS8 expression in genome-edited variants and wild-type maize plants.

ARGOS8 variants generated by CRISPR-Cas9 improve maize grain yield under field drought stress conditions Shi et al 2017 Plant Biotech. Jour. 15:207-216

Another way to look at plant breeding

• 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

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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

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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. https://mainichi.jp/english/articles/20170603/p2a/00m/0na/002000c

• China rice: Scientists identified a mutant gene (sdt) causing “semi-dwarf and high-tillering”, which when cloned onto super rice, resulting in increased yield of over 20 per cent http://www.scmp.com/tech/science-research/article/1805288/chinese-scientists-find-gene-improves-rice-yields-20-cent

• China rice: Genes NPT1 and DEP1 (Os09g0441900 γ subunit of G protein affecting Plant height Erect panicle Grain size) that enhances grain yield. https://news.cgtn.com/news/3d41444d3045544e/share_p.html

• Expression of barley SUSIBA2 transcription factor yields high-starch low-methane rice Su et al 2015 doi:10.1038/nature14673

• Expression of trehalose-6-phosphate phosphatase in maize ears improves yield in well-watered 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 27 1140-1146)

-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

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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. 2004. An approach to the genetics of nitrogen use efficiency in maize. J. Exp. Bot. 55:295-305

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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

Identification of candidate genes for drought tolerance by whole-genome resequencing in maize Xu et al 2014 BMC Plant Biol.14:83.

Annals of the Missouri Botanical Garden. 35: 255-276 (1948) THE SOUTHERN DENT CORNS: WILLIAM L. BROWN, Pioneer Hi-Bred Corn. Company, Johnston, Iowa EDGAR ANDERSON, Missouri Botanical Garden

• “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.

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?

Michael D. Edgerton Plant Physiol. 2009;149:7-13 ©2009 by American Society of Plant Biologists 28

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 1980-2002 •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 1109-1113

Post 1979 HUGE decline in use of publicly developed inbred lines as parents of hybrids

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1985 United States Farm Maize Germplasm Base and Commercial Breeding Strategies L. L. Darrah and M. S. Zuber 1986 Crop Sci 1109-1113

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. 32:598-604 (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. 31:893-899 (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. 46:1193–1205 (2006)

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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. 46:1193–1205 (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. 46:1193–1205 (2006)

Access to Competitor US maize germplasm for further breeding and commercialization 1980-2004

• 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. 103–111, 2004. [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. 9161–9166, 2001. [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, 2002. [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. 172–176, 2006.

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Genetic Composition of Contemporary U.S. Commercial Dent Corn Germplasm Mark A. Mikel Crop Sci. 51:592–599 (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.)

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Rate of loss Zero by

• Stiff Stalk 160/yr 2127

• Non Stiff-Stalk 100/yr 2240

• Iodent 450/yr 2037

ERAs 1=1950s 2=1970s 3= 1990s

From Van Heerwaarden et al 2012 Historical genomics of north American maize PNAS 109: 12420-12425

Rate of loss Zero by

• Stiff Stalk 0.3-0.65/yr 1995-2017

• Non Stiff-Stalk 1/yr 1998

• Iodent 0.15-1.7/yr 1993-2030

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.)

ERAs 1=1950s 2=1970s 3= 1990s From Van Heerwaarden et al 2012 Historical genomics of north American maize PNAS 109: 12420-12425

Part the Third 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

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 2017 http://www.nuffieldinternational2017.org/assets/FFFF%20presentations/4_Tina_Barsby.pdf

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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 1088–1092 | 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.

Evolution in breeding technologies facilitates access to genetic resources

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Create a molecular atlas to source new genetic diversity

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Results from Corn Breeder Questionnaire 2016

• Availability of a relatively limited array of diversity in well-adapted 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.

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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.

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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?

• 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!

The status of corn breeding in the United States: The beginning of the end, the end of the beginning, or somewhere in-between.

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Questions - Discussion