Category

Future Directions

Genetic Diversity in our Food Systems

By | Blog, Future Directions
Gurdev Khush at IRRI

Gurdev Khush at IRRI. Photo credit: IRRI photos. Reproduced under a Creative Commons license 2.0

This week’s blog post has been written by agronomist and geneticist Gurdev Khush. Gurdev had a major role to play in the Green Revolution, and while working at the International Rice Research Institute (IRRI) developed more than 300 rice varieties, one of which (IR36) became the most widely planted variety of rice. The impact and significance of his work has been recognized by numerous awards including the World Food Prize in 1996, the Wolf Prize in Agriculture in 2000, the Golden Sickle Award in 2007, and in 1987 the Japan Prize.

Our civilization developed with the domestication of plants for food, fiber and shelter about 10,000 years ago. Since then we have made constant improvements to these domesticated plants based on genetic diversity. It is the conservation, evaluation and utilization of this genetic diversity that will be essential for further improvements in our food crops and world food security.

Gene banks conserve biodiversity

The first important step in conserving biodiversity was the establishment of a gene bank by Nikolai Vavilov at the Leningrad Seedbank in Russia during the 1920s. In subsequent years more gene banks were created in developed countries, and the Green Revolution provided major impetus for the establishment of gene banks in developing countries. The first gene bank for the conservation of rice germplasm was organized after IRRI was established in the Philippines in 1960. Other rice growing countries followed suit and now most of them have their own gene banks.

The IRRI gene bank has over 120,000 entries

IRRI medium term seed store

The medium term storage unit of the IRRI seed bank. Photo credit: IRRI photos. Reproduced under a Creative Commons license 2.0.

The IRRI gene bank has progressively grown from a few thousand entries in 1962 to over 120,000 entries today, including accessions of all the wild species. The germplasm is stored under two-temperature and humidity regimes. The medium term store keeps seeds at 4ºC and a relative humidity of 35% for 30–40 years, while in the longer term store, maintained at –10ºC and a relative humidity of 20%, seeds are expected to remain viable for 100 years.

IRRI accessions are evaluated for morphological traits, grain quality characteristics, disease and insect resistance, and for tolerance to abiotic stresses such as drought, floods, problem soils and adverse temperatures. These are all important characteristics in terms of breeding resilient and high yielding rice varieties for the future.

Selection of new rice varieties

Numerous landraces have been utilized for breeding high yielding rice varieties. The first high yielding variety, IR8, was developed from a cross between two landraces, one from Indonesia and the other from China. Another variety, IR64, is one of the most widely grown rice varieties, and has 19 landraces and one wild species in its ancestry.

IR64

Rice variety IR64, one of the most widely grown rice varieties. Photo credit: IRRI photos. Used under Creative Commons license 2.0.

Ensuring future food security

Gene banks have played an important role in world food security. However, as the population grows there are now even bigger challenges for meeting demand. Climate change and increased competition for land and water resources further magnify the problem. We need to breed climate resilient crop varieties with higher productivity, durable resistance to diseases and insects, and tolerance to abiotic stresses. Success will depend upon the continuous availability of genetic diversity; we must redouble our efforts to unlock the variability currently preserved in our gene banks.

Diversity Seek Initiative

Establishment of the Diversity Seek Initiative (DivSeek) and the proposed Digital Seed Bank, under the auspices of the Global Plant Council, is a welcome development.

The aim of DivSeek is to develop a unified, coordinated and cohesive information management platform to provide easy access to genotypic and phenotypic data on germplasm preserved in gene banks. It is an international effort to bring together gene bank curators, plant breeders and biological researchers. To begin with, the project will develop standards and generate genotypic, transcriptome and phenotypic information for cassava, rice and wheat diversity. This will form the foundation of the Digital Seed Bank, a novel type of database containing standardized and integrated molecular information on crop diversity. The information from this database will be publicly available, and will be of enormous scientific and practical value. It has the potential to significantly increase our understanding of the molecular basis of crop diversity, and its application in breeding programs.

If your organization is interested in joining DivSeek, information can be found here. Alternatively, sign up to the mailing list to keep up to date with the initiative.

Providing For Our Brave New World

By | Blog, Future Directions
The Journal of Experimental Botany (JXB) published a special issue in June entitled ‘Breeding plants to cope with future climate change’

The Journal of Experimental Botany (JXB) published a special issue in June entitled ‘Breeding plants to cope with future climate change

By Jonathan Ingram

The Journal of Experimental Botany (JXB) recently published a special issue entitled ‘Breeding plants to cope with future climate change’.

More often than not, climate change discussions are focused on debating the degree of change we are likely to experience, unpredictable weather scenarios, and politics. However, regardless of the hows and whys, it is now an undeniable fact that the climate will change in some way.

This JXB special issue focuses on the necessary and cutting edge research needed to breed plants that can cope under new conditions, which is essential for continued production of food and resources in the future.

The breadth of research required to address this problem is wide. The 12 reviews included in the issue cover aspects such as research planning and putting together integrated research programs, and more specific topics, such as the use of traditional landraces in breeding programs. Alongside these reviews, original research addresses some of the key questions using novel techniques and methodology. Critically, the research presented comes from a diversity of labs around the world, from European wheat fields to upland rice in Brazil. Taking a global view is essential in our adaptation to climate change.

Avoiding starvation

Why release this special issue now?

Quite simply, the consequences of an inadequate response to climate change are stark for the human population. In fact, as previously discussed on the Global Plant Council blog, changing climate and extreme weather events are already having an impact on food production. For example, drought in Australia (2007), Russia (2010) and South-East China (2013) all resulted in steep increases in food prices. However, a positive side effect of this was to put food security at the top of the global agenda.

A farm in China during drought. Reduced food production can cause steep rises in food prices leading to socio-economic problems.  Photo credit: Bert van Dijk used under Creative Commons License 2.0

A farm in China during drought. Reduced food production can cause steep rises in food prices leading to socio-economic problems.
Photo credit: Bert van Dijk used under Creative Commons License 2.0

Moving forwards, researchers and breeders alike will have to change their fundamental approach to developing novel varieties of crops. In the past, breeders have been highly succesful in increasing yields to feed a growing population. However, we now need to adapt to a rapidly changing and unpredictable environment.

Dr Bryan McKersie sums this up in his contribution to the special issue. He commented: “Current plant breeding methods use large populations and rigorous selection in field environments, but the future environment is different and does not exist yet. Lessons learned from the Green Revolution and development of genetically engineered crops suggest that a new interdisciplinary research plan is needed to achieve food security.”

Driving up yields

So which traits should we be studying to increase resilience to climate change in our crops?

A potentially important characteristic brought to the foreground by Dr Karine Chenu and colleagues (University of Queensland, Australia) is susceptibility to frost damage. Although seemingly counterintuitive at first, the changing climate could result in greater frost exposure at key phases of the crop lifecycle. Warmer temperatures, or clear and cool nights during a drought, would allow vulnerable tissue to emerge earlier in the spring (Gu et al., 2008; Zheng et al., 2012). A late frost could then be incredibly destructive to our agricultural systems, causing losses of up to 85% (Paulsen and Heyne, 1983; Boer et al., 1993).

As explained by Dr Chenu, “Finding frost tolerant lines would thus help to deal with frost damage but also with losses due to extreme heat and drought – as they could be avoided by earlier sowings”.

The authors conclude that a “national yield advantage of up to 20% could result from the breeding of frost tolerant lines if useful genetic variation can be found”. The impact of this for future agriculture is incredibly exciting.

This study is just one illustration of the importance of thinking outside the box and investigating a wide range of traits when looking to adapt crops to climate change.

You can find the full Breeding plants to cope with future climate change Special Issue of Journal of Experimental Botany here. Much of the research in the issue is freely available (open access).

Journal of Experimental Botany publishes an exciting mix of research, review and comment on fundamental questions of broad interest in plant science. Regular special issues highlight key areas.

References

Association of Applied Biologists. 2014. Breeding plants to cope with future climate change. Newsletter of the Association of Applied Biologists 81, Spring/Summer 2014.

Boer R, Campbell LC, Fletcher DJ. 1993. Characteristics of frost in a major wheat-growing region of Australia. Australian Journal of Agricultural Research 44, 1731–1743.

Gu L, Hanson PJ, Post WM et al. 2008. The 2007 Eastern US spring freeze: increased cold damage in a warming world? BioScience 58, 253–262.

Paulsen GM, Heyne EG. 1983. Grain production of winter wheat after spring freeze injury. Agronomy Journal 75, 705–707.

Zheng BY, Chenu K, Dreccer MF, Chapman SC. 2012. Breeding for the future: what are the potential impacts of future frost and heat events on sowing and flowering time requirements for Australian bread wheat (Triticum aestivum) varieties? Global Change Biology 18, 2899–2914.

Nanopores: Next, next generation sequencing

By | Blog, Future Directions

Do you have a genome sequencer in your pocket or are you just happy to see me?

By Nikolai Adamski

On September 4 I attended an event sponsored by Oxford Nanopore Technologies (ONT) at Norwich Research Park, UK, which focused on nanopore technologies. This new technology has been dubbed ‘Next, next-generation sequencing’, and could have really exciting implications for the future of genome sequencing.

ONT has developed a pocked-sized genome sequencing device called the MinION that can sequence genomes in real time. Thanks to recent pop culture this generates visions of cuddly yellow creatures with an overly developed desire to serve super-villains. However, a MinION is actually a new genome sequencing device. To help confused readers, the figure below should help clarify the issue once and for all (Figure 1).

Figure 1: Demonstrating the difference between the pop culture Minion on the left and the genome sequencing MinION on the right.

Figure 1: Demonstrating the difference between the pop culture Minion on the left and the genome sequencing MinION on the right.

The striking thing about the MinION is its size. Sequencing machines these days vary in size from something that sits on a desktop, to something that fills half a student’s room. The MinION however, fits in the palm of your hand. This is possible thanks to highly miniaturized electronics.

So how does it work?

At the core of the MinION are two biological components: the nanopore protein, which gives the company its name, and a motor protein. The nanopore protein sits on top of an artificial layer and acts a microscopic sluice gate that controls how much of the sample solution passes through it into the lower layer. The sample solution contains DNA, but also ions that pass through the nanopore, thus creating a measurable electrical current. If a big molecule like a strand of DNA passes through the nanopore, the flow of ions is perturbed, which results in a change in the electrical current. These changes are recorded and interpreted to give the sequence of said DNA molecule.

Meanwhile, the motor protein sticks to a DNA molecule, attaches itself to the top of the nanopore, and feeds the DNA through the nanopore as a single strand at a certain speed. This process is similar to a ratchet. Each MinION device has thousands of nanopores allowing for as many molecules to pass through and be sequenced in real time. This is nicely illustrated in a video made by ONT, which you can see here which is well worth a watch!

The sequence data are sent to a cloud server in real time, where they are transformed and analyzed and the final data sent back to the user. This eliminates the need for an expensive computer infrastructure as well as the need for extensive training in bioinformatics.

Limitations of the technology

So far so good, but there are still some issues with the MinION system. One of these is the average length of the DNA molecules that can be sequenced. In theory, the MinION system is able to sequence DNA molecules of any length, although the data from users at last week’s event suggests that, at the moment, the average length of sequence obtained is around 6,000 base pairs (bp). This is still a great value, but there is room for improvement. Another issue is the amount of data generated by a single MinION run, which according to user experience is generally around 1Gb, approximately 200 times the size of the gut bacterium E. coli. Both of these issues can be easily remedied by running several MinION sequencers with the same sample.

A larger problem is the matter of sequencing accuracy, which is now somewhere around 90%, although it can be as low as 75%. This can in part be compensated for by the sheer amount of data generated. However, it would require a lot of sequencing to make up for these mistakes, and is a critical point that needs to be addressed by ONT in the future.

Current applications

The MinION system has been and is being used worldwide for a number of different applications. Scientists and medical doctors have used the MinION to monitor strains of the Ebola virus in different patients. Thanks to the real time sequencing data and cloud-based data analysis, patients could be screened within a few days as opposed to weeks. Another interesting example of the usefulness of the MinION system was when scientists travelled to the Tanzanian jungle to assess the biodiversity of frogs in the region.

There are many more fascinating applications for the MinION sequencer. Scientists who are interested can join the MinION Access Programme (MAP) to become part of the research and development community.

I very much enjoyed the ONT event and I am hopeful and curious about what the next few years will bring in terms of innovation and development.

______________________________________________________________________________________________________________________________________

About the Author:

nikolaiadamskiNikolai Adamski is a postdoctoral scientist working at the John Innes Centre in Norwich, UK, in the group of Cristobal Uauy. He studies yield and yield-related traits in wheat, trying to identify the underlying genes to understand the control and regulation of these traits.

 

You can follow him on Twitter @NikolaiAdamski

 

 

Plant Biology 2015: Introducing Plantae.org

By | ASPB, Blog, Future Directions, GPC Community, Plantae, Scientific Meetings, SEB
Minneapolis skyline. Photo by 'zman z28', Flickr, used under a CC BY-NC-ND 2.0 license.

Minneapolis skyline. Photo by ‘zman z28’, Flickr, used under a CC BY-NC-ND 2.0 license.

Ruth and I recently flew out to Minneapolis, Minnesota, USA, to attend the American Society of Plant Biologists’ (ASPB) annual conference, Plant Biology 2015.

Ruth did a sterling job of live-tweeting the scientific sessions she attended. She also spent some time stationed at the ASPB booth to talk to people about the Global Plant Council (GPC), as well as a big project we’re helping to bring to life: Plantae.org. I’ll talk more about what I did at the conference later… But first, what is Plantae.org?

The Evolution of Plantae.org

Some time ago, here at the GPC, we thought it would be a great idea if there was one, online location where plant scientists and teachers could go to look for and share new ideas, tools and resources for research and education. We tentatively called it the ‘Plant Knowledge Hub’, and set about looking for people or organizations that might be able to help us make it a reality.

In doing so, we discovered that the ASPB was interested in creating a kind of community networking and collaboration platform, for which they had the working title ‘Plant Science Exchange’. Joining forces, we decided to combine the two ideas into one big portal, now called ‘Plantae’. Extending beyond the ASPB membership, Plantae will be for plant scientists and educators all over the world. We hope it will become the leading plant science resource hub and community gathering place.

Lisa modeling her Plantae t-shirt!

Lisa modeling her Plantae t-shirt!

At this point, I should also mention the Society for Experimental Biology (SEB), without whose help the GPC would not have been able to move forward with this project. The SEB generously provided enough funding for my post! I joined the GPC in February as the Outreach & Communications Manager, so as well as looking after the GPC’s internal and external communications and helping to spread the word about the work of the GPC, one of my main duties is to identify and curate tools, resources and plant science information to upload to Plantae.

Building Plantae.org

I’ve made a few simple websites in the past, but nothing as complicated as an entire ‘digital ecosystem’ so taking the ‘Plant Science Knowledge Exchange Hub’ from an idea to the reality of Plantae.org was going to be a mammoth task. Fortunately we have had a lot of help!

Susan Cato, the ASPB’s Director of Member Services and Digital Marketing, and her team, have been doing a stellar job of pulling different stakeholder groups together to build and develop the Plantae platform. As well as a group of web architects to build the portal’s infrastructure, an agency called LookThink has been involved, with the unenviable task of optimizing the user experience. It’s no mean feat to take our ideas about what the platform should do, and the practicalities of how it can be built, to ensure that the final online product actually does what users want and need it to do in an intuitive, user-friendly way!

Ultimately, Plantae.org will have features such as Facebook or LinkedIn-style user profiles and groups, with the ability to ‘connect’, interact and send private messages. It will have public and private discussion boards where scientists can collaborate, talk about issues in science, or ask questions to the community and have them answered. It will eventually contain hundreds and thousands of pages of content including research papers, teaching resources, videos, posters and much more, some of which will be curated by groups like the GPC, and others uploaded directly by members. Underlying all of this, the portal needs a robust, intuitive search engine to allow users to find exactly the contact they are looking for.

User Testing the Beta Version

PlantBiology2015logoSo during the ASPB conference, I was to be found in a meeting room with Clare Torrans from LookThink, helping her to conduct some user experience analysis on an early beta version of the Plantae site. We recruited a range of potential Plantae users – from students through to senior professors – and asked them to tell us what they thought of the idea of Plantae, whether they would use it and find it useful, whether the icons, buttons and links on the screen did what they expected, and what else they would like Plantae to do.

I’d never consciously considered the ‘user experience’ of a website before, but having spent time with Clare, I now realize it’s a vital part of the build process – and now I’m analyzing every website I visit!

The feedback we received was varied: there were some clear patterns related to age, academic level, or previous experience with social media, some people pointed out elements of the site I hadn’t even noticed, or misinterpreted buttons I’d thought were obvious, but – positive or negative – all of the feedback we received was useful and will be fed back into the site development process.

When can I start using Plantae?

The site isn’t quite ready yet, but taking into account all of the data we obtained from the user testing sessions at Plant Biology 15, we will hopefully be ready for launch in the Autumn. Watch this space for more news!

GPC President Professor Bill Davies’ vision for the future

By | ASPB, Blog, Future Directions

Global Plant Council President Professor Bill Davies discusses his vision for the future of the GPC and its role in meeting some of the global challenges facing plant science and society today.

GPC President Professor Bill DaviesRaising the profile of plant science

As we face the task of sustainably feeding an ever-increasing global population, the issue of food security has never been more pressing, and of course, plant science plays a fundamental role in addressing this challenge. Professor Davies believes the GPC can have a major impact in raising the profile of plants in all parts of society, but perhaps most urgently with the policy makers who can drive investment into research.

He explains: “Plant science tends to have a lower priority with funding agencies. A number of years ago there was quite a lot of talk about plant science being a pretty mature subject and therefore we didn’t need much money for research. Fortunately the European Plant Science Organisation (EPSO) managed to convince the European Parliament and others that there was an important opportunity here, the funding continued and we’ve seen a lot of benefits from that – both in furthering plant science and enhancing food production”. He continues: “Raising the profile of plant science is key, and – more specifically – we need to think about ways in which, collectively, we could address some of these challenges”.

A global conversation

Genetic diversity research - CIAT

Image by Neil Palmer (CIAT). Used under: CC BY-SA 2.0

Professor Davies believes the GPC is well placed to tackle global problems on a worldwide scale, by providing platforms for member organizations and individuals to collaborate on a variety of issues: “There are some genuinely global challenges that the GPC could take on. We can try to provide more opportunities for people who might be interested in addressing things beyond the boundaries of their own national scientific societies”. He adds: “I’ve been a member of the Society for Experimental Biology (SEB) longer than I care to imagine, and it’s been a really important part of my life. It delivers a lot more than just good science. The SEB has made and continues to make a big effort to operate internationally, but there’s a limit, whereas there’s no limit for GPC.

“One of the things we’ve been talking about is whether there is more that we could offer societies, particularly in developing countries. Are we making resources available that can be as influential in Ghana, for example, as they might be in the United States? If there are opportunities to broaden the scope of that offering, particularly to address some of the areas where food security is a major issue, then we can do that and, I hope, help national societies in parts of the world where they are not as influential as they might be. I believe that there is strength in numbers.

“It seems entirely logical to me to address global challenges with a global organization”.

Building resources

One of the key goals of the GPC is to build up databases of information and resources that can be used by researchers, plant breeders, farmers and other agricultural stakeholders all around the world. This is being done both as part of the three main GPC initiatives (Diversity Seek, Biofortification, and Stress Resilience), but we are also collaborating with the American Society of Plant Biologists (ASPB) to launch an online platform for the plant science community this summer.

Gene bank - IRRI

Image credit: IRRI. Used under: CC BY 2.0

Professor Davies is keen to harness the power of the online community for cultivating a new excitement around plant science. He led a massive open online course (MOOC) about food security at Lancaster University last year, and was pleased to see how engaged the participants were. He explains: “We had 5000 students with a fantastic level of enthusiasm and commitment. At the end of it we were left with the feeling that people were keen to know more.

“My view is that if you listen to people talk about why they do the science they do, what’s involved, and to some extent how they do it, then I think you’re in a position to make a much more well-informed decision about the science in general or controversial issues, and to contribute to the debate”.

Professor Davies believes that the online plant science platform from the ASPB and GPC will provide useful resources for scientists, teachers and students alike: “I’m in this business because I was inspired by lecturers both as an undergraduate and in graduate school. If we can capture the drama and excitement of science, we can make it available to everyone. It’s a wonderful opportunity”.


Professor Bill DaviesProfessor William (Bill) Davies is the President of the Global Plant Council and Distinguished Professor of Plant Biology at Lancaster University, UK. His research into stress responses in plants and his involvement with many international projects aimed at improving global food security led to him being awarded a CBE award for services to Science in the 2011 Queen’s Birthday Honours list. For more information, click here.

The Next Generation

By | ASPB, Blog, Future Directions, GPC Community, SEB

Meet Amelia and Sarah, the two newest additions to the Global Plant Council team.

As a coalition of plant and crop societies from the around the globe, the Global Plant Council (GPC) aims to bring together scientists, policy makers and other stakeholders to engage in coordinated strategies to find solutions to global problems.

The GPC currently has 29 member organizations representing thousands of scientists in diverse disciplines around the world. Online media such as this blog and the @GlobalPlantGPC Twitter account provide a fantastic resource for our member organizations to stay in touch, share ideas and develop interdisciplinary collaborations.

For Spanish speakers, we’ve also recently launched a Spanish version of our Twitter feed at @GPC_EnEspanol, kindly translated for us by Juan-Diego Santillana-Ortiz, an Ecuadorian currently studying at Heinrich-Heine University in Düsseldorf, Germany.

Amelia is in the third year of her PhD at the John Innes Centre, Norwich UK. She is researching how altering the biochemistry of epicuticular waxes affects the physiology and ultimately yield of UK wheat. She tweets @AmeliaFrizell (https://twitter.com/AmeliaFrizell)

Amelia Frizell-Armitage is in the third year of her PhD at the John Innes Centre, Norwich UK. She is researching how altering the biochemistry of epicuticular waxes affects the physiology and ultimately yield of UK wheat. She tweets @AmeliaFrizell.

To further enhance this network, the GPC has awarded two New Media Fellowships to early career plant scientists Amelia Frizell-Armitage and Sarah Jose. The role of the Fellows will be to increase visibility of the GPC through managing this blog, devising new strategies to promote GPC activities and to increase traffic flow and engagement on Twitter.

A key priority will be to increase members’ contributions to this blog to promote their organizations and associated activities. Contributing to the blog is a fantastic way to interact with other GPC members, and we are always open to suggestions for guest posts. Perhaps you want to talk about a recent meeting or activity, discuss a particularly exciting piece of emerging research, promote a newly published book, or even just give some insight into your everyday life?

Sarah Jose is a third year PhD student at the University of Bristol, UK. She is investigating the link between wax biosynthesis and stomatal development in barley and Arabidopsis, and its potential impact on the water use efficiency of plants. Find her on Twitter @JoseSci.

Sarah Jose is a third year PhD student at the University of Bristol, UK. She is investigating the link between wax biosynthesis and stomatal development in barley and Arabidopsis, and its potential impact on the water use efficiency of plants. Find her on Twitter @JoseSci.

Whatever it is, we want to hear from you! Please get in touch on Twitter, via the comments section on the blog, or by emailing our Outreach & Communications Manager Lisa Martin.

It is an exciting year ahead for the GPC with the launch of a new online platform for the plant community that is being built in partnership with the ASPB and with support from SEB. There are also various fundraising initiatives in the works, and a Stress Resilience Forum coming up in October, which is being organized in collaboration with SEB.

Stay tuned to this blog to keep up to date with all our activities. The events calendar for member organizations is also looking busy and vibrant, and can be found here.

 

 

 

 

 

 

 

 

 

 

Can you crowdfund the sequencing of a plant genome?

By | Blog, Future Directions, Global Change
Dr Peng Jiang, University of Georgia, USA

Dr Peng Jiang, University of Georgia, USA

Peng Jiang and Hui Guo at the University of Georgia think you can! They are currently raising money via a crowdfunding approach to sequence the first cactus genome – but the question is: why would they want to? Peng explains all in this guest blog post.

A Prickly Proposal: Why Sequence the Cactus?
In these times of growing food insecurity due to climate change and population pressures, the prickly pear cactus (Opuntia ficus) has growing commercial and agricultural importance across much of the world – you will find it growing in Mexico and Brazil, Chile, large parts of India and South Africa, and in Spain and Morocco.

The goal of our proposal is to sequence the genome and transcriptome of the prickly pear cactus, a recognized food and forage crop in these challenging semiarid regions of the world.

With more than 130 genera and 1,500 species of Cactaceae, we will create a draft genomic and transcriptome database that would aid the understanding of this understudied plant family, and provide the research community with valuable resources for molecular breeding and genetic manipulation purposes. Here are some of the reasons why we think a first cactus genome would be so important:

The Prickly Pear Cactus

The Prickly Pear Cactus

1. Ecological Improvement
The beauty of the drought-tolerance cactus is that it can grow on desert-like wastelands. Nowadays, more than 35% of the earth’s surface is arid or semiarid, making it inadequate for most agricultural uses. Without efforts to curb global warming, “Thermageddon” may hit in 30–40 years time, causing desertification of the US, such that it may become like the Sahara. Opuntia helps create a vegetative cover, which improves soil regeneration and rainfall infiltration into the soil. This cactus genome research may help us to adapt our food crops to a much hotter, drier climate.

2. Food Crops, Feed and Medicine
The fruits of prickly pear cactus are edible and sold in stores under the name “tuna”. Prickly pear nectar is made with the juice and pulp of the fruits. The pads of prickly pears (“Nopalito”) are also eaten as a vegetable. Both the fruits and pads of prickly pears can help keep blood sugar levels stable because they contain rich, soluble fibers. The fruit contains vitamin C and was used as an early cure for scurvy.

Furthermore, there has been much medical interest in the prickly pear plant. Studies [1, 2, 3] have shown that the pectin contained in prickly pear pulp lowers cholesterol levels. Another study [4] found that the fibrous pectin in the fruit may lower a diabetic’s need for insulin. The plant also contains the antioxidant flavonoids quercetin, (+)-dihydroquercetin (taxifolin), quercetin 3-methyl ether (isorhamnetin) and kaempferol, which have a protective function against the DNA damage that leads to cancer.

3. Biofuels in Semiarid Regions
Planting low water use, Crassulacean acid metabolism (CAM; a water saving mode of photosynthesis) biofuel feedstocks on arid and semiarid lands could offer immediate and sustained biogas advantages. Opuntiapads have 8–12% dry matter, which is ideal for anaerobic digestion. With an arid climate, this prevents the need for extra irrigation or water to facilitate the anaerobic digestion process. Requiring only 300 mm of precipitation per year, Opuntiacan produce a large amount of dry matter feedstock and still retain enough moisture to facilitate biogas production. It’s possible to get as much as 2.5 kWh of methane from 1 kg of dry Opuntia.

4. Phylogenetic Importance
Trained botanists and amateurs alike have held cacti in high regard for centuries. The copious production of spines, lack of leaves, bizarre architecture and impressive ability to persist in the harshest environments on Earth are all traits that have entitled this lineage to be named a true wonder of the plant world.

The cacti are one of the most celebrated radiations of succulent plants. There has been much speculation about their age, but progress in dating cactus origins has been hindered by the lack of fossil data for cacti or their close relatives. Through whole genome sequencing, we help will reveal the genomic evolution of Opuntia by comparing this genome with that of other sequenced plant species.

Cacti are typical CAM plants. We will analyse the evolution of CAM genes in the cactus to help reveal the secret of drought tolerance. Furthermore, plant architecture genes and MADS-box gene family members will be analysed to reveal the specific architecture and structure of cactus.

Crowdfunding the Cactus Genome Project
Cactus has several fascinating aspects that are worth exploring, not just for its biology, but also its relevance to humanity and the global environment. We plan to generate a draft genome for Opuntia, and have launched a crowdfunding campaign to help fund this project – we have already raised $2300 USD (46% of what we need), but we only have 15 days to raise the rest. If you would like to help fund this project, please visit our Experiment page at: https://experiment.com/projects/sequencing-the-cactus-genome-to-discover-the-secret-of-drought-resistance.

If we are successful in raising enough money to initiate the Cactus Genome Project, not only will this be the first plant genome to be sequenced in the Cactaceae family, we will be releasing the results to the plant science community through GeneGarden, an ornamental plant genome database. Our citizen science approach is also allowing us to reach out directly to members of the public, creating exciting opportunities for outreach and engagement with plant science.

If you have any further questions, please contact project leader Dr Peng Jiang at pjiang@uga.edu.

This blog post is slightly adapted from a post originally appearing on GigaScience Journal’s GigaBlog. Reproduced and adapted with permission, under a CC-BY license.

References

  1. Wolfram RM, Kritz H, Efthimiou Y, et al. Effect of prickly pear (Opuntia robusta) on glucose- and lipid-metabolism in non-diabetics with hyperlipidemia – a pilot study. Wien Klin Wochenscr. 2002;114(19–20):840–6.
  2. Trejo-Gonzalez A, Gabriel-Ortiz G, Puebla-Perez AM, et al. A purified extract from prickly pear cactus (Opuntia fulignosa) controls experimentally induced diabetes in rats. J Ethnopharmacol. 1996;55(1):27–33.
  3. Fernandez ML, Lin EC, Trejo A, et al. Prickly pear (Opuntia sp.) pectin alters hepatic cholesterol metabolism without affecting cholesterol absorption in guinea pigs fed a hypercholesterolemic diet. J Nutr. 1994;124(6):817–24.
  4. Frati-Munari AC, Gordillo BE, Altamirano P, et al. Hypoglycemic effect of Opuntia streptacantha Lemaire in NIDDM. Diabetes Care. 1988:11(1):63–66.

Access to crop seeds through an SMTA: what is that?

By | Blog, Future Directions

Carolina Roa, Independent Consultant at CropIP

“We need a material transfer agreement”

Copyright: CIAT, CC BY-SA.

© CIAT, licensed under Creative Commons CC BY-SA.

As a plant breeder in the area of food and agriculture you look for well-characterized ­– or at least well-referenced – plant materials suitable for making crosses and generating populations to be tested for agricultural traits. If you or your organization don’t already have such materials, you are likely to contact people at seed or germplasm banks, research or breeding programs to obtain sexual or vegetative seeds.

Have the entities come back to you saying that to get access to the plant material you and/or your organization need to agree to the terms of a material transfer agreement (MTA)? Have they perhaps used the expression “Standard Material Transfer Agreement (SMTA)”? Likewise, if you wanted to provide germplasm to a colleague or a breeder/researcher at another institute, has your own organization told you that an MTA or an SMTA is required? You may be asking yourself, “What is an MTA or SMTA, and why are they required?” This article aims to address these questions.

International and national contexts behind the agreements

Around 20 years ago, no written agreement was necessary to exchange plant materials used for research, breeding or training in the area of food and agriculture, particularly if one was working in the public sector. A verbal agreement was likely to suffice. The latter, however, meant that access to plant materials depended in great measure on personal or inter-organizational relationships, geographic proximity, reciprocity and mutual gain, and interactions between governments1.

Maize active collection. © Xochilquetzal-Fonseca, CIMMYT, licensed under Creative Commons CC BY-NC-SA.

Maize active collection. © Xochilquetzal Fonseca, CIMMYT, licensed under Creative Commons CC BY-NC-SA.

In the early 1990s the situation changed with the advent of two major international treaties. The Convention on Biological Diversity (CBD), in force since 1993, deals with access to all biological diversity, including all genetic resources, as well as the sharing of benefits arising from their use. The International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA; referred to as the Plant Treaty), in force since 2004, carved a niche for plant genetic resources for food and agriculture (PGRFA) and created a multilateral system to facilitate access and benefit sharing for PGRFA deemed important for food security2.

A large number of countries are members of one or both of these treaties, currently 194 countries in the case of the CBD and 134 in the case of the Plant Treaty. The country members (called Contracting Parties) have implemented national laws and regulatory measures to adopt and adapt these regimes at national levels. Implementation, however, is not uniform. Some countries have amended existing national laws to incorporate the main aspects of the international treaties. Others have issued specific national laws that reproduce the international instruments and have added aspects pertinent to their national contexts, and a number of countries have not yet implemented the treaties at a national level. Therefore, as a plant breeder/researcher you are likely to encounter different rules and conditions for accessing or providing PGRFA, depending on whether the country where the materials are located have implemented the CBD, the Plant Treaty, both or none, and depending on the rules and regulations applicable at the organizations hosting/administering the plant materials, including your own institute.

MTA or SMTA? What’s the difference?

ILRI Forage genebank_ILRI-Stevie Mann-CC BY-NC-SA

ILRI forage genebank © Stevie Mann, ILRI, licensed under Creative Commons CC BY-NC-SA.

Whether an MTA with specific conditions of access and use, or the SMTA with standardized conditions applies for the plant materials to be exchanged depends on whether CBD-derived regulations apply, or whether the Plant Treaty operates. In case CBD rules apply, you or your institute, as a prospective recipient, will receive an MTA with conditions defined by the germplasm provider. You/your institute will need to accept the terms as they are, or try negotiating and modifying them to suit your purposes. This process normally takes time and legal skills. Going through this bilateral negotiation process every time new plant material is requested from another entity could be a deterrent to the research, and breeding work might not progress at the pace and scale that is needed to address growing food security challenges.

The SMTA, as its name indicates, was designed by the negotiators of the Plant Treaty as a standard and multilateral MTA with fixed terms and conditions of access and use, applicable to plant materials from 64 food and feed crops listed in Annex 1 of the Plant Treaty, which are under public management and control and in the public domain. This system is referred to as the Multilateral System of access and benefit sharing (MLS for short). The SMTA also applies to PGRFA placed voluntarily into the MLS by its holders. Therefore, if particular PGRFA required for research, breeding and/or training purposes are under the MLS, the SMTA as it is applies without the need to negotiate terms, saving time and costs.

At this point it is worth clarifying that PGRFA, even belonging to the crops listed in Annex 1 of the Plant Treaty, owned or administered by private corporate entities are generally outside the MLS. Likewise, PGRFA of the listed crops growing in farmers’ fields, or PGRFA under development by breeders or farmers (that is, not ready for commercialization and commonly referred to as ‘breeding materials’) may not be under the MLS. Their inclusion in the MLS is at the discretion of the owner/holder, the grower or the developer of the breeding materials. If they place such materials under the MLS, they will need to use the SMTA as the instrument for access and benefit sharing for the purposes specified in the Plant Treaty. However, the developer is entitled to add terms and conditions to the SMTA.

How the SMTA works3

CIAT Genebank_Luigi Guarino_CC BY

CIAT genebank © Luigi Guarino, licensed under Creative Commons CC BY.

Scope of use – PGRFA under the SMTA can be used for research, breeding and/or training in the fields of food and agriculture. If the intended use is different, e.g., extraction of compounds to be used for chemical or pharmaceutical applications, the SMTA is not the instrument to use. Other conditions dictated by national legislation, the holder/owner of the resources, or both may apply for non-food/feed applications.

Facilitated access – access to PGRFA should be free of charge and expeditious, without the need to track individual accessions. If a fee is charged, it should reflect ‘minimal costs’ related to shipment and transport costs. For instance, costs of seed maintenance, seed production, and the like should not be included.

Provider’s obligations and rights – the main obligations of PGRFA providers include (1) granting ‘facilitated access’ to PGRFA and associated passport data and non-confidential descriptive information, and (2) reporting periodically to the Secretariat of the Plant Treaty about the SMTAs entered into. As a provider and developer of breeding materials, you will have discretion on granting access to such materials while they are under development. If you grant others access to such materials, you’d be entitled to add terms and conditions to the SMTA, including aspects such as payments, limitations on subsequent transfers, etc.

Recipient’s obligations and rights – the main obligations that come with materials received under the SMTA include: (1) to exclusively use them for research, breeding, and/or training related to food and agriculture; (2) to not claim intellectual property rights or any other rights that may limit facilitated access; (3) to use a new SMTA for subsequent transfers; and (4) to report such subsequent transfer to the Secretariat of the Plant Treaty.

If the recipient were to subsequently transfer PGRFA under development, the recipient will act as a provider and in this case, s/he should (1) use a new SMTA; (2) identify in Annex 1 of the new SMTA the material from which the breeding materials were derived; and (3) report this transaction to the Secretariat of the Plant Treaty.

If additional conditions are added to the SMTA for the transfer (or the subsequent transfer) of PGRFA under development, they should go as a separate agreement to the associated SMTA and there is no need to report such add-on conditions to the Secretariat of the Plant Treaty. A recipient of PGRFA, whether under development or not, has no further duties with respect to the actions of a subsequent recipient.

Benefit sharing commitments – As a recipient, you are expected to share the benefits obtained from MLS materials with the agricultural community in general. As an example, granting access for further research and breeding to products developed by incorporating MLS materials received, is one of such benefits. In this case, you may also voluntarily contribute funds to the Benefit Sharing Fund, administered by the Plant Treaty, which finances food and feed-related research projects, mostly in developing economies. Conversely, if you decided to restrict further access to your MLS-derived products, you would be required to pay to the Benefit Sharing Fund either 0.77% or 0.5% of the sales of your product, depending on whether you opted to pay per accession received (first amount) or per crop accessed (second figure). The payment requirement operates regardless of how much MLS-derived material has been incorporated into your product and it will last as long as access to the product is restricted.

Duration – the particular SMTA you entered into will be valid as long as the Plant Treaty remains in force.

Genebanks using the SMTA

Rice seed varieties. Copyright: IRRI CC BY-NC-SA 2.0

Rice seed varieties. © IRRI, licensed under Creative Commons CC BY-NC-SA 2.0.

Apart from national seed collections of member countries, there are international institutions that have placed their seed holdings under the purview of the Plant Treaty.  The International Agricultural Research Centers of the Consultative Group on International Agricultural Research (CGIAR) are among those institutions. Eleven of the CGIAR centers, holding approximately 700,000 accessions of crops listed in Annex 1, as well as non-Annex 1 crops and breeding materials, use the SMTA to transfer these materials for the purposes specified by the Plant Treaty.

The individual websites of the CGIAR centers publish lists of available accessions, and requests can be placed electronically. As a prospective recipient, you should receive confirmation of availability of sufficient seed for shipping together with an electronic copy of the SMTA. You have the options to accept the SMTA terms through a mouse click, by signature, or by ripping the package containing the seed and a printed copy of the SMTA. From this point onwards, the rights and obligations of the SMTA for both providers and recipients start operating.

Therefore, next time you receive an SMTA don’t despair; come back to these notes and seek guidance from the legal or other pertinent office at your organization on how to proceed with this or any other kind of agreement. ©

 

REFERENCES

  1. Halewood, M (2013). What kind of goods are plant genetic resources for food and agriculture? Towards the identification and development of a new kind of commons. International Journal of the Commons 7(2): 278–312.
  2. Moore, Gerard and Tymowski. 2005. Explanatory guide to the International Treaty on Plant Genetic Resources for Food and Agriculture. IUCN, Gland, Switzerland and Cambridge, UK. xii + 212 pp.
  3. Standard Material Transfer Agreement (accessed at http://www.planttreaty.org/content/what-smta).

 

About the author: Carolina Roa is plant biologist and a legal professional with around 25 years of experience. She has worked for the public and private sector in different parts of the world on a range of legal and intellectual-property aspects related to agriculture and biotechnology. Carolina is currently the Principal Consultant at CropIP. She can be reached at carolina@crop-ip.info.

Yes, Africa will feed itself within the next 15 years

By | Blog, Future Directions

Africa will be able to feed itself in the next 15 years. That’s one of the big “bets on the future” that Bill and Melinda Gates have made in their foundation’s latest annual letter. Helped by other breakthroughs in health, mobile banking and education, they argue that the lives of people in poor countries “will improve faster in the next 15 years than at any other time in history”.

Their “bet” is good news for African agriculture: agronomy and its natural twin, agricultural extension, are back on the agenda. If Africa is to feed itself, the women and men who grow its crops need access to technical expertise on how to manage their variable natural resources and limited inputs and market intelligence on what to grow, what to sell and what to keep.

New tools in the hands of farmers

The Gates foundation report outlines that African countries spend $50 billion a year importing food. Nigeria alone imports $500m of rice from Vietnam each year.

But there is no quick fix that will transform African agriculture without skillful agronomy and intelligent extension. Whatever the promises brought by new, drought-tolerant varieties of crops such as maize, they cannot achieve their potential without the wise management of fertilisers, timing of cultivations and appropriate crop rotations.

Bill & Melinda Gates Foundation 

As the graph above shows, sub-Saharan Africa’s crop yields remain very low compared to the rest of the world. Sadly, in our rush for only genetic solutions to increasing agricultural yields, we have ignored the fields and landscapes in which crops are grown. The consequence has been a missing generation of scientifically trained agronomists and agricultural extension workers – who help teach farmers about new farming practices – with the skill sets required to manage resources and apply principles.

Meanwhile, powerful tools such as geospatial mapping, predictive modelling, remote-sensing (using aerial imaging to assess the state of vegetation) and mobile technologies have advanced to a stage where they are of practical use to the scientific agronomist, educated extensionist and literate farmer. We now have a real opportunity to link genetic advances and improved management with the social and economic drivers for African agriculture. This “research value chain” between grower and consumer requires that each research discipline plays an interconnected role with the end-user always in sharp focus.

Soils and sustainability

So, what are the priorities for African agriculture in the next 15 years? First, we must rehabilitate its soils. Since 2015 has been declared as the UN International Year of Soil, we need to recognise that Africa has some of the world’s frailest soils, which have suffered most from “cereal abuse” through the almost continuous cultivation of cereal crops. These monocultures have left Africa’s soils tired and impoverished. Applications of fertilisers will not, by themselves, be enough to save them.

For sustainable agricultural systems, we need to reconsider our addiction to major cereals grown as monocultures and move from “calorie security” to “nutritional security”. For this, nitrogen-fixing leguminous crops have to be part of any solution. In his Noble Peace Prize address in 1970, Norman Borlaug, the father of what became known as the “green revolution” in South Asia, recognised the imbalance between research advances on the major cereals and those on all other crops:

The only crops which have been appreciably affected up to the present time are wheat, rice, and maize… nor has there been any appreciable increase in yield or production of the pulse or legume crops, which are essential in the diets of cereal-consuming populations.

Approaching 50 years later, the situation remains similar. Clearly, improvements in leguminous crops (such as beans and lentils), both in their own right as nutritious sources of food and as rehabilitators of soil, are long overdue. Since 2016 has been declared as the UN International Year of Pulses, there is no better opportunity to redress the historical imbalance noted by Borlaug.

Crops for the future

We also need to recognise that most African family farmers are women. Often the species they cultivate are not the major cash crops grown by men as mechanised monocultures. Rather, they are local “underutilised” species, often legumes and vegetables, which families cultivate in complex landscapes for their own sustenance.

These crops, and the multiple cropping systems which support them, have few influential champions and rarely feature in the research strategies of national and international agencies. But it is crops and agricultural systems such as these that will help Africa feed itself sustainably.

In a very real sense, these “crops for the future” will help diversify Africa’s agriculture to meet the volatile physical and economic climates that lie ahead. Unlike the major crops which have received billions of dollars of support over generations, underutilised crops deserve a “big bet” over the next 15 years if they are to help achieve major breakthroughs for most people in most poor countries.

The Conversation

This article was written by Sayed Azam-Ali, CEO of the Crops for the Future Research Centre and Professor of Global Food Security at University of Nottingham, and originally published at The Conversation.

Read the original article.

B.B. Singh’s quest to make cowpea the food legume of the 21st century

By | Blog, Future Directions

4fig3In 1944, the year Bir Bahadur (B.B.) Singh was born in the state of Uttar Pradesh in India, Indian agriculture was in shambles. During nearly 200 years of British rule, the country’s agricultural enterprise had been turned over to commodities such as cotton, indigo, and sugarcane for export; what little food was grown hinged on rainfall and the soil’s natural fertility—or lack of it. Crop yields were often abysmal as a result, and famine was common. So when India won independence from Britain in 1947, the Indian government enacted a sweeping program of nationwide, agricultural education.

That’s why when Singh graduated in 1956 from his village school with good grades and an interest in science, he found himself at one of India’s newly minted agricultural high schools. It was the only nearby school where he could study science, Singh says, as well as the closest high school to his home. Plus, his father wanted him to attend, saying, “Why don’t you study agriculture and see what help you can give to our people,” Singh recalls.

“So I was okay with going to an agricultural high school, and that later became my good luck,” he says. Turns out it also became the good luck of millions of the world’s smallholder farmers.

Today, Singh is among the most revered breeders of legume—or pulse—crops, credited with improving the diets, incomes, and lives of farming families across Africa, Asia, and South America. In the late 1960s and 1970s, for instance, the ASA and CSSA Fellow not only established the first systematic breeding program for soybean in India, but was also pivotal in bringing the novel food to millions of Indian people. Soybean production has since grown in India from just 5,000 tons in 1961 to about 12 million today. Yet this was only the start.

“Of course, B.B. is best known for his work with cowpea,” says Bill Payne, an ASA, CSSA, and SSSA Fellow who was at Texas A&M and CGIAR in Ethiopia before becoming dean of agriculture at the University of Nevada–Reno this winter. “Almost anywhere in the world, you cannot work on cowpea without running into him in some way, fashion, or form.”

imagesKnown also as black-eyed pea, cowpea is a staple crop in many tropical areas, and Singh’s signature achievement is a fast-maturing variety that fits into the rotational niches between wheat, maize, and rice. Due largely to this advance, worldwide cowpea production rose from 1.3 million to 7 million tons between 1981 and 2013—the only food legume to enjoy such an upswing. But the crop scientist, now in the 48th year of his career, isn’t content to stop there.

“I think there’s a very good possibility that we will have a surge in pulse production in the coming decades,” says Singh, who currently splits his time between Texas A&M University and India’s G.B. Pant University. The title of his new book, Cowpea—The Food Legume of the 21st Century asserts the same.

Those who know him don’t doubt it. “He’s just tenacious,” says CSSA President David Baltensperger, also an ASA and CSSA Fellow. He often compares Singh’s success with cowpea to Norman Borlaug’s accomplishments with wheat. “One of the secrets to B.B., like Dr. Borlaug, has been his ability to keep his eye on what he considers to be really powerful fundamentals. That leads to a lot of success over a long career.”

Good decisions… and a little luck

Focus is indeed crucial for a researcher, and other colleagues add that Singh is highly intelligent, full of energy, and a careful listener—as well as supremely dedicated to helping farmers.

“He is an excellent scientist—I mean, he publishes a lot,” says Ken Dashiell of the International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria, from which Singh retired in 2006. “But he probably spends 98% of his energy on getting the best cowpea varieties for the farmers, and 2% of his energy on publishing.”

What Singh himself says is that he’s been lucky. “At every stage of my life, some good people have come, given me direction, and good things have happened,” he says. The first stroke of luck came when his father pushed him toward an agricultural high school because it helped gain him admission in 1960 to India’s first agricultural university: Uttar Pradesh Agricultural University (now Pant University).

4fig3Singh then earned a scholarship in 1963 to do graduate studies in plant breeding at the University of Illinois, where again he made a fateful choice. After learning how much research was already under way to improve cereals, Singh resolved to study legumes to help India’s vegetarian multitudes meet their need for protein. And at the University of Illinois, that meant one option: soybean.

“So, that’s how I decided to work on soybean,” he says, “and it was one of the best decisions that I took in my life.”

Soybean contains roughly twice the protein of other pulses, he explains, and by the time he earned his Ph.D., USAID and the University of Illinois were already trying to bring soybean to countries beset by malnutrition, including India. Meanwhile, the dean of agriculture at Pant University was monitoring Singh’s progress, and in 1968 sent him a “very personal and emotional letter,” Singh says. It offered him—now a postdoc at Cornell—an assistant professorship at Pant that included 50% more salary than what a new assistant professor in India typically earned.

Singh had two competing offers from U.S. universities for substantially higher pay, but he never gave the decision a second thought. Later that year, he returned to India to begin the work that would transform soybean from an agricultural novelty into one of the nation’s principal foods.

He might have stayed at Pant for the rest of his career. But in 1977, a change in university administration led to major campus unrest, including the shooting of several staff. Hoping to get away for a “breathing spell,” Singh began looking for other opportunities and was immediately offered soybean breeding positions by the United Nation’s Food and Agriculture Organization (FAO) in Zambia and by IITA in Nigeria. Opting for IITA because of his interest in research, he intended to stay abroad for just two years, but “then based on my work, they kept me there forever, and I spent my life there,” he says.

They asked something else of him, as well: to work not on soybean, but cowpea.

Continue reading this story in the Oct. 2014 issue of CSA News magazine…

This blog was first published by the American Society of Agronomy

https://www.agronomy.org/science-news/bb-singhs-quest-make-cowpea-food-legume-21st-century