Resilient cropping systems for the future

Dr John Kirkegaard

Dr John Kirkegaard, CSIRO, Australia

Last year Dr John Kirkegaard (CSIRO, Australia) gave a fantastic presentation to the Stress Resilience Forum hosted by the Society for Experimental Biology and the Global Plant Council. He discussed the need for resilient cropping systems to enhance yields, and described the success of the National Water Use Efficiency Initiative (2009-2013) in discovering the synergies between new crop varieties and better crop management.

Here, Dr Kirkegaard, who was recently elected as a Fellow of the Australian Academy of Science, describes the work of the National Water Use Efficiency Initiative and the exciting new discoveries made by farmers and scientists already being used to shape resilient cropping systems for the future.

 

Could you begin by explaining how and why the National Water Use Efficiency Initiative was established?

Despite the semi-arid conditions, rain-fed agriculture is by far the most common form of farming in Australia, especially for grain crops such as wheat and canola. The National Water Use Efficiency Initiative was established in 2009 by the Grains Research and Development Corporation (GRDC), a research-funding organization that collects levies from farmers to support agricultural research. They provided $17 million over five years to growers and research organizations to tackle the challenge of increasing water use efficiency (the amount of grain produced per mm of rainfall) of grain farming systems by 10%.

Wheat in Australia

Wheat is New South Wales, Australia. Image credit: Tim J. Keegan. Used under license: CC BY-SA 2.0.

Growers could suggest ways in which they believed this could be achieved and CSIRO scientists provided farming systems research assistance to test and validate the ideas and ensure a consistent and scientific approach was taken.

 

How has modeling been used to guide the research?

Pre-experimental modeling was used to determine which interventions looked most promising. This early modelling suggested there were huge opportunities to catch and store summer rainfall in better ways, and to sow crops earlier to utilize water more efficiently.  Experiments were then designed to test and validate those ideas on-farm, in experiments run by the farmers in their own fields.

 

What synergies have you found between management practices in semi-arid agriculture?

Canola in Australia

Canola growing in New South Wales, Australia. Image credit: Jan Smith. Used under license: CC BY 2.0.

In wheat farming, we found that adopting a good crop rotation, controlling summer weeds, maintaining stubble cover and sowing earlier at lower crop densities was very successful. Capturing and storing water in the summer facilitates early sowing because crops can be planted without waiting for rain, and choosing a wheat variety that flowers at the right time makes best use of the seasonal rainfall. This combination of management and variety was very powerful, leading to a doubling in yield.

We are now investigating similar interactions in canola. Sowing canola early helps the plant to avoid heat and water stress at the end of the season, increasing its biomass production and grain yield potential, and improving its water use efficiency.

 

Poppy and wheat

Vigorous wheat varieties may be able to choke out weeds, like this field poppy. Image credit: Tony Smith. Used under license: CC BY 2.0.

Have you discovered any other genotype x management (G x M) relationships, where a particular cultivar contributes to crop management?

Vigorous wheat varieties can have beneficial interactions with management. For example, more vigorous crops cover the ground quickly and reduce the direct loss of soil water through evaporation, and can improve water use efficiency. In addition, vigor can also make the wheat more competitive with weeds and provide a non-chemical form of weed control to reduce the overreliance on herbicides as part of an integrated weed management approach.

 

What advice do you have for researchers or breeders developing a new cultivar? How can they test its interaction with crop management?

In some cases, depending on the genetic change that is present in a new variety, there may be little interaction with management. However, large and obvious changes in crop traits, such as changes in crop vigor or root and shoot architecture, may interact strongly with numerous aspects of management (e.g. sowing date, sowing density, nutrient management, weed management). It would be wise to test some of these interactions before crop release, so that the new variety is released WITH a package of sound management strategies to maximize productivity.

 

Stubble cover

Leaving stubble on a field maintains water and increases soil organic matter. Image credit: USDA NRCS South Dakota. Used under license: CC BY-SA 2.0.

How will the findings of the National Water Use Efficiency Initiative be built upon in the future?

I believe we have had an impact on the way research is approached. Rather than assume that a single intervention or new variety will have a large impact, people are now more interested in what packages of management and varieties will be most successful. It’s like always asking “what else do I need to add to my innovation to get the most out of it?” Testing some of the G x M interactions experimentally during the pre-breeding process may be a fruitful area to identify likely synergies well ahead of cultivar release.

Large increases in system productivity rarely come from a single transformational change; they arise when several interacting factors combine, such as in the first agricultural revolution in Europe, or the Green Revolution in India and Asia. New crop types combined with management packages to fulfil the higher potential is what made the difference. We need to envisage what combination might provide those synergies for the crops of the future and be sure we organize ourselves and capture those possibilities by NOT staying in comfortable discipline siloes.

 

Let’s get Plantae!

So you’re hearing good things about the new plant science networking platform Plantae and want to get involved? You’ve come to the right blog post! Read on to learn how to set up your profile, find friends and get involved with the community.

Who are you?

Plantae profile

Filling in your profile is easy!

Plantae is a great place to network with researchers around the world, so you’ll want your profile to be as detailed as possible.

As a minimum, add your name, a profile photo, your professional affiliations and a summary of who you are and what you do. This will help your colleagues and friends to find you, and break the networking ice with new connections!

What makes a good bio? Give the reader a little information about your fields of interest, background, plant science outreach, new papers, favorite plant, whatever you like (related to plants and plant science, of course!). Remember that Plantae is a professional networking site, so don’t put anything on there that you wouldn’t want your boss (current or future!) to see!

Where can I find out more about this interesting person?

Plantae social media

Don’t forget to add your social media and researcher profiles

A great feature of the Core Profile is the ability to add your social media profiles, website, and enhance the visibility of your research by adding researcher profiles, for example your ORCID, Mendeley, or ResearchGate account. To ensure that the accounts connect properly, add the full URL of each profile, not just your account name.

 

Will you be my friend?

From the Community homepage you can choose to see the recent activity of your friends, but only if you’ve added them first!

Add a friend on Plantae

How to add a friend on Plantae

To find colleagues, click on ‘Members’ and you can search for a name, or filter all members by city, state or country. Click on your friend’s name to go to their profile. On the left sidebar, you’ll see a button named ‘User Actions’, which when clicked brings up the option to add them as a friend. After they accept your request, you’re officially friends. Congratulations!

Branching out

Plantae groups

Join a group to continue networking

Now you’ve added everyone you know, it’s time to connect with people that you don’t! Get over to the Discussion boards and let everyone know how you feel about the latest hot paper or public engagement scheme. Or you could join a Group of users who share your interests, location, or love of plant-themed poetry (disclaimer: the latter is currently not a Plantae group – feel free to start it!). It’s easy to join conversations or start one of your own.

Finding funding, jobs and resources

Plantae is a hub of plant science resources, including research news, funding opportunities, job advertisements, science policy news and a wealth of education and public engagement tools. Log in regularly to see up and coming events, grant calls, opinion pieces and more, or maybe upload some of your own!

Join us!

There you have it. Now you know the basics, reach out to the Plantae network, get involved in exciting plant science discussions, make the most of funding and job opportunities, and, pretty please, fill in your profile!

A typical day for PhD students in Japan

Akiko Nakazaki

Akiko Nakazaki, PhD student at Kyoto University

Kon-nichiwa! (Hello!) I am Akiko Nakazaki, a PhD student studying plant molecular cell biology at Kyoto University in Japan.

I’m interested in plant defense – specifically the glucosinolate-myrosinase defense system, which is specific to Brassicales such as Arabidopsis thaliana. Glucosinolates are a group of secondary metabolites stored in separate cells to myrosinases, the enzymes that break them down. Upon tissue damage, the glucosinolates and myrosinases are released from their cells and combine. The glucosinolates are hydrolyzed to volatile repellent compounds such as isothiocyanates and nitriles.

Glucosinolate myrosinase defense system

When damaged, cells containing glucosinolate and myrosinase are ruptured, releasing their contents. The glucosinolate is broken down by the myrosinase into volatile compounds that repel herbivores

I was impressed by this ingenious and rational survival strategy! I want to reveal this defense system at the cellular level, and am researching it in Arabidopsis thaliana by performing microscopic observations, bioassays with insects, and so on.

A day in the lab

Are you interested in how PhD students from other countries spend their day in the laboratory? I am! Let me tell you about my typical day in the lab.

I wake up at 8:30am, and have morning coffee and toast for breakfast while reading a newspaper. Then, I get dressed and ride on my bicycle to the University. During the ride (about 10 minutes), I remind myself of the day’s schedule. I get to the lab at 10am and take my seat. All the members of the lab have their own desk and workbench. I turn on my computer and check my emails.

In the daylight, I basically do experiments and read papers. I start doing microscopic observations and lose track of time until I hear my stomach growling and realize that it is almost 2pm. I have lunch at the eating space in lab. In this room, there are always some lab members who are eating, discussing their research, playing social games, etc. After lunch, I report the result of my microscopic observations to my boss and we have a brief discussion about it.

Microscopic_observations

Then, I return to my seat and realize the primers I ordered yesterday have arrived. I perform a PCR and prepare an agarose gel for electrophoresis. While I am waiting for the PCR to end, I search PubMed and Google Scholar for new papers to read. I load the PCR products to the gel and check that the PCR worked. In the evening, I allocate myself free time for doing more experiments, reading more papers, preparing research presentations, discussions, etc.

I’ve sought a more effective way to advance my research through trial and error. For example, when I started researching in the lab I was a little too ambitious, and planned my schedule too tightly. I sometimes felt tired and depressed when my research was not right on schedule, as is often the case. In these negative moods I couldn’t enjoy my work, so I adopted a schedule with more free time. Because of this change, I’ve come to be able to work flexibly and keep a positive frame of mind.

I’m home between 10pm and midnight. At home, I have a late dinner and take a good long soak in the bath (my favorite time of day!). I go to bed at 2am.

Free weekends!

On weekends I enjoy playing badminton, learning traditional Japanese dance and shopping. I try to make plans without lab work as much as I can, however I’m not able to do avoid it sometimes when I am struggling to get new data before academic conferences and progress reports. Leaving the lab allows me to get rid of stress and feel refreshed for a healthy next week. Furthermore, I devise ways to work more efficiently on weekdays, because I am required to take time off at the weekends.

Treasure every encounter

My boss always says, “It is important to value encounters with people and things.” It wasn’t until recently that I finally understood that message! I have found that experiments may not always work well, but when I look at it from a different angle, even experiments that haven’t gone the way I’d wanted could make me aware of something new and interesting. This awareness could also be brought about through discussions with others.

I am grateful for being able to receive this opportunity. Thank you.


Akiko Nakazaki is in the first year of her doctoral program in the Department of Botany, Graduate School of Science, Kyoto University, Japan.

 

Protecting plants, protecting people

Professor Sophien Kamoun

Professor Sophien Kamoun (The Sainsbury Lab, UK)

This week on the blog, Professor Sophien Kamoun describes his work on plant–pathogen interactions at The Sainsbury Lab, UK, and discusses the future of plant disease.

Could you begin by describing the focus of your research on plant pathogens?

We study several aspects of plant–pathogen interactions, ranging from genome-level analyses to mechanistic investigations focused on individual proteins. Our projects are driven by some of the major questions in the field: how do plant pathogens evolve? How do they adapt and specialize to their hosts? How do plant pathogen effectors co-opt host processes?

One personal aim is to narrow the gap between research on the mechanisms and evolution of these processes. We hope to demonstrate how mechanistic research benefits from a robust phylogenetic framework to test specific hypotheses about how evolution has shaped molecular mechanisms of pathogenicity and immunity.

 

Phytophtora ramorum

Sudden oak death is caused by the oomycete Phytophthora ramorum. Image from Nichols, 2014. PLOS Biology.

Tree diseases such as sudden oak death, ash dieback and olive quick decline syndrome have been making the news a lot recently. Are diseases like these becoming more common, and if so, why?

It’s well documented that the scale and frequency of emerging plant diseases has increased. There are many factors to blame. Increased global trade is one. Climate change is another. There is no question that we need to increase our surveillance and diagnostics efforts. We’re nowhere near having coordinated responses to new disease outbreaks in plant pathology, especially when it comes to deploying the latest genomics methods. We really need to remedy this.

 

The wheat blast fungus recently hit Bangladesh. Could you briefly outline how it is being tackled by plant pathologists?

Wheat blast has just emerged this last February in Bangladesh – its first report in Asia. It could spread to neighboring countries and become a major threat to wheat production in South Asia. Thus, we had to act fast. We used an Open Science approach to mobilize collaborators in Bangladesh and the wider blast fungus community, and managed to identify the pathogen strain in just a few weeks. It turned out that the Bangladeshi outbreak was caused by a clone related to the South American lineage of the pathogen. Now that we know the enemy, we can proceed to put in place an informed response plan. It’s challenging but at least we know the nature of the pathogen – a first step in any response plan to a disease outbreak.

 

Which emerging diseases do you foresee having a large impact on food security in the future?

Obviously, any disease outbreak in the major food crops would be of immediate concern, but we shouldn’t neglect the smaller crops, which are so critical to agriculture in the developing world. This is one of the challenges of plant pathology: how to handle the numerous plants and their many pathogens.

European Corn Borer

European corn boreer. Image from Cornell University. Used under license CC BY 2.0.

As far as new problems, I view insect pests as being a particular challenge. Our basic understanding of insect–plant interactions is not as well developed as it is for microbial pathogens, and research has somewhat neglected the impact of plant immunity. The range of many insect pests is expanding because of climate change, and we are moving to ban many of the widely used insecticides. This is an area of research I would recommend for an early career scientist.

 

What advice would you give to a young researcher in this area?

Ask the right questions and look beyond the current trends. Think big. Be ambitious. Don’t shy away from embracing the latest technologies and methods. It’s important to work on real world systems. Thanks to technological advances, genomics, genome editing etc., the advantages of working on model systems are not as obvious as they were in the past.

 

How can we mitigate the risks to crops from plant diseases in the future?

My general take is to be suspicious of silver bullets. I like to say “Don’t bet against the pathogen”. I believe that for truly sustainable solutions, we need to continuously alter the control methods, for example by regularly releasing new resistant crop varieties. Only then we can keep up with rapidly evolving pathogens. One analogy would be the flu jab, which has a different formulation every year depending on the make-up of the flu virus population.

 

Blight Potato

Potato with blight, caused by the oomycete Phytophthora infestans. Image credit: USDA. Used under license CC BY-ND 2.0.

Is there anything else you’d like to add?

I read that public and private funding of plant science is less than one tenth of biomedical research. Not a great state of affairs when one considers that we will add another two billion people to the planet in the next 30 years. As one of my colleagues once said: “medicine might save you one day; but plants keep you alive everyday”.