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.

2015 Plant Science Round Up

Following on from last week’s post, Now That’s What I Call Plant Science 2015, we bring you a year in Plant Science!



Image credit: Jean Weber. Used under license CC BY 2.0.

The year began with a surprising paper that turned our understanding of the phytohormone auxin on its head. Researchers in China and the USA created Arabidopsis knockout mutants of AUXIN BINDING PROTEIN 1 (ABP1), expecting them to fail to respond to auxin and have developmental defects, as previously seen in the abp1-1 knockdown mutant. Instead, these plants were indistinguishable from wild type plants, leading the authors to conclude that ABP1 is not required for auxin signaling or Arabidopsis development as previously believed.

Read the paper in PNAS: Auxin binding protein 1 (ABP1) is not required for either auxin signaling or Arabidopsis development.

A paper later in the year from the same authors found that the embryonic lethality of the abp1-1 mutant is actually caused by the off-target linked deletion of the adjacent BSM gene.

Read this paper in Nature Plants: Embryonic lethality of Arabidopsis abp1-1 is caused by deletion of the adjacent BSM gene.

The tale of ABP1 was examined in more detail on the GARNet blog, Weeding the Gems, which concluded: “In many ways this story is an excellent example of how science should work, where claims are independently tested to ensure that earlier experiments have been conducted or interpreted correctly.” Click here to read more.



A clever experiment from Germany led to a significant breakthrough in crop protection from insect pests.

When double-stranded RNA (dsRNA) is present within a eukaryotic cell, it is cleaved by the Dicer enzyme to form short interfering RNAs. These can bind to complementary RNA within a cell to target it for destruction, thus silencing the corresponding gene expression. This process is known as RNA interference (RNAi).

RNAi has previously been used to tackle insect herbivory by expressing insect-specific dsRNA in plants; however the protection has previously been incomplete. In this new study, published in Science, researchers produced dsRNA within chloroplasts, which do not have RNAi machinery. When dsRNA is expressed in the cytoplasm, the plant’s own Dicer enzyme breaks most of it down. When expressed in the chloroplasts, the dsRNA remained intact when eaten by insects, which proved much more effective at killing these pests.

Read the paper here: Full crop protection from an insect pest by expression of long double-stranded RNAs in plastids.



Another crop protection study followed in March, when researchers in China cloned the genetic locus in rice that confers broad-spectrum resistance to planthoppers – insect pests that cause the loss of billions of dollars of crops per year. Three lectin receptor kinase genes were found in rice cultivars from the Philippines, which enable plants to survive an infestation of insects. When cloned into a susceptible rice cultivar, these genes conferred resistance to two different planthopper species.

Understanding the genetic basis of resistance is very important as marker-assisted breeding and selection could be used to develop resistant rice varieties, and potentially utilized in other species of cereal.

Read the paper in Nature Biotechnology: A gene cluster encoding lectin receptor kinases confers broad-spectrum and durable insect resistance in rice



A European collaboration led to the development of 3DCellAtlas, a computational approach that semi-automatically identifies cell types in a developing 3D organ without the need for transgenic lineage markers. This program will enable the interpretation of dynamic organ growth and the spatial and temporal context of developmental cell divisions that produce the resultant plant. It could be integrated with growth in different conditions or with developmental mutants to examine exactly how these processes affect growth in 3D.


Image credit: Montenegro-Johnson et al., 2015. Digital Single-Cell Analysis of Plant Organ Development Using 3DCellAtlas. The Plant Cell, vol. 27 no. 4, 1018–1033.



A special issue of the Plant Biotechnology Journal was published in May, focusing on the amazing advances in molecular farming. While the entire issue is worth delving into, we were particularly intrigued by the review on moss-made pharmaceuticals, which outlines the rapid progress made in the field.

The model moss Physcomitrella patens has rapidly become one of the organisms of choice in biotechnology, with a fully sequenced genome and an outstanding toolbox for genome-engineering. The authors describe how moss-made pharmaceuticals can easily be produced while remaining remarkably more stable from batch to batch than cultured animal cells. The system is easily scalable, making their production highly cost effective, and safe. The first moss-made pharmaceuticals are currently in clinical trials, so keep an eye out for much more from this field over the next few years.

Read the review: Moss-made pharmaceuticals: from bench to bedside.



In June, US researchers discovered a new role for chloroplast stromules, protrusions that extend from the surface of all plastid types. The function of stromules has been difficult to determine, but this research, published in Developmental Cell, suggests that they may provide a mechanism by which plastid signals are conveyed to the nucleus. The paper shows that chloroplast stromules are induced by defense responses such as programmed cell death signaling, and that the stromules extend to form dynamic connections with the nucleus. The stromules may therefore aid in the amplification and/or transport of immune response signals into the nucleus.

Read the paper: Chloroplast Stromules Function during Innate Immunity.



Extracellular self-DNA

Image credit: Veresoglou et al., 2015. Self-DNA: a blessing in disguise? New Phytologist, vol. 207, no. 3, 488–490.

In late 2014 and early 2015, Italian researchers published a set of articles showing that extracellular self-DNA, DNA from conspecifics, could inhibit the growth of organisms from a wide range of taxa, including plants, bacteria, fungi and animals. Conversely, these organisms were not affected by extracellular DNA from other unrelated species.

In July, New Phytologist published a letter offering an interpretation of the data as it relates to plants. Plants could interpret extracellular self-DNA as an indicator of intraspecific competition (which seeds could use as a cue to remain dormant) or of a hostile environment that has already caused the death of conspecifics, signaling them to ramp up their pre-emptive immune response to increase survival after neighbors have been damaged or killed. There are still a lot of mechanisms and ecological effects to be investigated in this new field, but this letter suggests several interesting avenues to investigate.

Read the article: Self-DNA: a blessing in disguise?

Original research papers in New Phytologist:

Inhibitory and toxic effects of extracellular self-DNA in litter: a mechanism for negative plant–soil feedbacks?

Inhibitory effects of extracellular self-DNA: a general biological process?



A US study in August revealed a surprising degree of conservation in gene expression patterns across a wide range of plant taxa during root development. This was particularly interesting because the spikemoss Selaginella was shown to use many of the same genes as the evolutionarily distant angiosperms, despite the fossil record suggesting that roots evolved independently in these two lineages. Perhaps roots in these two groups evolved by independently recruiting the same developmental program, or perhaps by elaborating on a previously unknown proto-root that existed in the common ancestor of vascular plants.

Read the paper in The Plant Cell: Conserved Gene Expression Programs in Developing Roots from Diverse Plants.



Salt stress can significantly reduce the growth and yield of plants. Researchers in Germany identified two components of the cellulose synthase complex that directly interact with the microtubules and promote their dynamics, which interestingly were highly produced during salt stress conditions. During salt stress, cellulose microtubules depolymerize, however the newly discovered compounds, known as Companions of Cellulose Synthase, promote the reassembly of the microtubule to allow cellulose synthesis to continue.

Read the paper in Cell: A Mechanism for Sustained Cellulose Synthesis during Salt Stress



Throughout the year the GM debate in Europe reached several important milestones. In January the European Union (EU) changed its rules, giving individual countries more flexibility to decide for themselves whether or not to plant GM crops. In February, the UK Science and Technology Committee report stated that EU regulations preventing GM crops are not fit for purpose, and that they should be replaced with a trait-based system.

In October, EU member states revealed their stances on GM crops, with over half of Europe opting out of growing GM crops. Germany was the largest country to opt out of growing GM. The full list can be viewed here: Restrictions of geographical scope of GMO.

Read the news articles here:

EU changes rules on GM crop cultivation – January 2015

EU regulation on GM Organisms not ‘fit for purpose’ – February 2015

Half of Europe opts out of new GM crop scheme – October 2015



A collaboration between South African and UK scientists revealed how plants can use their circadian clock to pre-emptively boost their immune resistance at dawn, when fungal infection is most likely. Plants tend to decrease in susceptibility at dawn, but those with dysfunctional circadian clocks remained highly susceptible throughout the day. The research also showed that jasmonate signaling plays a crucial role in the circadian timing of resistance.

Read the article in The Plant Journal: Jasmonate signalling drives time-of-day differences in susceptibility of Arabidopsis to the fungal pathogen Botrytis cinerea.



Single nucleotide exon

Image credit: Guo & Liu., 2015. A single-nucleotide exon found in Arabidopsis. Scientific Reports, 5:18087.

Researchers in China published the surprising finding that a single-nucleotide exon exists in the APC11 gene in Arabidopsis. This is the smallest exon ever to be discovered before. The team used an elegant set of APC11-GFP constructs to show that intron splicing around the single-nucleotide exon is effective in both Arabidopsis and rice. This finding has implications for future genome annotations, which might reveal many more single-nucleotide exons.

Read the paper in Scientific Reports: A single-nucleotide exon found in Arabidopsis.


What a wonderful year of science! What new knowledge will 2016 bring?