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De-balkanizing crop genomics

Genomics has a data problem, according to Nature. Not perhaps as big as YouTube’s, but…

Nevertheless, Desai says, genomics will have to address the fundamental question of how much data it should generate. “The world has a limited capacity for data collection and analysis, and it should be used well. Because of the accessibility of sequencing, the explosive growth of the community has occurred in a largely decentralized fashion, which can’t easily address questions like this,” he says. Other resource-intensive disciplines, such as high-energy physics, are more centralized; they “require coordination and consensus for instrument design, data collection and sampling strategies”, he adds. But genomics data sets are more balkanized, despite the recent interest of cloud-computing companies in centrally storing large amounts of genomics data.
…
Astronomers and high-energy physicists process much of their raw data soon after collection and then discard them, which simplifies later steps such as distribution and analysis. But genomics does not yet have standards for converting raw sequence data into processed data.

Leave aside for a minute that last sentence, which is generating some heat on Twitter…

…it is certainly worthwhile highlighting the balkanization of genomics datasets. But then, why not mention that in at least one area — crop diversity — there are some useful initiatives underway, like DivSeek. Which Nature knows about.

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Invisible Angola

Kew botanist David Goyder had a thought-provoking blog post a couple of days back describing the relative lack of floristic data from Angola. Here’s his map of plant collection data for southern Africa, from GBIF:

GBIF Angola_2015_6a

Angola emerges quite clearly as a gap, particularly the interior. There’s lots of reasons for that, not least landmines, as Goyder points out, and there are also efforts underway to redress the situation. But the thought that the map provoked in me was, of course, whether the situation was similar for crops. So here’s what Genesys knows about crop germaplasm collections in southern Africa:

Angola genesys

It seems the answer is a pretty resounding yes. Again, you can clearly trace the borders of Angola by where the genebank accessions end. There is, in fact, though, a very active national genebank in Angola, which has been collecting the country’s crop diversity for years, landmines or no landmines:

A total of 441 accessions were collected during a mult-crop collection in Huila province, Namibi province and Malanga province in 2004. With these collections, NPGRC now has a representative sample from 55% of the total number of districts in the country and representing 60% of the recognized agricultural zones (MIIA).

But when will we be able to see the data?

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Climate smart agriculture = diverse agriculture, and vice versa

USAID is seeking feedback on the climate smart agriculture (CSA) strategy of its Feed the Future programme. Recall that CSA has three objectives 1

  • Sustainably increasing agricultural productivity and incomes.
  • Adapting and building resilience to climate change.
  • Reducing and/or removing greenhouse gas emissions, where appropriate.

So it’s that triple-win we’re after, and it’s good to see diversification being highlighted in that context by the strategy document:

In general, Mission FTF programs work within diversified production systems that reflect farmer choice around crops, livestock or fish although one value chain may be the focus. Diversification includes not only the number of crops, but also using a wider range of improved varieties and staggered planting times for a given crop. Over a longer time period, crop choices by farmers may shift as risks with one crop rise while another crop option is viewed as a safer bet. Thus diversification can be a strategy for managing risk and optimizing returns, particularly when informed by information on potential shocks, seasonal forecasts and long term climate trends. Ultimately, it will be farmers who directly determine their risks, but FTF programs can help widen the array of appropriate options that confer greater resilience as well as more efficient production with a concomitant reduced GHG footprint.

But why a wider range of only improved varieties? Don’t landraces or varietal or other types of mixtures have any role to play at all? And why mention staggered planting times, but not intercropping, say?

And, most importantly, why no mention at all of conservation of crop diversity as a prerequisite for diversification, and the role of genebanks in that? After all…

…it is likely that some (if not all) countries will need germplasm that is currently grown elsewhere to adapt.

And where is that going to come from if not genebanks? You can let USAID know until noon on August 14, 2015.

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Nagoya marches on in the EU

It seems that an attempt by Dutch and German plant breeders to get the EU to reconsider its ratification of the Nagoya Protocol has been unsuccessful. The breeders had said that the regulation…

…was insufficiently clear and created disproportionate red tape and additional expenses for their businesses.

Ouch. But what of the International Treaty on Plant Genetic Resources for Food and Agriculture? Wouldn’t the quite different access and benefit sharing system it established alleviate at least some of the breeders’ concerns? Well, maybe.

Regarding other avenues for plant breeders specifically, Article 2(2) of the Regulation in principle allows an exemption for genetic resources for which alternative “access and benefit-sharing” mechanisms are governed by “specialised international instruments”. Some commentators have argued that this could in theory allow at least some plant breeders to evade 2 the Nagoya Protocol using the benefit-sharing procedures of the International Treaty on Plant Genetic Resources for Food and Agriculture, as some industry leaders have also suggested. However, it remains untested, whether such an exemption would be upheld in practice.

To which I would say: why don’t the breeders in question do that testing? I’m not sure whether any of the ones involved in querying Nagoya specialize in breeding for organic agriculture, 3 but if it’s true what they’re saying about “additional expenses,” the new regulations would hit that segment particularly hard. A recent report points out that:

Organic plant breeding is of common interest and requires long-term funding. It is a common good with socio-environmental benefits greater than are mirrored by the modest royalties of its market value.

All the more reasons to test the International Treaty, and indeed make sure it works. Incidentally, recommendation 6 of the report (p. 19) will resonate with breeders — organic, and not so much — everywhere. And it might also be extended to genebanks (which unfortunately the report doesn’t mention):

Public awareness about the importance of plant breeding should be dramatically enhanced. It is literally in everybody’s best interest to develop an awareness of the foundational role that seeds play in health and nutrition. Since this topic is not always easy to communicate, new forms of communication should be sought. Hitherto, only breeders have been pushing for organically bred plant varieties, now consumers should start pulling retailers to further develop the market.

Meanwhile, various stakeholderts are gearing up to enforce the new rules, and monitor compliance, for example in the UK. The International Treaty came into force years ago in the EU, but I don’t recall frantic meetings being organized at the time to cope with it.

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An evolving genebank in farmers’ fields

News that the Organic Research Centre has launched the ORC Wakelyns Population, an unusual new wheat “variety”, inspired Dr Salvatore Ceccarelli to write this blog post for us about his own efforts in a similar vein. He describes a different breeding paradigm, one based on providing farmers with lots of diversity, rather than with a single Next Big Thing.

One of the global issues most frequently debated today is the loss of biodiversity. What’s not often mentioned is that this can happen within agricultural as well as natural ecosystems, and that it can then have an effect on the ability of farmers to adapt to climate change, on food security and on human health.

In 2008, at ICARDA, we dusted off the old idea of evolutionary breeding 4 to bring biodiversity back into farming systems. We made large, widely diverse populations of barley, bread wheat and durum wheat by mixing lots of F2 lines. And I mean lots: 1600 in the case of barley, 2000 in the case of bread wheat and 700 for durum wheat. The populations went to different countries, including Jordan, Algeria, Eritrea, Iran, and lately even Italy. In Ethiopia, a specific population was made based more specifically on Ethiopian germplasm.

sicily wheat

The objective was to provide farmers with what could be defined as an evolving gene bank. Because of natural crossing, the seed which is harvested from these populations is never genetically the same as what was sown. In other words, the populations evolve continuously, becoming progressively better adapted to the conditions (soil, climate and agronomy) in which they are grown — and in the long term to climate change.

We thought that as the populations evolved, farmers would be able to use them as a source from which to select, possibly with the participation of scientists, ever better adapted varieties. However, it went further than that. Iranian farmers started reporting that the evolutionary populations could themselves be used as crops, as they were high yielding, stable and did not require chemical protection against pests. As a result, the evolutionary populations of barley and wheat spread through 17 provinces in Iran, and new evolutionary populations are being established in rice and corn.

But perhaps the best finding was the one made by Iranian bakers: the bread made with the evolutionary population of bread wheat soon became a commercial success, not only because of its taste and flavour, but also because it was tolerated by people affected by allergies.

iranian bread

We are now having the same experience in Italy, where evolutionary populations of barley, durum wheat and bread wheat are grown in several regions: in Marche, bread made with the flour of the bread wheat population is now in great demand.

pizza and bread

And an evolutionary population of zucchini, of all things, is currently grown by an organic farmer and new populations are being formed in beans and lettuce.

All these cases show that cultivating diverse populations can combine increasing biodiversity in farmers’ fields, adapting crops to climate change, and producing more, healthier, tastier food.