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Crop wild relatives get special treatment

…this Special Volume of Plant Genetic Resources, Characterization and Evaluation is very timely as CWR science finally moves beyond the theoretical to the increasing applied, to meet breeders and consumers growing demands. It includes prioritized CWR inventories at different geographical levels viz. national (Bissessur et al., 2019; Dickson et al., 2019), regional (Allen et al., 2019; Fitzgerald et al., 2019) levels. Tools to facilitate conservation planning have also been developed (Magos Brehm et al., 2019; Holness et al., 2019), and regional conservation strategies and approaches have been developed (Allen et al., 2019; Kell et al., 2016).

Ok, the whole thing is not open access, but at least the introduction to the Special Issue is. And since I’m on the subject, there’s a nice summary just out of the state of wild Coffea in Madagascar. Coincidentally, one of the paper in the special issue is on the CWR of Mauritius, among which Coffea features very prominently.

The wild coffee species that grow in northern Madagascar are genetically similar to Coffea species found on Grande Comore in the Comoros – a volcanic archipelago off the east coast of Africa, near Mozambique. Other species have spread from Madagascar to Mauritius and Reunion Island.

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Brainfood: Sinotato, Photophenomics, Bangladesh lentils, Vernalization gene, Droning on, Pathogen identification, Human domestication, Citrus cryo, Purple rain, Teff diversity, Mining biodiversity lit, Wild dates, Buckwheat improvement, Panicum genome

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Global seed companies and the pragmatic agrobiodiverse portfolio

Coosje Hoogendoorn, Senior Research Lead on the Access to Seeds Index at the Royal Tropical Institute (KIT), and an old friend of the blog, has a bone to pick with us on a recent Nibble: “I don’t really agree with your ‘Not much change, alas’ – companies are doing more, and telling us a lot more. The order of companies has not changed a lot, same champions. Although we have runners up. The champion, East-West Seed, is however hard to catch in Asia and worldwide. And for your information, there are indeces for Sub-Saharan Africa forthcoming (March), and a synthesis report that brings the whole story together.” And to help us along, she is contributing the following blog post, and is looking forward to feedback. Thanks, Coosje.

Seed companies are often seen as the nemesis of agricultural biodiversity. At the same time, farmers around the world, big and small, are in dire need of good quality seed to produce the food needed for 9 to 10 billion people. What is the state of the balance between agrobiodiversity, world food production, and the seed industry? The Global Access to Seeds Index 2019, published on 28 January 2019, provides some insights on this dilemma.

The Index takes stock of to what extent, and how, the seed industry provides good quality seed of suitable crops and varieties to smallholder farmers – the base of the world’s agricultural pyramid.

Overall, 13 leading global seed companies were found to address climate change and nutrition needs, but to reach only around 10% of the world’s small farmers. Lack of crop diversity is a major constraint; hybrid seed dominates while legumes are largely ignored.

While the focus of the Index is wider, insights on how seed companies deal with agrobiodiversity is part of the picture. In this blog post I provide a preliminary analysis.

Companies have diverse portfolios, sort of

The Access to Seeds Index investigated whether companies sell major field crops and vegetables, ones that are important for food and nutrition security and require at least annual replanting. Companies were found to develop and market varieties of many such crops, but with a very clear gap for dry legumes. Not one company was found to market groundnut, pigeonpea or cowpea, and only single companies have dry bean and chickpea in their portfolio.

Neglected crops are getting attention: about half of the companies invest in local crops, providing professional quality seed and/or setting up breeding programs. Most local crops – 15 – were found in company portfolios in South and Southeast Asia; there were only two such crops in Latin American portfolios. East-West Seed, across the world, with 14 local crops, and Limagrain with seven local crops in its portfolio, are leading in investments in agrobiodiversity through local crops. Yardlong bean can be called a ‘global-local’ crop, since it is being sold in all four regions, and by three companies.

As far as variety development is concerned, in addition to yield, companies give very high priority to breeding for local adaptation through breeding for tolerance to abiotic stress and pest and disease resistance. But fewer than half breed for local tastes and preferences.

Global seed companies contribute to formal genetic resources conservation

To a large extent, companies are actively involved in developing workable global Access and Benefit Sharing arrangements, and have suitable track and trace systems. Most collaborate with CGIAR in genetic resources matters. A majority have active ‘in-kind’ collaborations, for example through testing and multiplication of (local) genebank materials. Some have made considerable financial donations to the Plant Treaty’s Benefit Sharing Fund and/or the Global Crop Diversity Trust. But no company was found to support in situ conservation efforts or community genebank initiatives.

Companies are flexible on intellectual property when it concerns small farmers

Most companies support the breeders’ exemption under plant variety protection regulations, allowing varieties to be used by other breeders. Also, most companies do not block on-farm seed saving of their commercial varieties, with several being particular lenient when it concerns smallholder farmers. However, a focus on developing hybrids, as opposed to ensuring the availability of OPVs, effectively restricts the practice. Only East-West Seed, Advanta, Sakata and Limagrain have a company policy to sell OPVs in addition to hybrids because of their smallholder farmer clientele.

Agrobiodiversity is on company radar screens, but…

What did we learn? The global companies studied were found to take agrobiodiversity seriously, both expressed by company portfolios and by the sector’s willingness to contribute to ABS, its recognition of the breeder’s exemption and – with some clear reluctance – its respect for non-commercial on-farm seed saving. But obviously there are gaps. There is a clear lack of interest in in situ and community conservation of genetic resources, showing that companies prefer to stay on one side of the line between formal and informal genetic resources conservation activities. And companies are shying away, probably presently for good commercial reasons, from legumes.

This story isn’t finished yet. What is the contribution of regional and local seed companies to conservation and use of agrobiodiversity? The final synthesis report of the Access to Seeds Index 2019, that will bring insights together across regions, and across global, regional and local companies, will be released in May 2019. So watch this space for further updates, and in the meantime keep checking out the Access to Seeds Index website.

LATER: Coosje’s colleague Ido Verhagen adds his own take in this interview.

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Detecting Wisconsin’s Wild Cranberries from Space

This is a guest post by Vanesa Martin, Anastasia Kunz, Nicole Pepper and Eli Simonson of the NASA DEVELOP Colorado office. Many thanks to all of them. And thanks also to Colin Khoury for helping to make it happen.

NASA DEVELOP, as a part of NASA’s Applied Sciences Program, addresses environmental issues through interdisciplinary research projects that apply the lens of NASA Earth Observations to community concerns around the globe. Over the last year, researchers at the USDA ARS National Plant Germplasm System (NPGS) in Fort Collins, Colorado approached the NASA DEVELOP program to determine whether NASA satellites could be used to monitor and map Crop Wild Relatives (CWR) more efficiently than standard field methods alone. This collaboration has created a push to experiment with the mapping of different types of CWRs, in the hope of eventually producing an operational method to accurately monitor CWRs globally.

In the fall of 2018, our NASA DEVELOP team was formed to focus efforts on using satellite information to map the distributions of wild cranberries within a Landsat scene in northern Wisconsin. Previously, the USDA ARS’s method for mapping species distribution had exclusively considered bioclimatic and environmental factors, and these provided only a rough prediction of possible cranberry presence that looked like this:

With the aim of narrowing down the areas of predicted presence, the team used cranberry presence data from publicly available databases like GBIF and BISON to train initial habitat distribution models through Software for Assisted Habitat Modeling (SAHM). In addition to publicly available cranberry presence data, we incorporated bioclimatic and topographic variables derived from WorldClim (a global climate database with 1 km resolution) to mirror the current practices of USDA. We later incorporated ClimateNA data (a national climate database with 30m resolution) to assess whether our distribution maps improved.

The publicly available presence data we used was not suitable for remote sensing purposes, given that remote sensing requires highly accurate location information where the spectral signatures of the target species is clearly discernible. Consequently, we generated our own predicted presence points in order to incorporate spectral data and NASA Earth Observations into these models. These user-generated points, which we based on research we did of our two target cranberry species, were sent to our field cranberry experts to verify that they actually represented sites of probable cranberry presence.

After getting their approval and employing the user-generated points, we incorporated spectral detection into the models, creating maps based on the detection of the spectral signature of these species instead of predicting their possible locations based on suitable environmental conditions. This was the result, with red being the likeliest locations of cranberry presence:

One way we assessed the accuracy of our detection method was by overlaying a commercial cranberry layer we obtained from the Wisconsin Department of Natural Resources on to our maps to see how well they aligned with our binary detection maps. The binary detection maps did indeed locate commercial cranberry crops, despite the fact that we did not use any commercial cranberry presence points to train our models. With this assurance in hand, we felt more confident in sending our final incorporated maps to our field partners and experts for a final verification.

We hope to be able to continue working with our partners to conduct in-field verification of our maps. For now, however, it’s apparent that spectral data can positively influence the research efforts of our partners at the USDA ARS, and their larger goals of improved food security and biodiversity.

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Brainfood: Intensification, Yemen ag, Czech barley, Bangladesh community genebank, Agrobiodiversity Index, North American CWR, Israeli genebanks, Biofortified wheat, QDS, Collecting Miscanthus, Ethnobotany, NUS, Pecan diversity, Korean ponds, CWR gaps double, Salty rice