A Pioneer website states that grain sorghum x Johnsongrass hybrids rarely occur and are almost always sterile. I don’t doubt this, but the extreme abundance of this weed easily beats any numbers game – especially with the intense selection of regular herbicide applications. I don’t know the agronomy of this system or whether the total cultivation/pesticide strategy does anything special to mitigate the risk of ALS/FOP resistant Johnsongrass emergence, but I’m going to assume it’s an absolute sure thing unless someone has data to the contrary.

The non-transgenic status of these plants in no way lessens or ameliorates this risk. The method of genetic change is completely inconsequential. I’m usually a big fan of herbicide resistant crops, but this just sounds like a terrible idea to me all around. Anyone know otherwise?

h/t: Jesse Bussard @cowgirljesse (who wrote about Jgrass here)

* I know of one house where it has apparently replaced the ornamental grasses in the center of the homeowner’s garden.

I’m very impressed by the fact that these blue potato chips exist. It’s no small feat to create a good-frying potato with excellent agronomic qualities in itself. I can’t imagine crossing in blue coloring (anthocyanin expression) on top of this in a reasonable amount of time – especially since potatoes aren’t true to seed. Non true to seed crops like potatoes have messy, highly heterozygous genomes that when crossed (or selfed) produce offspring that segregate for all the traits you care about. I’ve been told that potato breeders typically make a bunch of crosses in the first year of their program – and then spend the rest of their careers evaluating and propagating the resulting segregants asexually.

Though the chips really are purple, not blue…

Among plant geneticists, breeders are always held up as the pragmatic experts who know what matters in the Real World. But not all fields perceive breeders this way…

Sustainable agriculture was a popular session topic at the tri-societies joint meeting in San Antonio. More specifically, many speakers took pleasure (rightly so) in pointing out the subtle complexities of local agricultural systems that many of us in breeding gloss over when trying to help.

Some highlights:

1. Agronomy comes first. In most situations, productivity is most directly limited by poor agronomic practices. For example, it’s not uncommon for poor field design and maintenance practices to route only 10-30 % of rainfall within reach of the crop. The majority runs off the surface, scraping away much of the organic matter in the process. And while there’s lots of potential for more complex intercropping, aquaculture, perennials etc., you need to settle the basics (a productive, reliable staple harvest) first.
2. The right varieties already exist. Multiple speakers implored breeders to stop arbitrarily improving varieties and traits they hope to be useful. Instead they emphasized that major improvements can be made simply by introducing modern varieties that are appropriate to the respective region. Additionally, no crop is grown in a vacuum (i.e. iron biofortification of grain is not super useful if a higher yield of grain could be used to raise livestock). 
3. Infrastructure is essential. Producing higher yields is virtually worthless if you can’t get it to a market. Some groups are finding that helping villages safely store extra grain is one of the most valuable things that can be done for poor farmers. This not only protects against famine but allows farmers to spread out when they sell their harvest, thus obtaining better prices. And farmers can’t plant improved seed in the first place if there’s no local shops that sell (the right) seed. And this is all worthless without roads.
4. Risk matters as much as payoff. Farmers aren’t going to (and hopefully won’t) invest in fertilizers, higher quality seed, or putting a lot of extra effort into their crop in general if there’s a good chance drought will wipe out everything despite it – or if they don’t have a way to get surplus yield to a market. For example, many of those farmer suicides occurred because farmers were convinced to take out loans on extra supplies but weren’t able to recoup the investment. 
5. Don’t forget the social system! Some crops are traditionally tended by (and benefit) men and others by women (and children). One study argued that while grains may not be super nutritious, a reliable staple harvest will encourage farmers to invest more of their remaining effort/time/resources on nutritious garden crops and profitable market crops. Finally, another study found that one of the main results of introducing grain silos was that farmers directed more of their harvest to raise livestock (with positive health outcomes).

“Many administrators, private and public, have decided that the future of plant breeding lies in genomics, relying on claims that molecular genetics has revolutionized the time frame for product development. ‘Seldom has it been pointed out that it is going to take as long to breed a molecular engineering gene into a successful cultivar as it takes for a natural gene’” - Goodman 2002

Traditional breeding essentially consists of the repeated selection of the best individuals of a plant population over time. This can be accomplished by farmers, hobbyists or professionals and ranges radically in sophistication from the inadvertent selection of genotypes that grow best in a given cultivated environment to massive multi-year statistical studies on large pedigreed families grown in multi-location trials. Regardless of the methods used, breeders are unified in their selection of traits based on phenotype and NOT on genotype (with some limited MAS). Breeders generally don’t know (or care) why a plant has a certain trait. They just want it to work. This approach is the strategic opposite of genetic engineering, which aims to first understand the specific mechanism of a given trait first so that it can be consciously and directly modified.

New Sources of Germplasm: Lines, Transgenes, and Breeders*
The end of breeding has been repeatedly and falsely prophesied for going on two decades now – yet even after hundreds and hundreds of millions of dollars of research, only a handful of transgenic traits have been successful. To some extent, it’s an unfair comparison as applied genetic engineering has been virtually crippled by regulation. Yet all the same, the above paper by Goodman (2002) does a nice job of outlining all the complications that genetic engineering enthusiasts tend to gloss over in their zeal to take crop improvement beyond breeding.

Far and away, I think the most important reason that genetic engineering has not replaced breeding is that overenthusiastic proponents fail to understand how much of the genetics upon which breeding is built remains unknown. Genotypes can perform radically different in very similar environments and genes can perform radically different within similar genotypes (and of the tens of thousands of genes in any crop, we have a hint of only what a few of them do). Breeding succeeds in the face of these tremendous unknowns because it selects blindly based on phenotypic results.

This distinction between consciously engineering a system and improving it by trial and error (generating many, possibly random iterations and just seeing which works best) is a fundamental distinction seen in many fields from drug discovery to mechanical engineering (to evolving computational cars!). Whether you’re trying to improve biological, technological or social systems, iterative selection is best when you don’t really understand how your system works – but once you do understand it well enough to make accurate predictions, rational engineering allows massive leaps in what you can accomplish.

Currently, our knowledge of plant biology is nowhere near complete enough to allow wholesale engineering – but it does allow us to make some very small, targeted changes that can occasionally have very big effects (e.g. herbicide and pest resistance). Ten years after Goodman’s paper, there is still much that we can hope that genetic engineering will accomplish – but breeding will continue to be the bread and butter of crop adaptation and yield improvement for the foreseeable future.** In 2002, he warned:

“Plagiarizing N.W. Simmonds (1991), we can add MAS, genomics, and possibly even transgenics to the bandwagons we have known. These include (but are certainly not restricted to): induced polyploids, haploids, mutations, overdominance, genetic variances harvest index, high-lysine, small tassels, nitrogen fixation, nitrate reductase, somaclonal variation, bracytic dwarfs, leafy hybrids, precision agriculture, high-oil topcrosses, ag chemical/seed synergy.

Simmonds’ observations merit repeating even after more than a decade, “The bandwagon, as it applies to plant breeding, is expensive and damaging. Resources are being diverted from doing genuinely useful jobs to the pursuit of trendy irrelevance; biotechnology is, I think, accelerating the collapse of proper agricultural research.”

Clearly this is an overstatement (now that we’re in the future). In particular precision agriculture has gone mainstream and genomics and MAS have been paying dividends. All the same, his ending plea to remember that breeding is the core of crop improvement holds true. Private companies haven’t forgotten this (for the few crops and market classes they work on), but our public breeding programs (that cover every other crop) are being rapidly hollowed out and dissolved.

I once heard a nice analogy of genetic engineering vs. breeding.*** Emphasis on genetic engineered “traits” are like drop-in widgets for cars: electric starters, GPS, halogen headlights, etc. But breeding is what shapes the chassis, drivetrain and body. It’s great to have all those bells and whistles, but they’re more useful on some cars than others…

* Goodman, M.M. (2002). New Sources of Germplasm: Lines, Transgenes, and Breeders Memoria congresso nacional de fitogenetica
** Of course my department, Applied Systems Biology, is one of many groups trying to change this…
*** Rabobank presentation from Genomics in Business, 2011

The September issue of CSA news has a nice (open access) article entitled: “Do polycultures have a role in modern agriculture?”

Some key caveats:
* While diverse plant mixtures have been associated with many benefits, high biomass yield (i.e. what farmers get paid for) is usually not one of them.
* It’s very difficult to maintain complex plant mixtures – usually a single species will come to dominate.
* Our crop monocultures represent those crops that are best adapted to a given region.
* Establishing, maintaing and harvesting polycultures will require significant effort, risk, investments and training for farmers.

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They conclude that polycultures are intriguing but definitely require more (agronomically realistic) research.

Thoughts?

Someday you’ll be able to use CAD software to draw up what you want a plant to look like and the software (containing detailed growth models) will tell you what genetic constructs you need to bring it into the world…

But for now we barely understand how natural morphological variation is controlled. So I was excited to see this paper out of the van der Knaap and Francis labs. In it, they review some of the known levers by which tomato plants control fruit shape and investigate their historical appearance.

Many species of wild tomatoes grow along the western coast of South America, from above the snowline in the Andes to the cloud forests and desert valleys below. Despite this great ecological diversity, most of them produce little, green fruit (that are often covered with fur). These wild species are generally bitter and inedible, but a few species make sweet, red ripe fruit. Some have suggested that Solanum lycopersicum var. cerasiforme (the cherry tomato) is the ancestral domesticated tomato. More recently, others have suggested it is a feral mix of domestic and wild tomatoes. One way or another, the few centuries of domestication since have witnessed and enormous diversification of fruit shape (and flavor!) as it was tracked from the Americas to Europe and back – with each culture adapting it to their unique cultures and cuisines.

Today, tomatoes come in all shapes and sizes from small round cherries to large, lumpy, many-loculed heirlooms. The authors worked to track the morphological history of this fruit by looking for associations between alleles with known impacts on fruit shape and germplasm of known origins.

They began by assembling 368 heirloom, modern and wild genotypes from Europe and the Americas, which they then classified into 8 fruit shape categories: flat, rectangular, ellipsoid, obovoid, round, oxheart, long and heart. 4 genes (SUN, OVATE, FAS and LC) have so far been discovered to make major contributions to these differences in fruit shape. The SUN mutation creates elongated fruit, apparently due to a misregulation of the phytohormone auxin (thanks to the influence of a retrotransposon). The OVATE mutation (an early stop codon) creates pear shaped fruit. FAS (FASCIATED) and LC (LOCULE NUMBER) both contribute to tomato size and locule number.

The authors looked for associations among these alleles and the shape classifications in their diverse germplasm collection. They found the SUN mutation in 88% of long and 83% of oxheart-shaped fruit. The OVATE mutation was present in 83% of ellipsoid, 59% of rectangular and 48% of oxheart-shaped fruit. 82% of flat fruit had the LC mutation and 28% had the FAS mutation. 63% of long fruit also had LC.

While all 4 gene mutations are present in both modern and heirloom fruit, their presence in older varieties is indicative of their evolution. Little is known about what tomatoes looked like when Columbus first encountered them, but we know his compatriots tracked them from Mexico to Spain and Italy soon after they were discovered. The first written account of these fruit in 1544 describes them as flat and segmented, and soon after as fasciated – suggesting that LC and FAS were already present in Latin American varieties by this time. The next novel tomato fruit shape (pear) wasn’t mentioned until 1813, possibly indicating that OVATE was brought to Europe in a later wave of germplasm. This allele proliferated in Italy and is now present in 71 out of 109 elongated accessions, where it’s responsible for the classic Italian paste tomato shape.

SUN arose much later than OVATE and FAS and can now be found in half of US heirlooms (especially those of northern European origin) and Spanish regional accessions with elongated fruit shapes (but not Latin American or wild accessions). This suggests that SUN originated in Europe rather than the Americas – Northern Europe to be specific, as only 6 of 109 Italian fruit varieties contain it. SUN probably first appeared in an LC background because older heirloom and regional varieties with SUN also have LC except for recent exceptions like Banana Legs.

It’s exciting to witness these early steps towards understanding how plants work, but I’m really looking forward to that CAD software…


Rodríguez GR, Muños S, Anderson C, Sim SC, Michel A, Causse M, Gardener BB, Francis D, & van der Knaap E (2011). Distribution of SUN, OVATE, LC, and FAS in the Tomato Germplasm and the Relationship to Fruit Shape Diversity. Plant physiology, 156 (1), 275-85 PMID: 21441384
Xiao, H., Jiang, N., Schaffner, E., Stockinger, E., & van der Knaap, E. (2008). A Retrotransposon-Mediated Gene Duplication Underlies Morphological Variation of Tomato Fruit Science, 319 (5869), 1527-1530 DOI: 10.1126/science.1153040
Liu, J. (2002). A new class of regulatory genes underlying the cause of pear-shaped tomato fruit Proceedings of the National Academy of Sciences, 99 (20), 13302-13306 DOI: 10.1073/pnas.162485999

It was striking how much of what was old is new again. One of the earliest priorities of government leaders was to stock their “new” continent with as diverse of seed as possible. They not only promoted the adoption of proven Amerindian crops, but encouraged immigrants to bring their own favorite seeds with them and even sponsored botanical expeditions to the far corners of the world to discover potential new crops. Thomas Jefferson went so far as to smuggle rice seed out of Italy in his pockets – a crime punishable by death!

The young U.S. government not only encouraged the use of diverse, locally appropriate seed but actually provided it to farmers. For years, farmers spurned much of the offerings of the young seed industry due to the reliably superior quality of government seeds.* In what would become a recurring theme, the beleaguered seed industry formed a trade association and successfully lobbied the government to leave seed production to them.**

As the U.S. matured from a rural frontier to an industrial power, the people slowly developed an appreciation for what regulation could do for them (which is a good reminder for all of us from time to time). The Jungle was written to reveal the exploitative working conditions of industrial food processing factories, but the public’s outrage (to Sinclair’s frustration) was consumed by the disgusting revelation of what was going into their dinners. It gave me a new appreciation for the FDA to hear some of the early practices they were tasked with addressing – including chemical adulteration that made exploding ketchup bottles and child deaths from candy consumption common.*** As was also a recurring theme, food processing businesses protested these new regulations full-throated, but the overwhelming demands of the people eventually held the final say.

Along the way, the government kept working to educate farmers and the public on best practices to profitably produce and safely consume the nation’s food, mediating conflicts between the two, and nudging both towards behaviors that were in everyone’s interest. Government efforts in social engineering include rationing during the World Wars (“Meatless Mondays” was invented by the Hoover administration), promotion of home gardening and canning (which I believe was at one point responsible for 40% of all produce consumed by the public), the establishment of the classic American meal of affordably nutritious potatoes + meat + vegetables, the now-infamous ag subsidies and the school lunch program.
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Much of the exhibit was dedicated to the always-evolving efforts of the government to keep its people healthy – from early efforts to ensure that everyone had affordable access to basic nutrition, to burgeoning biochemical understanding of the nutrient components of food (and a seeming “vitamin” craze) to the recognition of obesity as a serious health threat. It was illuminating to walk these displays with my nutrition/social science gf, who explained where and how some education efforts succeeded and others failed.

D wasn’t the first vitamin to be accused of causing widespread deficiency-induced malaise. A pet theory that Americans were in need of more thiamine (vitamin B1) led to the fad of donuts as health food (as they apparently contained a fair amount of it). In this case, the FDA stepped in – allowing advertisement of “enriched wheat donuts,” but not “enriched donuts” or “vitamin donuts.” If I remember correctly, it was this passing emphasis on the biochemistry of food that inspired the now ubiquitous FDA “Nutrition Facts” label.

I balked at the American public’s repeated gullibility in the face of health claims in food marketing (from “vitamin” donuts to “whole grain” sugary breakfast cereals), but gf pointed out that nutrition science is inherently complex, frequently changes and has generally been poorly distilled into simple to understand and follow messages. It’s no wonder that the public is quick to grab products that associate themselves with whatever is seen as healthy at the moment (apparently even green packages are associated with healthiness). She contrasted our complex nutrition education materials (e.g. the terrible interactive food pyramid website) with simple public health education campaigns (e.g. wash your hands to prevent the flu, use clean needles and condoms to prevent HIV).

I asked her to give an example of what she thought nutrition education materials should look like. She re-emphasized that it had to be targeted to the needs, education and attitudes of each given demographic, but that, for example, the core message for many children might be: “exercise a lot more, drink water instead of sugary drinks.” I was encouraged to hear that many on-the-ground nutrition educators already take this approach. She thought the new USDA Food Plate was a step in the right direction as it’s simple and works at the level of a meal (most people don’t have a good idea of everything they eat in a day or a week, and certainly don’t understand how much a “serving” is).

I definitely recommend checking out the exhibition’s preview on the National Archives website, and stopping in if you’re in the area. I just wish it was a lot bigger! In conclusion, I’ll leave you with a quote from one of the displays that I couldn’t resist (and an unrelated poster advertising an early farmer education campaign).

“Many urbanites held on to the agrarian myth—the belief that the family farm stood for all that is pure and good in America—but demanded the cheap food that large agribusiness could supply.”

* If you know more about this program, I’d love to hear it!
** Later, dairy farmers united to compel the government to impose massive taxes on margarine butter substitutes. People were thrown in federal prison for breaking these draconian “oleomargarine laws.” Eventually, the added expense of these taxes was repealed under increasing protests from the public.
*** Industrial ketchup was invented as both a shortcut for busy home cooks and a way to use the dregs of tomato harvests (e.g. cores and skins) made edible with vinegar, red dye and preservatives that built pressure within the containers. According to this exhibit, Heinz was the first to demonstrate that ketchup could be made without these bottle-busting chemicals. Oh, and by the way – ketchup is originally descended from Asian fish sauces. Crazy!

The “perennial grain” story seems to pop up every few months. The basic idea is that perennial crops would have higher yields and lower environmental impacts than their annual kin.

The picture on the left explains pretty clearly why – large permanent root systems secure the topsoil, exhaustively scavenge water and nutrients and support more vigorous shoot growth over a longer season.

This week, it’s perennial maize.

One thing that I think is funny about these stories is that they inevitably herald the accompanying freedom from multinational seed companies. Aside from the fact that no farmer’s forced to buy seed, I don’t see any reason why companies wouldn’t jump on a perennial grain bandwagon.* Companies like Monsanto are already selling/developing advanced varieties (e.g. Bt/Roundup) of perennial crops like alfalfa and sugarcane.**

Companies don’t have to sell seed every year to make money. In this case, I’ve heard they’ll be offering an annual license agreement (e.g. you buy the seed the first year and pay a license fee each following year that you continue to cultivate the crop). I think it shows a lack of creativity that people always pin the blame on what they don’t like about the state of agriculture on the “need” for companies to sell seed every spring. There’re lots of ways to do business.

Which isn’t to say I’d expect companies to make the initial investment – jumpstarting speculative new technologies and industries is the role of governments and non-profits. According to Ed Buckler (in the article), an easy $15-30 million should do this. This is an inconsequential speck in the U.S. budget and we should probably just get it done.

h/t: Agricultural Biodiversity Weblog

* I heard that a coalition of wheat farmers actually petitioned companies like Monsanto to begin reinvesting in transgenic wheat varieties since wheat yields have fallen so far behind other crops like maize.
** Pest and herbicide resistance is particularly valuable in perennial systems as bugs and weeds tend to build up over years without tilling or rotation.
*** It might also be a concern how you can maintain a high genetic gain in yield year-by-year and decade-by-decade when you switch an annual to a perennial, but I imagine the gains inherent to perennialism paired with our incredible current breeding technology should make this well worth it.

It’s 3 am local time and I’m wide awake, fixated on the challenge of brand differentiation in ketchup…

I recently spoke with one of the ketchup tomato breeders I know. Among other topics, he lamented the consumer’s irrational fixation on price. He pointed out that most of us won’t hesitate to grab a generic bottle of ketchup over a trusted brand for a difference of only 20 cents – which breaks down to no difference over the months it sits in your fridge: How do you sell a better product to a customer who’s not willing to pay 1 cent more per week?

It’s the advantage (and burden) of major brands that they specialize in making a high-quality, consistent product over years and decades. (If there was an outbreak of botulism in a Campbell’s or Del Monte, would you ever buy that brand again?) Meanwhile, generic food companies can just grab whatever ingredients are cheapest at the moment, throw them together and ship them out. A less than ideal batch may sneak its way into various supermarket generics once in awhile, but even if one generic brand gets associated with poor quality, they can just come up with a new (equally generic sounding) name. So how can a branded food company make a profit when they have to put all this extra effort into product quality and consumers nonetheless treat it like a commodity? And, of course, it doesn’t help when consumers perceive your product as a low-rent item in the first place…

This probably sounds like a “who cares? / too bad for them” type of problem but it has repercussions outside of the ketchup game. People have the same attitude towards all products – including fresh fruits and vegetables. Now I, as I imagine many of you would, quickly protested this idea. Unlike ketchups, I perceive huge difference between “high” and “low” quality apples and oranges. I won’t touch anything that looks like a Red Delicious and I don’t even buy tangerines (let alone oranges) unless they’re specifically labelled as clementines.** He took my point and then asked if I cared what variety my apple was (so long as it exceeded my stated threshold). I said “no” and he elaborated on the problem – that although I have a threshold for apple quality, the likelihood of the apple product I would buy on a given week (or whether I’d buy apples at all) was very strongly linked to what was on sale at the time.

So how does all this relate to transgenic food? People like myself have been flogging the idea that the public resistance to transgenic food is due in part to the lack of a consumer benefit – all the traits so far benefit the farmer (by yield, convenience and lower risk). This will all change, so the story goes, when transgenic Botrytis-proof strawberries hit the supermarket shelves. “Ah!,” the customer will shout, “Look at these beautiful strawberries surrounded by ones gray with mold!” This only works though if customers are really dedicated to buying strawberries when they head to the supermarket. If instead the customer doesn’t really care whether he can get strawberries on any given day, he just won’t buy strawberries on the days when the choice is between gross molded “generics” and expensive transgenics.*** Maybe he can just buy strawberries another day.

The breeder definitely had a point, but I immediately brought up the hordes of people I know who gladly hand over extra cash to get perceived superior quality (or merely philosophy) from the Trader Joe’s and Whole Foods of the world. But, he emphasized, these are the same people who are most opposed to GM foods.

It was a disheartening series of arguments. Though, of course, if you can find a way to make a consistent profit branding something as ordinary as ketchup, it seems like there should be a place for a slightly more expensive fresh market (out of season) tomato that still tastes like a tomato…

* “Food” brands that are actually vertically integrated enough to do their own breeding include Campbell’s, ConAgra (Hunt’s), Heinz, Land’O Lakes, Frito-Lay and Orville Redenbacker. 
** Well, when I’m too far from the West Coast, that is.
*** Although a difference in price will be less inevitable if regulations get pared back

“Heirlooms were varieties that were so unsuccessful that they wouldn’t be sold today…

Every product declines until it’s replaced by new heirlooms.”

The backlash was inevitable.

What are heirlooms? A 1949 article in the New York Times defined them as “open pollinated varieties [i.e. genetically stable lines, not F1 hybrids] that are more than 50 years old and have been handed down through generations.” It fits the modern technical definition – but not the contemporary consumer’s expectation for a primary focus on taste.

Plant breeding is an always ongoing process. Breeders grow out their core collection of genotypes every year, cross them and collect seeds from the best individuals. Occasionally new genotypes with new properties are added to the mix, but for the most part a breeding program is a conveyer belt that continuously improves the quality and performance of a given crop.

People in the past never viewed their crops as perfect – they were always trying to improve their favorite varieties, whether to get better production, to fit changing fashions, or to excel in new environments. As voiced in the above article, “A 1902 cabbage by Burpee was a perfectly good cabbage by 1902 standards… But none of our ancestors ever viewed these things as done. You never stopped breeding your livestock. You never stopped selecting your cabbage.” People tend to lock onto the idea that older varieties tasted better while forgetting that, even when taste was excellent,* reliable performance in the garden was often not.