The Scientist Gardener

Monsanto's GM Drought Tolerant Corn

2012-08-24T07:54:00.001-04:00

DroughtGardTM maize will be the first commercially available transgenic (GM) drought tolerant crop if it's released in 2013 as planned. Hybrid seed sold under this trademark will combine a novel transgenic trait (based on the bacterial cspB gene) with the best of Monsanto's conventional breeding program.

The Union of Concerned Scientists threw their usual wet blanket on the development. I think their gloomy assessment of transgenic drought tolerance is pretty biased but they do make a few good points that the public should understand. Primarily, "drought tolerance" does not mean that these plants can be grown with little to no water.

A typical maize crop burns through over half a million gallons of water on the way to harvest - and the physics of turning sunshine, minerals and water into over a hundred bushels per acre of grain doesn't leave much room for improvement. To paraphrase a scientific presentation I once saw, modern maize varieties are like high performance racecars. You could re-engineer your racecar to get 50 mpg, but it won't be very fast anymore and you won't make any money. All the same, getting more grain per input water (generally referred to as water use efficiency) remains of major interest.

Drought tolerance is different than water use efficiency and can operate in complex and unpredictable ways (as plant physiologists have been shouting for years). For example, it's a glaringly common mistake in the literature to announce some new "drought resistance" gene that allows Arabidopsis to survive longer without water - only to reveal that the "resistant" plants grow slower and therefore simply take longer to drink up their little ration of soil water. This way of measuring drought is of questionable usefulness because helping a drought-ravaged crop to survive a few days longer is commercially worthless. As you've likely seen in the news this year, a maize crop that has been subjected to serious drought has absolutely no chance of producing enough grain to justify harvesting - either in the costs of harvest (e.g. diesel) or the value of crop insurance. Reducing growth rates generally also results in lower biomass and grain yield under good times, which farmers have zero tolerance for. Alternatively, reducing yield losses under minor to moderate drought (while delivering maximum yield under well-watered conditions) is a very valuable trait in the North American maize seed market. While this modest goal is nonetheless important (and very difficult to achieve!), the public should understand what 'drought tolerance' really means and hold their expectations accordingly.

DroughtGard maize contains the gene for "cold shock protein B" (cspB) from Bacillis subtilis. Cold shock proteins were discovered (and named) due to their rapid accumulation in cold shocked bacterial cells. Some CSPs such as CSPB act as RNA chaperones, which help to maintain normal physiological performance during stress events by binding and unfolding tangled RNA molecules so that they can function normally. Castiglioni et al., 2008 describes Monsanto's initial research demonstrating cold resistance of Arabidopsis plants transformed with cspA and cspB, followed by cold, heat and drought resistance of similarly transformed rice plants. It might seem odd to spend time testing genes in Arabidopsis and rice prior to getting around to testing in the crop of interest but this is the appeal of model organisms - genes can be screened much more efficiently in small, quick and easy growing model organisms compared to often finicky and cumbersome crop species. This is critical as companies may need to consider hundreds of thousands of transgenic constructs for each one that becomes a successful product.

Following these initial experiments, maize was transformed with cspB and was assessed in a series of field experiments of increasing complexity and realism. First, 22 independent cspB transgenic events (i.e. independent transfers of the DNA construct into 22 maize plants) were crossed into commercial grade maize. These were tested in a preliminary field trial where they were exposed to drought stress during the two week period immediately preceding anthesis (flowering), when cereals are most susceptible to yield losses. Drought-induced biomass losses that occur early in the season and grain filling losses that occur after flowering can be partially compensated for if sufficient rains return. Drought stress that occurs adjacent to anthesis, however, leads to the abortion of individual grains, with an irreversible impact on yield. This first field experiment was designed so that non-transgenic plants subjected to drought suffered from a 50% reduction in growth rate relative to the well-watered control. Within this scheme, cspB transgenic maize lines exhibited up to a 24% increase in growth rate under drought conditions (accompanied by improved chlorophyll content and photosynthetic rates), while performing normally under well-watered conditions. Grain measurements demonstrated a 4% increase in the number of plants with kernel-bearing ears and a 11.7% increase in the number of kernels per plant for cspB transgenic lines under drought. Thus, the cspB gene appeared capable of minimizing kernel abortion, an irreversible (and therefore very important) component of yield loss under drought.

Larger grain yield trials were then performed on 10 cspA and 10 cspB lines at four locations. Again, the drought treatment was applied immediately before flowering, at a severity that produced a 50% yield loss for non-transgenic genotypes. Here, cspA lines showed an average yield increase of 4.6% while cspB lines had an average yield increase of 7.5%. The best performing lines of cspA and cspB showed increases of 30.8% and 20.4%, respectively. The best two cspB lines (CspB-Zm event 1 and 2) also showed significant gains in leaf growth, chlorophyll content and photosynthetic rates.

The most promising line, CspB-Zm event 1, was then assessed in several years of field trials. The transgenic locus was crossed into three different hybrid genotypes, which were tested under three controlled watering conditions (well-watered, drought immediately preceding flowering, drought during grain fill) at five replicated locations. Non-transgenic controls suffered 50% or 30-40% yield losses under the two drought stresses, respectively, while cspB lines produced 11-21% relative yield gains. The yield stability of CspB-Zm event 1 was also analyzed over four years of testing in three hybrid test-crosses, where cspB provided an average yield benefit of 10.5% (with a range of 6.7-13.4%). CspB lines were also tested under dryland (non-irrigated) conditions with a field design that approximated normal commercial planting densities (rather than a more open field plot design). Of the sites that happened to experience seasonal drought during the experimental timeframe, the maximum yield gain of the transgenic lines was 15%.

Monsanto conducted much more field testing than was described in this paper. Typically, genes are discovered in a model organism prior to testing in a pilot field trial under controlled conditions. Promising lines are ramped up into multi-location/year field trials of increasing size and agronomic realism until they're eventually tested in preliminary farmer trials and prepared for commercial release. In this promotional presentation, Monsanto illustrates their network of 200 testing locations across different climatic regions of the United States. This entire process (for one transgenic variety) takes about 12 years.

In addition to field testing for agronomic performance, Monsanto had to generate huge amounts of data in order to petition for deregulation to allow their novel transgenic product to be grown in the U.S. and imported to foreign countries. If you'd like to get into the weeds on this, you can climb into this 500+ page Petition for the Determination of Non-Regulated Status for MON 87460). I looked through it to see some additional yield data and it appears consistent with what they stated in Castiglioni 2008.

According to the Plant Pest Risk Assessment for MON 87460 Corn, the final variety contains a single insertion of the following DNA sequences:

Part of the TDNA border

used to insert genes into plants with A. tumefaciens

Promoter, leader and intron from rice actin gene, Ract1

appears to drive constitutive (always on) expression of the cspB gene

Full length coding sequence of cold shock protein B (cspB) from Bacillus subtilis

functional cspB RNA chaperone protein

3' nontranslated terminator sequence of the transcript 7 gene from A. tumefaciens

a terminator in molecular biology is a signal sequence at the end of a gene that induces transcriptional proteins to stop copying the DNA sequence (e.g. by physically disrupting the copying process). It has nothing to do with hypothesized "Terminator genes."

a short length of noncoding DNA to separate the two genes
loxP sequence from Bacteriophage P1 for Cre-lox recombination

potentially allows the whole nptII cassette to be specifically snipped out of the plant once its no longer needed, though they appear to have left it in

P-35S promoter for the 35S RNA of Cauliflower mosaic virus

most famous promoter in plant molecular biology, drives constitutive expression of nptII

CS-nptII coding sequences from Tn5 from E. coli

protein that confers neomycin and kanamycin resistance, which allows original plantlets that have been successfully transformed to be selected for by applying antibiotics that kill any non-transgenic plants. Once plants with functional gene insertions are identified, antibiotic resistance is no longer needed and can be removed.

T-nos 3' nontranslated sequence from nopaline synthase (NOS) gene from A. tumefaciens

terminator sequence for nptII gene

loxP sequence from Bacteriophage P1 for Cre-lox recombination
Part of the TDNA border

From what I've heard, the yield gain of this variety under drought occurs because it slows its growth specifically under drought stress such that existing soil moisture is saved for the critical period surrounding flowering, resulting in less kernel abortion, higher harvest index and greater yield. This is certainly ironic given the expectations of many field physiologists and breeders. It also occurs to me that this is consistent with the thesis of Denison's Darwinian Agriculture - that evolution has already maxed out our crops' ability to deal with most stresses and environments, and that the greatest potential for improvement exist in traits that only work in an ecosystem (such as a farm field), where plants aren't in competition with their neighbors.

DroughtGard will begin its limited commercial rollout in the Western Great Plains (from South Dakota down to Texas). This is the initial target environment for many drought tolerant maize products as it's far enough west to experience regular drought, but not so far that irrigation is common. It's convenient for Monsanto that their new variety will be ready for its first season following a major drought. Farmers are generally most willing to invest in premium traits like drought tolerance when memory of major yield losses are fresh on their minds.

Of course the real test will be in farmers' fields over the next couple of years. It will be interesting to see how well this variety sells and performs.

Monsanto DroughtGard, Genuity webpages and brief video on product rollout

Castiglioni P, Warner D, Bensen RJ, Anstrom DC, Harrison J, Stoecker M, Abad M, Kumar G, Salvador S, D'Ordine R, Navarro S, Back S, Fernandes M, Targolli J, Dasgupta S, Bonin C, Luethy MH, & Heard JE (2008). Bacterial RNA chaperones confer abiotic stress tolerance in plants and improved grain yield in maize under water-limited conditions. Plant physiology, 147 (2), 446-55 PMID: 18524876

Herbicide Resistant Johnsongrass: Coming soon to a farm near you!

2012-01-31T22:55:00.001-05:00

Pioneer and K State are jointly releasing a set of new herbicide resistant sorghum varieties, which will incorporate resistance to ALS and FOP herbicides. Ironically, these non-genetically modified varieties invoke one of the classic bogeymen of anti-GM thinkers - herbicide resistant weeds.

In the past, I've heard a couple pro-genetic engineering scientists give herbicide resistant sorghum as an example of a potentially irresponsible creation. This is because another Sorghum species is a notorious noxious weed throughout much of the world: Johnsongrass. Presumably, herbicide resistance alleles in a grain sorghum variety could quickly jump to Johnsongrass, where it would subsequently burn through the rural landscape, making the associated herbicides useless. Johnsongrass is without a doubt one of the most strikingly common weeds in roadside ditches and farm fields here in rural West Virginia and Maryland.* This new potential threat of herbicide resistant Johnsongrass is ironic not only because the resistant grain sorghum varieties were created by non-transgenic methods, but also because these varieties were developed specifically as a control for Johnsongrass!

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?

[Also posted at Biofortified]

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.

Practical Agricultural Development

2011-11-10T22:53:00.003-05:00

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:

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.
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).
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.
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.
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).

Genetic Engineering vs. Breeding

2011-10-13T22:54:00.001-04:00

"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

openSNP and Personal Genomics

2011-10-04T22:38:00.000-04:00

So if you haven't heard, Direct to Customer (DTC) genomics has hit the mainstream. Multiple companies (23andMe, deCODEme, etc.) will now genotype you, providing you with a detailed rundown of all your genetic traits and tendencies...
Well, not exactly.

The promise of personal genomics/personalized medicine is that doctors will someday be able to prescribe medicines and lifestyle recommendations that are customized to how YOUR body works, not to some statistical average of how most studied human bodies work. The rub is that identifying genes that control these individual responses to drugs, foods and experiences is really really hard.

I won't describe it all in detail, but the short story of how personal genomics works is as follows:

Find a big group of people
Identify genetic markers that differ between human genomes (SNPs, currently)
Do math to see what SNP markers are associated with the trait you care about
Check your own genome to see which version of the SNP (and trait) you have

In reality it's not so simple because most traits are controlled by many genes, and many different (but rare) alleles can have the same effect on a trait. This is referred to as the "missing heritability problem." It's not unusual to have an extremely heritable trait (where the value of two parents is very similar to the value of their offspring) yet where (across a population) the presence of specific alleles don't explain much of this association. It's a sticky statistical problem and one that many famous geneticists have declared cannot be fixed no matter how many markers or individuals you add to your study.*

So back to openSNP...
openSNP is an effort to put the power of personal genomics and association mapping (aka linkage disequilibrium, aka GWAS) studies into the hands of the people. The idea is that everyone will upload their SNP marker genotype to this common database (along with whatever part of their own phenotype they want to share) in order to create a shared resource. While published data is already freely available (another site, SNPedia, aggregates these peer-reviewed results), the people behind openSNP protest that databases owned by these personal genomics companies are not available to the public.

I love open source/access efforts and citizen science in general, but they're definitely trying something audacious. I'm not going to underestimate the application of the internet to a difficult problem, but they definitely have it cut out for themselves. I think I'd be hesitant to upload my own genotype due to privacy concerns but it's definitely an interesting project. I haven't considered paying to get my genotype though I did sequence a segment of my mitochondrial genome (which was inherited from my mom's mom's mom's mom back in Abruzzo) while I was in grad school.

Incidentally, I came across openSNP first in the DIYbio google group.
It's worth checking out.

* Association mapping seems to work much better in domesticated plants than in natural populations of humans and other creatures. If you're interested in more detail, these papers are a great start.
** The only reason this works at all is because DNA sequencing has become so cheap that it's already revolutionized how biology is studied. Sequencing costs per basepair is actually falling faster than Moore's Law.

Zhu, C., Gore, M., Buckler, E., & Yu, J. (2008). Status and Prospects of Association Mapping in Plants The Plant Genome Journal, 1 (1) DOI: 10.3835/plantgenome2008.02.0089
Hamblin MT, Buckler ES, & Jannink JL (2011). Population genetics of genomics-based crop improvement methods. Trends in genetics : TIG, 27 (3), 98-106 PMID: 21227531

California Almonds

2011-10-02T22:50:00.001-04:00

I recently got a tour of some Cali Central Valley almond farms from the Almond Doctor.

The nuts were in the process of being harvested. The first step is to shake the nuts off the tree with a machine that grabs them around the trunk (here's a video*). One way you can tell almond and peach (both Prunus species) orchards apart is to look at how low the first branches are. Almond trees are trained to branch higher above the ground to give the machine room to grab them. Peach trees are trained to branch almost immediately above the ground to help most of the canopy stay low enough to be reached without ladders (due to the increased chance of injuries). Maximum canopy height is more rigorously limited in peaches for the same reason.

Step two is to let the almonds dry on the ground. At this point every edible almond nut is surrounded by a hard shell (like a peach pit), which is itself surrounded in a somewhat green, rubbery hull (like the fruit of a dried up peach).

Step three is to blow the almonds into windrows and collect them for transport to the local processor.

Almond hulls and shells used to just be burned or thrown away, but now they're used to supplement the feed of local dairy cattle and assorted other uses. The hulls are sweet, which the cattle love and are pretty healthy for them. The shells are basically wood and can be used accordingly - from adding fiber to the cattle's diets, to use as their bedding to manufacturing fiberboard.

The Almond Doctor pointed out how much modern farmers rely on other industries (like animal ag) to support their operations through the purchase of byproducts. It's also much more efficient and sustainable to feed your scraps to another industry than to burn or bury them. Agriculture is very industrial and very BIG in the Central Valley, which certainly helps every farmer and processor get the most of their products and byproducts.

It also is interesting to drive north on a highway lined with processors; smelling first onions (from the onion dehydrating plant), then wine (from some kind of raisin processing plant), then cattle (less pleasant of course...). I mentioned to him of my friend who lives near the Nabisco plant in Paterson, NJ. Every time it rains, it smells like chocolate chip cookies...

Finally, here's a picture of a chopped up melon weed out in an almond test plot. I never knew that melon species could be weeds...

* "Industrial ag" has a negative connotation to most, but I think the increasing presence of crazy machines and robots is pretty cool.

Blue Potato Chips

2011-09-29T22:53:00.000-04:00

JetBlue airlines now gives out blue potato chips as their "official" snack.

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...

Polycultures in Modern Ag?

2011-09-21T00:08:00.001-04:00

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.

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

Thoughts?

Evolution of Fruit Shape in Tomato

2011-09-05T21:06:00.003-04:00

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

I have a yard!

2011-08-14T23:05:00.001-04:00

I spent the day moving the first of my stuff into the new house I'm renting. I'm very excited to finally be somewhere besides a one bedroom apartment. The yard's pretty shady but presents some interesting gardening opportunities that I'm working over in my head.

This picture shows a small patch of grass completely encircled by deck and walkway in the backyard. It's a bit shady but the concrete border will make a useful edge and it's out of sight from the road. It's also about as far from intrusive tree roots as anywhere in the yard and is conveniently close to the back door. I think I'll set up a compost pile against the deck so I can easily toss in kitchen scraps during the winter. It's not a ton of space but will be a great start for intensive cycling of brassicas and tomatoes at least. I'll probably tuck in other (especially more ornamental) crops throughout the property.

The soil's pretty lousy; compacted and light in color. I'm kinda burned out from vegetable gardening this year so I think I'll go right to making an investment in the spring. I'll dig up this whole section (and maybe borrow a rototiller) then seed in some cover crops. CU has a pretty awesome guide for cover cropping for vegetables. Cover crops are planted for many reasons - most notably to prevent erosion, increase nitrogen and soil organic matter and suppress weeds.

It looks like oats and red clover would be a good mix for me. They'll grow deep roots that break up the soil structure, increase nitrogen content and produce lots of organic matter. The oats will die and begin decomposing during the winter, which should leave the soil fairly easy to work come early spring (when I'll likely install a low tunnel for an early start on greens!).

I should probably think about what else I want to start now for 2012. Maybe asparagus? garlic? some spring bulbs or a few perennials?

More to come...

Putting up Hay

2011-08-08T10:10:00.002-04:00

It used to be a common sight for me this time of year (on the way to the maize experimental fields) to see straw and hay being raked into windrows by hay rakes (video 1 2). Though most of us tend to use these words interchangeably, hay is a crop grown specifically for animal feed and straw is the leftover stems and leaves of a harvested grain that may be used for animal feed, bedding or construction. Common annual and perennial hay crops include legumes (e.g. alfalfa and clover) and grasses (e.g. timothy, brome, orchard grass and tall fescue). Straw usually comes from whatever grain is being grown in your area (e.g. wheat or barley).

Straw and hay are commonly cut and piled into windrows to dry before being packed up and removed from the field. Either may be baled into big blocks or cylinders for storage and distribution. Those bales wrapped tight in white plastic are actually silage, which can also be made by piling green vegetation into silos or trenches. This process preserves the material by fermentation, which maintains greater nutrient value than allowing it to dry.* In cold northern places like Upstate NY and parts of the Upper Midwest (where dairy is king), maize is often grown for silage. Silage maize is harvested whole before the grain is fully mature. This captures much of the energy of maize grain where seasons are not reliably long and warm enough to get the more valuable fully mature grain product.

Traditionally (into the early 1900s), straw and hay were stored in stacks. I think it's a testament to our culture's agrarian past that all of us are familiar with these stacks as passed down in children's stories. In his classic DIY grain gardening book, Gene Logsdon describes how his family used to create these stacks (with the help of their neighbors) and how the stack played a central role in the life of the farm year round - for both people and livestock.

Dry straw was removed from the outside of the stack each day for fresh animal bedding, opening up access to fresher vegetation within. The cows would continuously root out these inner layers, slowly transforming rounded stacks into (eventually unstable) mushroom shapes, while pigs and chickens kicked through the fallen debris looking for seeds. On cold and wet days, livestock would huddle under the ledges of these eroded stacks. A used up stack left a patch of extremely fertile composted soil in its place, which was apparently perfected for watermelons.

Haystacks shouldn't be confused with shocks (aka sheaves), which are small stacks of grain that has been cut but not threshed. Before combines, cutting grain with scythes was the first step of harvesting, followed by bringing in the sheaves and threshing and winnowing them. In pre-industrial times, the metals that were used to make scythes required constant sharpening in the field. I think this painting demonstrates how fun the use of such relatively primitive tools probably was.

At the end of last July, I watched the barley field by my apartment transformed to straw. A combine harvester combines cutting and cleaning the grain: reaping, threshing and winnowing. The most sophisticated (and incredibly expensive!) combine models can harvest huge amounts of grain, storing it in a bin and dropping finished bales of straw. In modern industrial ag, some farmers have left their own fields to become professional combine owner-operators, traveling throughout the U.S. grain belt, selling their services to farmers who can't afford to own and maintain their own combines.

The grain was poured into some waiting trucks (spilling only a little). Straw was left behind in windrows (and presumably baled up later - but I left town before I saw it).

Returning on the trail to my apt, this deer crashed by me on its way from one woods to another.

* One of the reasons those plastic wrapped bales have become popular is that you don't need to maintain a silo (or move the hay back and forth from it). I've heard that the fermentation process also increases the protein content of hay, but wikipedia seems to dispute this.
** Some more reading on how to grow your own hay
*** There's a real science to knowing what kind and richness of hay to feed animals at different times of the year to keep them healthy, but I don't know the details.
**** I know there's U.S. regional variation in the phrase "putting up hay" to refer to harvesting and storing hay, but I can't remember or find it now...

First! (to harvest garden sweet corn)

2011-06-28T20:11:00.002-04:00

Well, it's not from the garden, per se. It's from the greenhouse.

When I got the keys to my greenhouse space, one of the first things I did was sow a bunch of field crop seeds. I didn't know if there would be a need for me to grow them in the greenhouse, but I did know that it can be a tricky proposition. Better to sketch out a quick SOP now than wait till I need one and then add a 6 month delay to the project as I figure it out on the fly...

So a couple seeds bought for my garden and 3 months later, and I had some sweet corn with dinner. You can see how poor pollination was (as I didn't make much of an effort to pollinate it myself). Still, not too bad considering the stand only had a half-dozen plants.

Neglect left the plants savaged by aphids and spider mites towards the end - which is just as well as I'd probably have left the ears till they were dry if I had kept waiting in vain for them to get to full size.

They did taste good though!

What's Cooking, Uncle Sam?

2011-06-13T21:50:00.006-04:00

I just went to the new "What's Cooking, Uncle Sam?" exhibit at the National Archives. It tells the history of the government's role in U.S. food and agriculture - a story of market protectionism, social engineering and the regulated tension between the aspirations of business and the demands of the people...

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 (who is quoted on the sidebar of this blog) 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.

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 preview on the 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.
*** 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.

Twitter Update

2011-06-02T21:12:00.001-04:00

I love this stupid service. I can flag all the interesting papers and articles I find in a week (with room for a little commentary) but without needing to sit down and come up with a coherent 500 word essay!

I could automatically feed these tweets into the blog, but it would just clog my page up with text. If you're interested in tapping this new stream, just add my twitter account to your blog rss feed. I promise not to gum it up with updates on what I'm eating.

I'll probably continue to write actual blog posts at about the rate I've settled into.

Now on Twitter

2011-05-13T22:19:00.000-04:00

Thought I'd give this stupid twitter thing a shot...

Seems like a good way to share links and blog post updates for those times that I don't feel like putting hours into a full post. Follow me.

Commercial Perennial Crops?

2011-05-13T21:56:00.000-04:00

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.

Weed Seedling ID

2011-05-09T00:08:00.001-04:00

I've spent the past hour reacquainting myself with the likely weeds I'll find in my plot, which ones are useful and what they look like.

While pulling up some chenopods among other weed seedlings, it occurred to me that some of these "volunteers" would be worth sparing. I went through my "Wild Plants to Eat" book along with a mess of extremely helpful extension weed seedling ID websites and came to the conclusion that I'll spare the two little dicotyledonous pseudograin weeds: amaranth and quinoa.

Lamb's quarters (first picture) is easily recognized by its leaf shape and frosted leaves. It's closely related to quinoa, and like other members of the Chenopodioideae (spinach, beets and chard) produces young leaves that are edible raw and older leaves that better cooked. My direct-sowed greens are all off to a slow start so it'll be good to take alternatives where I can.

Amaranth species are popular ornamentals, commonly known as "pigweed" where weedy and closely related to chenopods. Like their kin, they produce edible seeds and leaves, but unlike all my other greens they grow well in sticky, hot weather - no doubt a useful salad trait in the great swamp that is the District.

I've been impulsively grabbing more seed from the big box store (it's so cheap and there's still so much room in my plot!).* Maybe I'll get some ornamental amaranth too. I'll let you know how good they taste and if I decide to cultivate any other weeds this year.

* New additions: nasturtiums (salad and putative pest repellence), marigolds (like the smell and putative pest repellence), cauliflower and collars (for fall), lime and regular basil (for fun)

** I found a volunteer potato on the edge of my plot today. I was very excited since I missed the opportunity to get seed potatoes this spring and the store ones all shriveled up. I moved it to a better spot with well chopped up soil. I also spared two mint volunteers.
*** Volunteers = crop plants that manage to survive the winter

Opportunistic Gardening

2011-05-05T23:52:00.006-04:00

It's amazing what you can accomplish with some reckless enthusiasm and an emergency shovel.

I've been out of grad school/postdoc for half a year now but have been slow to acclimate to my new budget. After spending 75 bucks to rent my garden plot, I couldn't help but balk at the idea of spending hundreds more on tools, containers, plants and fencing - so I started cutting corners.

Warning: irrational frugality will be a theme here...

After last year's disaster, I knew there wasn't any point in renting a plot unless I was ready to take weed control seriously. Our plots were tilled and staked the first week of April, but I'd been kept out of the field by work and family events for the past couple weeks and was dreading the green plague that would begin consuming my 20 ' x 25 ' plot. Luckily for me, the weed pressure (so far) is nowhere near what I experienced in Ithaca - probably because this garden is barely big enough to meet local demand and they kick people out who don't tend their plots.

The War on Weeds.
It started with a trip to the big box store for some weed fabric. The first roll only covered about a fifth of my plot, but it was enough to direct sow some of the cold weather seed. A few days later, the greenhouse manager asked if I wanted to use some old plastic potting soil bags he'd been saving, hoping for a way to recycle them. I took him up on the offer and have been pretty happy with the results. I laid out a couple rows of plastic bags, covered and staked them down with mulch. Two thirds of the plot was now mulched with plastic or cloth covered in bark with thin strips of soil in between.

Since then, the weeds have really made their move - mostly crab grass and bindweed. It's incredible how fast they can become big robust plants while my seeds have barely germinated and the transplants are still settling in. They're now forcing themselves through the weed cloth, crawling out from under the plastic and generally bursting up from the depths. I'm kinda dreading what's up with West Neighbor, who hasn't touched his plot yet and will soon have a closed canopy of weeds advancing on my border.

With my warm weather crop transplants outgrowing their pots and the weeds taking off, I forced myself out into the field after work earlier this week. I spent a couple hours hand tilling the rain soaked clay with my trusty emergency shovel. Doing this on the whole plot would probably be the same losing proposition it was last year, but it seems fine so far for the 1/3 of the field that's not covered in mulch. I barely finished before it was completely dark but I'm satisfied with the results (and getting a lot of exercise without having to go to the gym). I stopped in today to play catch up and I'm pretty confident I can keep ahead of the weeds one way or another.

I'm holding off on installing fences until I see to what extent my neighbors continue to build metal fortifications all around me. I've only ever had critter problems later in the season and I haven't seen so much as a single deer since I moved here, so we'll see...

The Tragedy of the Commons is rented land. I've heard a number of ag economists explain recently that the main reason many mainstream farmers don't take full advantage of soil-building rotations is that they no longer own their own land. It doesn't make sense to invest in a cover crop year if you're not sure you'll get to plant in a cash crop the following spring. Similarly, while I'm a huge proponent of composting and working on soil structure, I still live in an apartment - so I just did what I could to loosen the heavy clay to crumbs around each plant and will start dousing them with miracle gro once they get established and the weeds fall back. The greenhouse manager emphasized (unfortunately after most of my transplants were in) the importance of breaking up the clay. Apparently if you plant trees and shrubs into too hard of clay soil, the roots can fail to penetrate from the potting soil into the earth and just grow in circles as if they were still pot bound.

The Summer of Intercropping.
I really enjoy finding excuses to "do stuff" out in the garden during the summer and this will be my most intensively managed garden yet. I'm gonna see how far I can push mixing fast and slow growing crops within the same personal space and sowing successive generations of determinate ones like maize and salad greens. As the garden starts to fill in, I'll see where I still have some extra room to tuck in some additional plants and will start more cold weather crops in another month or two for fall harvest transplants. The first row of maize is planted and I'll add more each week or so. I'm putting it along the back (in an North-South line!) up against the other titans (squash, watermelon, etc.) with the hopes they can slug it out to use up all the available space and choke out the weeds.

It began with seed. I had planned on ordering from Seed Savers this year but despite their many unique offerings, they didn't have all my staples. I still look forward to supporting them in the future, but this year I went with Johnny's, which I've been very impressed with in the past. They also had lots of seed on sale and would save me from two S&H fees. I don't know what kind of self-respecting ag scientist I'd be if my garden fails to yield more than I spent for a second time - so I bought lots of seed on sale, F1 hybrids where available.

The Essentials.
I started with the stuff I really like, really wanted to experiment with, or have had great luck with in the past.

Lettuce mix (Tango, Red Salad Bowl, Salad Bowl, Parris Island, Dark Lollo Rossa, Deer Tongue, Firecracker, Spock)
Carrot (Early Nelson F1) - because carrots were foolproof in Cali
Brussels sprouts (Churchill F1) - because I just discovered they taste awesome roasted
Broccoli Raab (Specialty Spring) - because I'm half wop
Thai basil (Queenette) - because I'm trying to perfect my curry recipe
Cilantro (Calypso) - to make better Mexican and Indian food
Beet (Merlin F1) - for something different
Sweet corn (Bicolor BRD 275A F1) - I'll hand-pollinate it at a later date in a how-to blog post (and to ensure proper pollination with the sh2 allele)
Green onions (Nabechan F1) - for my gf
Snap pole beans (Fortex) - because I can use up a lot of time training their tendrils
Tomato (Heirloom Tall Vine Rose) - I'd also have grown Joseph's breeding line again but have not been able to find them among my moving boxes :p

The Extras.
The greenhouse manager offered me some extra seed of his. Conveniently, we have similar taste in veggies.

Okra
Peppers (Serrano, Tabasco, Bell)

The Produce Section.
I also planted a bunch of stuff from the store. This isn't a good practice if you want good yields of good-tasting food, but I just wanted to play around with some plants I haven't grown before.*

Potatoes were cut up and set in the sun, but didn't manage to overcome dormancy/anti-sprout coatings. I dropped the shriveled up slices in the ground for the heck of it.
Garlic is usually planted in the fall but I wanted to try it anyway. It's sprouting fine so far.
Sweet potatoes are sitting in water, slowing growing leaves and roots. It's probably a little too cold to put them out yet anyway. Hopefully they'll keep growing because I have a big empty spot ready for them.

Filling it in.
I couldn't resist some impulse additions as it became clear 20 x 25 is a little bigger than I had thought.

Cherry tomatoes (Red Currant)
Straightneck summer squash (Saffron)
Mini watermelon (Bush Sugar Baby)
Tobacco (Wisconsin 38) is a lab rat that the lab manager grows routinely for the scientists. It's a virtually flavorless binder variety but I'm curious to grow it anyway.

If you're working the land at Woottons Mill, feel free to come over to #17 and say hi!

* Store-bought fruits and veggies have genetic backgrounds primed for yield and shipping quality more than flavor. Plus, tubers are prone to be riddled with viruses, ruining your chance of getting amazing amounts of food. They also tend to be sprayed with anti-sprouting chemicals that will make it pretty difficult to turn them back into plants.

Wednesday Links

2011-04-27T20:50:00.000-04:00

Man, oh man. Possibly the coolest website ever and more chemical ecology than I know what to do with (and here's another). h/t OrchidGrownMan from Biofortified
Open source Legos for grownups. Can I have a microtractor? or a microcombine? or a dimensional sawmill? Pleeeease?
More scientific sour grapes. Why won't grad students sacrifice their entire careers to do what we think is important?
And, as always, maps! This time, watch agriculture spread. h/t Seed.Feed.Food

Ketchup and the Future of GM Food

2011-04-20T23:04:00.001-04:00

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

Craziest Landscape Tree Pruning Ever

2011-04-16T12:05:00.001-04:00

It's how the Dutch do it.

A couple people told me it's common to see trees pruned like this out in rural areas - particularly willows. I assume the traditional purpose is to coppice for fuel and baskets - and here it's nostalgia for the countryside.

Heirlooms are Obsolete

2011-04-11T22:48:00.001-04:00

"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.

In light of inevitable reality, the executive director of Seed Savers suggests that the term "heirloom" include all of the following:

Family legacies - e.g. some special plant rediscovered growing in someone's garden
Old (obsolete) market varieties - e.g. the Danvers carrot and Rutgers tomato**
Modern heirlooms - e.g. the sugar snap pea, developed by a vegetable breeder in the 1970s
Mystery heirlooms - e.g. varieties that have been preserved by farmers and gardeners

Ultimately, the age of the variety doesn't really matter. Gardeners who understand value heirlooms for their diversity and the invitation to participate in the ownership and future of agriculture and self-sufficiency. I'd like to see potential amateur plant breeders out there shift their thoughts on heirlooms from the past to the future. As said in the article: "The great bank of heirloom seeds is ripe for fresh creations and practical improvements."

There's a place for celebrating classic technologies (and crop varieties), but I'm more interested in seeing people move beyond a fixation on an overly idealized past to create their own future.

h/t: Plant Breeding News (3/2011)

* One Dutch friend told me that, contrary to the popular perception that foods were better during our youth, the tomatoes he grew up with were huge and red - but watery and tasteless. Commercial tomatoes available in the Netherlands today are much tastier.
** The Rutgers tomato, released in the 1930s, was one of the earliest mass-market tomato varieties. It was bred largely as a processing tomato (i.e. paste and ketchup, not fresh eating). It's ironic that the same people who turn their noses up at modern commercial varieties would embrace an obsolete version of the same thing.

Spring arrives in Metro DC

2011-04-10T19:28:00.000-04:00

It showed up a couple weeks earlier in the heat island of the city proper.
The cherries bloomed first in DC, than along the highways and now in my apartment complex. I imagine my neighbors around the courtyard wished these Bradford pears smelled like cherry trees. I don't mind. The scent reminds me of my suburban street hockey days.

"car! ... game on!"

Genomics in Business Meeting, Amsterdam

2011-04-01T11:20:00.000-04:00

Anyone going to the Genomics in Business meeting in Amsterdam next week?

In hindsight, I should have asked earlier but it's been a crazy couple weeks...

Better Chemistry Through Breeding

2011-03-22T21:30:00.003-04:00

I recently had the opportunity to visit the fabled heart of the USDA-ARS empire: Beltsville.

I heard all about the tornado that knocked down all the campus trees, smashed in the greenhouses and threw doors down hallways a few years ago, visited their food sensory lab (a controlled environment where fruit samples are passed through a wall to waiting taste testers), and saw greenhouses packed full of cacao (where research on one of my favorite fungi, Crinipellis perniciosa, is co-funded by M&M Mars Inc.).

But I was there mostly to visit the pepper breeding program.

One of the goals of this particular program is to breed baby bell pepper (C. annuum) varieties that are equally ornamental and edible. It was an amazingly vibrant greenhouse scene in the middle of a brown winter day: bright green, dark purple and variously variegated bushes of leaves tufted from twisted woody stems and were spotted with flowers and fruit of most colors imaginable. It was a striking demonstration of segregating traits and the heart of what plant breeding is all about. Appropriately, these guys have released a few varieties to the public (including the striking Black Pearl).

The Colors of Peppers

Plants are green due to chlorophylls, orange and red thanks to carotenoids and red, purple and blue (sometimes yellow or orange) because of anthocyanins.* Anthocyanin pigments (actually dyes) are the reason why stressed plants tend to turn purple - especially when exposed to too much sun. Like other plant pigments, they also play important roles attracting pollinators and seed dispersers and protecting the plant from stresses (in this case, UV light) by acting as antioxidants.

The typical bell pepper (C. annuum) is a green plant with green fruit that gradually turn orange, then red as they ripen. In the process, chlorophyll is broken down in the fruit as carotenoids accumulate. Although you won't likely see these varieties in stores, C. annuum can also produce immature fruit that are dark purple or almost black (containing normal chlorophyll and anthocyanins) or violet (lacking chlorophyll but containing anthocyanins). Either way, the black or purple fruit will turn orange and red as carotenoids replace chlorophylls and (in this case) anthocyanins. There are also varieties that lack chlorophyll (and anthocyanins) in immature fruit - and therefore start from white or yellow-green and ripen through orange to red. It's a pretty powerful visual statement to see rows of pepper plants with masses of mixed green-orange-red, white-orange-red or purple-orange-red fruit. The dark purple and violet-fruited peppers also tend to have dark purple foliage and if they happen to contain the genetic locus for foliar variegation, the whole plant may be a mix of purple and white (see first picture). Oh, and the flowers can be purple too (instead of the normal cream color).

So in summary:

Leaves can be green, violet, black or variegated cream
Fruit ripen from green, cream, yellow-green, violet or purple through orange to red
Flowers may be cream or purple!

A Pigment Called Delphinidin

In addition to being surprisingly ornamental, chili peppers turn out to be a great model for anthocyanin development in plants. Structurally, anthocyanins consist of a 3-ring core (the "aglycone" anthocyanidin) that's ornamented with any number of glycosyl (sugar), acyl, methyl and hydroxyl functional groups. While the aglycone component is fundamentally responsible for color, it's also positively charged and inherently unstable at neutral pH. Functional groups not only help stabilize these anthocyanins, but also play important roles modifying the hue and intensity of color (along with associated co-pigments and the pH and metal ion concentration of the relevant cellular compartment). While this produces an extremely diverse and dynamic chemical family, there are only three primary aglycone anthocyanidins: cyanidin, pelargonidin and delphinidin.

Delphinidin anthocyanins are usually the most blue of these due to their large number of hydroxl groups. The absence of delphinidin anthocyanins in most roses, carnations, chrysanthemums and lilies is the reason why blue versions of these flowers have long been lacking. These molecules also become bluer as they receive aromatic acyl groups, are stacked with flavone and flavonol co-pigments and metals and are subject to neutral/alkaline pH. Therefore, even though tulips have no shortage of delphinidin anthocyanins, the intracellular environment prevents these molecules from appearing blue (in this case, due to iron levels). Similarly, the well-known ability of Hydrangea macrophylla flowers to change from pink to blue with soil pH is due to the pH-mobilization of delphinidin-influencing aluminum ions.

The chain of enzymes that are needed to build anthocyanins have been known for some time, but as is often the case, we're still figuring out exactly how different regulatory mechanisms manage to fine-tune the flow of precursors through the various steps of the biosynthetic pathway. In this case, the purple color is almost entirely due to a single anthocyanin:

delphinidin-3-p-coumaroyl-rutinoside-5-glucoside

(It's probably a safe bet where the aglycone was first discovered)

While a whole series of enzymes are needed to build this delphinidin glucoside, whether the purple end product is actually present in a given C. annuum variety is determined by the A locus, which encodes a MybA transcription factor gene.** This MYB protein is thought to bind with a particular WD40 protein, which in turn binds to a MYC protein to form a single protein complex that works together to turn on one of the specific enzymes in the anthocyanin biosynthetic pathway. A naturally occurring mutation in MybA apparently changes the property of this protein such that this regulatory MYB-WD40-MYC complex fails to assemble (and no purple is made!). Quantitative variation in the amount of purple in peppers that contain a functional version of MybA is controlled by an additional gene, moA (aka modifier of A). However, neither the identity of moA nor the more complex regulatory structure that controls purple accumulation in leaves seems to have been figured out yet.

So what's next for chili peppers? Lightbourn et al. suggest that as there are no pH differences between purple and black-fruited varieties, there're might be an opportunity to create blue peppers by selecting parents with more alkaline pH (to modify the hue of the delphinidin anthocyanin from purple to blue). There are already 2 known genes in petunia that modify vacuole pH. As both petunia and peppers are in the same family (Solanaceae), there's a chance it'd be pretty straightforward to find a pepper version of these genes to make the intended changes.

There have been lots of attempts to engineer anthocyanin synthesis, largely in flowers and mostly unsuccessful. Early on, it was expected that some simple changes would allow major color changes to be made to plants (e.g. "blue" roses), but for the most part it's turned out to be trickier than hoped. In hindsight, it shouldn't be so surprising considering the extent to which color is influenced by pH, metal ions and various pigments and co-pigments (that often have to be shuttled among different cellular compartments). It's difficult enough with current technology to optimize the expression of multiple genes at one time, but the complications of biochemistry really push the envelope.

Even if some very talented scientist-artist manages to engineer a flower with really unique coloring, it's unlikely we'd see it in our gardens anytime soon. The path to commercialization is just soaked with regulation, all of which differs from country to country (which is even more complicated due to the frequency with which flowers are often grown, warehoused and sold in different countries). Existing regulations are already pretty burdensome for major traits in major crops where your chance of recouping your expenses are at their best. The floriculture market is incredibly segmented and the sales per any one cultivar are relatively small. Until regulation gets streamlined, no company is likely to be bankrolling any sci-fi new flowers.

   Lightbourn, G., Griesbach, R., Novotny, J., Clevidence, B., Rao, D., & Stommel, J. (2008). Effects of Anthocyanin and Carotenoid Combinations on Foliage and Immature Fruit Color of Capsicum annuum L. Journal of Heredity, 99 (2), 105-111 DOI: 10.1093/jhered/esm108
   Stommel, J.R., & Griesbch, R.J. (2008). Inheritance of Fruit, Foliar, and Plant Habit
Attributes in Capsicum J. Amer. Soc. Hort. Sci., 113 (3), 396-407
   Stommel, J.R., Lightbourn, G.J., Winkel, B.S., & Griesbach, R.J. (2009). Transcription Factor Families Regulate the Anthocyanin Biosynthetic Pathway in Capsicum annuum. J. Amer. Soc. Hort. Sci., 134 (2), 244-251
   Tanaka Y, Brugliera F, Kalc G, Senior M, Dyson B, Nakamura N, Katsumoto Y, & Chandler S (2010). Flower color modification by engineering of the flavonoid biosynthetic pathway: practical perspectives. Bioscience, biotechnology, and biochemistry, 74 (9), 1760-9 PMID: 20834175

* Plants in the Caryophyllales (beets, swiss chard, cacti and many carnivorous plants) rely on betalains (which are red or yellow) instead of anthocyanins - and no plant is known to be capable of making both.
** chalcone synthase -> chalcone isomerase-> flavanone 3-hydroxylase-> dihydroflavonol 4-reductase-> anthocyanidin synthase -> UDP-glucose-flavonoid-3-O-glucosyltransferase
*** As usual, my reports of what other scientists are up to is limited to what is publicly available. Don't want to cause someone to get scooped!