Roots of a second green revolution

This week we spoke to Professor Jonathan Lynch, Penn State University, whose research on root traits has deepened our understanding of how plants adapt to drought and low soil fertility.



Could you begin by giving us a brief introduction to your research?

We are trying to understand how plants adapt to drought and low soil fertility. This is important because all plants in terrestrial ecosystems experience suboptimal water and nutrient availability, so in rich nations we maintain crop yields with irrigation and fertilizer, which is not sustainable in the long term. Furthermore, climate change is further degrading soil fertility and increasing plant stress. This topic is therefore both a central question in plant evolution and a key challenge for our civilization. We need to develop better ways to sustain so many people on this planet, and a big part of that will be developing more resilient, efficient crop plants.


Drought is devastating for crops

Drought and low soil fertility are devastating for crops. Image credit: CIAT. Used under license: CC BY-SA 2.0.


What got you interested in this field, and how has your career developed over time?

When I was 9 years old I became aware of a famine in Africa related to crop failure and resolved to do something about it. I studied soils and plant nutrition as an undergraduate, and in graduate school worked on plant adaptation to low phosphorus and salinity stress, moving to a research position at the CIAT headquarters in Colombia. Later I moved to Penn State, where I have maintained this focus, working to understand the stress tolerance of staple crops, and collaborating with crop breeders in the USA, Europe, Africa, Asia, and Latin America.


Your recent publications feature a variety of different crop plants. Could you talk about how you select a species to study?

We work with species that are important for food security, that grow in our field environments, and that I think are cool. We have devoted most of our efforts to the common bean – globally the most important food legume – and maize, which is the most important global crop. These species are often grown together in Africa and Latin America, and part of our work has been geared to understanding how maize/bean and maize/bean/squash polycultures perform under stress. These are fascinating, beautiful plants with huge cultural importance in human history. They are also supported by talented, cooperative research communities. One nice feature of working with food security crops is that their research communities share common goals of achieving impact to improve human welfare.


Common bean (Phaseolus vulgaris)

The common bean (Phaseolus vulgaris) is an important staple in many parts of the world. Image credit: Ervins Strauhmanis. Used under license: CC BY 2.0.


Many researchers use Arabidopsis thaliana for plant research, but are crops better suited for root research than the delicate roots of Arabidopsis? Are crop plants more or less difficult to work with in your research than Arabidopsis?

The best research system is entirely a function of your goals and questions. We have worked with Arabidopsis for some questions. Since we work with processes at multiple scales, including crop stands, whole organisms, organs, tissues, and cells, it has been useful to work with large plants such as maize, which are large enough to easily measure and to work with in the field. The most interesting stress adaptations for crop breeding are those that differ among genotypes of the same species, and at that level of organization there is a lot of biology that is specific to that species, that cannot readily be generalized from model organisms with very different life strategies. There has been considerable attention to model genomes and much less attention to model phenomes.


You have developed methodologies for the high-throughput phenotyping of crop plants. What does this technique involve and what challenges did you have to overcome to succeed?

We have developed multiple phenotyping approaches – too many to summarize readily here. Our overall approach is simply to develop a tool that helps us achieve our goals. For example, we have developed tools to quantify the root architecture of thousands of plants in the field, to measure anatomical phenotypes of thousands of samples from field-grown roots, to help us determine which root phenotypes might affect soil resource capture, etc. Working with geneticists and breeders, we are constantly asked to measure something meaningful on thousands of plants in a field, in many fields, every season. ARPA-E (the US Advanced Research Projects Agency for Energy) has recently funded us to develop phenotyping tools for root depth in the field, but this is the first time we have been funded to develop phenotyping tools – generally we just come up with things to help us do our work, which fortunately have been useful for other researchers as well.


Could you talk about some of the computational models you have developed for investigating plant growth and development?

The biological interactions between plants and their environment are so complex, we need computational (in silico) tools to help us evaluate them. Increasingly, in silico tools can integrate information across multiple scales, from gene expression to crop stands. These tools also allow us to evaluate things that are difficult to measure, such as phenotypes that do not yet exist, or future climates. In silico biology will be an essential tool in 21st Century biology, which will have access to huge amounts of data at multiple scales that can be used to try to understand incredibly complex systems, such as the human brain or roots interacting with living soil. Our main in silico tool is SimRoot, developed over the past 25 years to understand how root phenotypes affect soil resource capture.

Check out a SimRoot model below:


You have been working on breeding plants that have improved yield in soils with low fertility. What have you achieved in this work?

In collaboration with crop breeders and colleagues in various nations we have developed improved common bean lines with better yield under drought and low soil fertility that are being deployed in Africa and Latin America, improved soybean lines with better yield in soils with low phosphorus being deployed in Africa and Asia, and are now working with maize breeders in Africa to develop lines with better yield under drought and low nitrogen stress. Many crop breeders are using our methods for root phenotyping to target root phenotypes in their selection regimes in multiple crops.


What piece of advice do you have for early career researchers?

You are at the forefront of an unprecedented challenge we face as a species – how to sustain 10 billion people in a degrading environment. Plant biologists are an essential part of the effort to reshape how we live on this planet. Do not doubt the importance of your efforts. Do not lose sight of the very real human impact of your scientific choices. Do not be deterred by the gamesmanship and ‘primate politics’ of science. You can make a difference. We need you.

Early Career Researcher travel bursary to attend the State of the World’s Plants Symposium 2017

The Society for Experimental Biology have very kindly offered to sponsor one early career researcher (PhD student or postdoctoral researcher within five years of obtaining PhD) to attend the State of the World’s Plants Symposium 2017 at the Royal Botanic Gardens, Kew (UK). The recipient will receive up to £1000 to support their meeting registration, travel, and accommodation costs to attend the meeting, which will be held at the Jodrell Laboratory, RBG Kew, on the 25th and 26th May 2017.

The bursary is offered to promote the international collaboration goals of the Society for Experimental Biology and the Global Plant Council, and applications from all countries are welcomed.

In return for this generous bursary, the student will be expected to write a 500-1000 word blog post about the meeting for the Global Plant Council blog.

In order to be eligible for the State of the World’s Plants bursary, you must be:

  • An early career researcher (PhD student or postdoctoral researcher with less than five years of experience after completing PhD) in plant science.
  • Available and able to attend the State of the World’s Plants Symposium 2017.
  • A member of the Society for Experimental Biology or willing to join if you are awarded the bursary.


To apply for this bursary, please send an email containing the following information to Sarah Jose ([email protected]) by 9 am (BST) on Tuesday 18th April 2017:

  • Name
  • Institutional address
  • Research topic
  • Why would attending this meeting help your future career? (250 word limit)
  • What else would you gain from attending? (250 word limit)
  • Do you intend to present a poster at the meeting?
  • A signed statement from your PhD supervisor/Head of Department confirming that you are a student or an early career researcher (please scan this and send as an attachment).

How to publish your work in New Phytologist

Reproduced with permission

In two short videos, New Phytologist Editor-in-Chief Prof Alistair Hetherington provides a step by step guide for early career researchers, intending to publish their work in New Phytologist.

“One of my top tips would be: get the author list decided very early on.”


Alistair talks through the process of working out whether research is within the scope of the journal, deciding the author list, and submitting a presubmission enquiry.

“Remember, the Editor will use the covering letter to help him or her decide whether or not to send your work out for review. You need to put your work in context, and describe how your findings are novel, and exciting.”


In part two, Alistair explains the submission process, including what should be included in the covering letter. He then describes the peer review process at New Phytologist and what to do after you’ve received a decision on your manuscript.

Read the transcript of both videos on the New Phytologist blog. The audio from the videos is available to download under a Creative Commons licence from the New Phytologist Soundcloud page. You are welcome to redistribute this for teaching purposes.

Reproduced with permission.

Connecting Plant Science Researchers, Entrepreneurs and Industry Professionals

From Lab Bench to Boardroom

From Lab Bench to Boardroom workshop at Botany 2015

This blog post was written by Amanda Gregoris and R. Glen Uhrig who organized a workshop entitled “Lab Bench to Boardroom” at the Botany 2015 meeting in Edmonton, Alberta, Canada.

Our motivation behind holding this workshop was to engage graduate students and post-doctoral fellows to consider the science behind biotechnology. We designed this workshop to be an opportunity to expose students and post-doctoral fellows to how industry experts and entrepreneurs develop ideas, and how they refine those ideas to make them attractive business opportunities for investors. We created an environment where students and post-doctoral fellows could ‘pitch’ their own plant science business ideas to a panel of industry experts. Through cooperative idea development with the panel and audience members, presenters were able to learn how to evolve their ideas, as well as how their peers viewed their proposed ideas.

Workshops such as Lab Bench to Boardroom are of central importance given the limited availability of academic positions. In light of this fact, students and post-doctoral fellows alike need to consider career options outside of academia prior to completion of their degrees, contracts or fellowships. It is imperative that early career researchers invest time to maximize long-term career outcomes. Workshops like ours and others assist in this by developing a thorough understanding of the non-academic opportunities available.

If you are an early career researcher looking to move away from academia, some industry positions for graduates and post-doctoral fellows may include:

  • research and development,
  • quality control,
  • marketing,
  • market research analyst,
  • business development manager,
  • competitive intelligence analyst,
  • product manager, and
  • management consulting.

Notice that these opportunities are not only based at the lab bench, but can be in more managerial or consulting positions. Your experiences as a researcher have given you highly valued skills, so don’t limit your options! Of course, industry is not the only option, and other opportunities may include working in a government lab, public policy, science writing, herbarium curation or patent agent.

The question of whether enough is being done to inform graduate students and post-doctoral fellows of alternative, non-academic career paths is one often asked, and is one that varies by institution. In our experience, universities have taken a largely standard approach, offering lectures by professionals from industry, as well as informal social gatherings aimed at connecting students to industry. Although these are good opportunities, they represent just the tip of the iceberg in terms of what could be done to inspire entrepreneurship amongst the upcoming generation of plant scientists, and better assist them with the transition from an academic focus to an industry focus.

Workshop concepts similar to Lab Bench to Boardroom could be developed at the departmental level, or by university career centers, to allow graduate students and post-doctoral fellows to gain an elevated understanding of non-academic career opportunities. Some universities have made great strides in this area, creating internship resources for current graduate students in the areas of biotechnology and public policy. Along these lines, university career centers will usually have databases of current job postings that can assist students in the search for life after grad school.

In the end, it is imperative that universities, governments and industry continue to work to develop strategies that assist graduate students and post-doctoral fellows in the transition from academics to successful non-academic careers. This can be accomplished either individually, or through partnerships between these groups. We believe that developing these strategies is undoubtedly essential to the sustainable development of new ideas and technologies in the plant sciences that will be required to address the current and future needs of society.


Amanda Gregoris is a Ph.D. candidate in the Department of Biological Sciences at the University of Alberta, Canada and Dr. R. Glen Uhrig is a post-doctoral fellow at the ETH Zurich, Switzerland. Both are members of the Canadian Society of Plant Biologists

Glen Uhrig

Glen Uhrig

Amanda Gregoris

Amanda Gregoris