This week’s post was written by Jonathan Ingram, Senior Commissioning Editor / Science Writer for the Journal of Experimental Botany. Jonathan moved from lab research into publishing and communications with the launch of Trends in Plant Science in 1995, then going on to New Phytologist and, in the third sector, Age UK and Mind.
Botanic gardens are also part of the picture. In another paper in the same issue, Yang Li et al. from the Key Laboratory of Tropical Plant Resources and Sustainable Use at Xishuangbanna Tropical Botanical Garden in Kunming (Yunnan) and the University of the Chinese Academy of Sciences in Beijing present research on DELLA-interacting proteins in Arabidopsis. Here the authors show that bHLH48 and bHLH60 are transcription factors involved in GA-mediated control of flowering under long-day conditions.
Naturally, research on rice is important. Wei Jiang et al. from the National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University (Wuhan) describe their research on WOX11 and the control of crown root development in the nation’s grain of choice, which will be important for breeders looking to increase crop yields and resilience.
Shenzehn has grown rapidly and is now highly significant for life science as home to the China National GeneBank (CNGB) project led by BGI Genomics. The vision as set out by Huan-Ming Yang, chairman of BGI-Shenzhen, is profound – from sequencing what’s already here, often in numbers per species, to innovative synthetic biology.
Shenzehn is also home to another significant institution, the beautiful and scientifically important Fairy Lake Botanic Garden. At the IBC, the importance of biodiversity conservation for effective, economically focused plant science, but also for so many other reasons to do with our intimate relationship with plants and continued co-existence on the planet, was a central theme.
The research highlighted in Journal of Experimental Botany is part of the wider, positive growth of plant science (and, indeed, botany) not just in China, but worldwide. The Shenzehn Declaration on Plant Sciences with its seven priorities for strategic action, launched at the congress, will be a guide for the right development in coming years.
This week’s blog was written by Dr Craig Cormick, the Creative Director of ThinkOutsideThe. He is one of Australia’s leading science communicators, with over 30 years’ experience working with agencies such as CSIRO, Questacon and Federal Government Departments.
So what do you think CRISPR cabbage might taste like? CRISPR-crispy? Altered in some way?
Professor Stefan Jansson, one of the workshop organizers, has grown the CRISPR cabbage (discussed in his blog for GPC!) and not only had it included on the menu of the workshop dinner, but also had samples for participants to take away. Some delegates were keen to pick up the samples while others were unsure how their own country’s regulatory rules would apply to them
The uncertainty some delegates felt about the legality of taking a CRISPR cabbage sample home was a good demonstration of the diversity of regulations that apply – or may apply – to new breeding technologies, such as CRISPR and gene editing – and there was considerable discussion at the workshop on how European Union regulations and court rulings may play out, affecting both the development and export/import of plants and foods produced by the new technologies.
A lack of certainty has meant many researchers are unable to determine whether their work will need to be subjected to costly and time-consuming regulations or not.
The need for new breeding technologies was made clear at the workshop, which was attended by 70 people from 17 countries, with presentations on the need to double our current food production to feed the world in 2050 and reduce crop losses caused by problems such as viruses, which deplete crops by 10–15%.
The two-day workshop, held in early July, looked at a breadth of issues, including community attitudes, gene editing success stories, and tools and resources. But discussions kept coming back to regulation.
Outdated regulations
Regulations of gene technologies were largely developed 20 years ago or so, for different technologies than now exist, and as a result are not clear enough for researchers to determine whether different gene editing technologies they are working on may be governed by them or not.
The diversity of regulations is also going to be an issue, for some countries may allow different gene editing technologies, but others may not allow products developed using them to be imported.
That led to the group beginning to develop a statement that captured the feeling of the workshop, which, when complete, it is hoped will be adopted by relevant agencies around the world to develop their own particular positions on gene editing technologies. It would be a huge benefit to have a coherent and common line in an environment of mixed regulations in mixed jurisdictions.
CRISPR cabbage
And as to the initial question of what CRISPR cabbage tastes like – just like any cabbage you might buy at your local supermarket or farmers market, of course – since it is really no different.
A man stacks sugarcane at the Ver-o-Peso (Check the Weight) market in Belem.
Currently, it is common for producers to raise sucrose levels in sugar cane by applying artificial growth regulators or chemical ripeners. This inhibits flowering, which in turn prolongs harvest and milling periods.
One of these growth regulators, ethephon, is used to manage agricultural, horticultural and forestry crops around the world. It is widely used to manipulate and stimulate the maturation of sugarcane as it contains ethylene, which is released to the plant on spraying.
Ethylene, considered a ripening hormone in plants, contributes to increasing the storage of sucrose in sugar cane.
“Although we knew ethylene helps increase the amount of sugar in the cane, it was not clear how the synthesis and action of this hormone affected the maturation of the plant,” said Marcelo Menossi, professor at the University of Campinas (Unicamp) and coordinator of the project, which is supported by the Brazilian research foundation FAPESP.
To study how ethylene acts on sugarcane, the researchers sprayed ethephon and an ethylene inhibitor, aminoethoxyvinylglycine (AVG), on sugar cane before it began to mature.
After spraying both compounds, they quantified sucrose levels in tissue samples from the leaves and stem of the cane. They did this five days after application and again 32 days later, on harvest.
Those plants treated with the ethephon ripener had 60 per cent more sucrose in the upper and middle internodes at the time of harvest, while the plants treated with the AVG inhibitor had a sucrose content that was lower by 42 per cent.
The researchers were then able to identify genes that respond to the action of ethylene during ripening of the sugar cane. They also successfully identified the genes involved in regulating sucrose metabolism, as well as how the hormone acts on sucrose accumulation sites in the plant.
Based on the findings, the team has proposed a molecular model of how ethylene interacts with other hormones.
“Knowing which genes or ripeners make it possible for the plant to increase the accumulation of sucrose will allow us to make genetic improvements in sugarcane and develop varieties that over-express these genes, without the need to apply ethylene, for example,” explained Menossi.
This research could also help with spotting the most productive sugar cane, as some varieties that do not respond well to hormones, he added. “It will be possible to identify those [varieties] that best express these genes and facilitate the ripening action.”
[SYDNEY] The increasing use of groundwater for irrigation poses a major threat to global food security and could lead to unaffordable prices of staple foods. From 2000 to 2010, the amount of non-renewable groundwater used for irrigation increased by a quarter, according to an article published in Nature on March 30. During the same period China had doubled its groundwater use.
The article finds that 11 per cent of groundwater extraction for irrigation is linked to agricultural trade.
“In some regions, for example in Central California or North-West India, there is not enough precipitation or surface water available to grow crops like maize or rice and so farmers also use water from the underground to irrigate,” the article says.
“When a country imports US maize grown with this non-renewable water, it virtually imports non-renewable groundwater.”
Carole Dalin, Institute for Sustainable Resources at University College, London
The article focused on cases where underground reservoirs or aquifers, are overused. “When a country imports US maize grown with this non-renewable water, it virtually imports non-renewable groundwater,” Carole Dalin, lead author and senior research fellow at the Institute for Sustainable Resources at University College, London, tells SciDev.Net.
Crops such as rice, wheat, cotton, maize, sugar crops and soybeans are most reliant on this unsustainable water use, according to the article. It lists countries in the Middle East and North Africa as well as China, India, Mexico, Pakistan and the US as most at risk.
“Pakistan and India have been locally most affected due to groundwater depletion and exporting agricultural products grown with non-sustainable groundwater. Iran is both exporting and importing and The Philippines is importing from Pakistan, which is non-sustainable. China is importing a lot from India. Japan and Indonesia are importing, mainly from the US,” says Yoshihide Wada, co-author of the report and deputy director of the International Institute for Applied Systems Analysis’s Water Programme, Laxenburg, Austria.
Agriculture is the leading user of groundwater, accounting for more than 80 to 90 per cent of withdrawals in irrigation-intense countries like India, Pakistan and Iran, according to the report.
The researchers say efforts to improve water use efficiency and develop monitoring and regulation need to be prioritised. Governments must invest in better irrigation infrastructure such as sprinkler irrigation and introduce new cultivar or crop rotation to help producers minimise water use.
Wada suggests creating awareness by putting water labels, along the lines of food labels, “showing how much water is used domestically and internationally in produce and whether these water amounts are from sustainable or non-sustainable sources”.
Andrew Western, professor of hydrology and water resources at the University of Melbourne’s School of Engineering, suggests enforceable water entitlement systems and caps on extraction. “In recent decades, water reform in Australia has led to water having a clear economic value made explicit by a water market. This has enabled shifts in water use to cope with short-term climate fluctuations and has also driven a trend of increasing water productivity,” he says.
This post is republished with the kind permission of the Australian Plant Phenomics Facility (APPF).
We at the APPF love visits from our global plant science community, so it was a treat to host Ruth Bastow, Executive Director of the Global Plant Council (GPC), this week.
While she was here, we took the opportunity to ask a few quick questions:
Ruth Bastow, Executive Director of the Global Plant Council in high-throughput phenotyping Smarthouse™ at the Australian Plant Phenomics Facility’s Adelaide node
Ruth, could you tell us a little bit about the GPC?
The GPC is a not-for-profit coalition of national, regional, and international societies and affiliates representing thousands of plant, crop, agricultural, and environmental scientists. We bring together all those involved in plant and crop research, education and training, to provide a body that can speak with a single, strong voice in the policy and decision-making arena, and to promote plant science research and teaching around the world.
What do you do there?
As Executive Director of the GPC I am responsible for the day to day management of the organisation.
What is the reason for your visit here?
To meet up and discuss GPC initiatives with colleagues here at the University of Adelaide, to further develop current collaborations and hopefully initiate new ones.
For example the Australian Plant Phenomics Facility (APPF) is partner of the Diversity Seek Initiative (DivSeek). DivSeek is a global community driven effort consisting of a diverse set of partner organisations have voluntarily come together to enable breeders and researchers to mobilise a vast range of plant genetic variation to accelerate the rate of crop improvement and furnish food and agricultural products to the growing human population. DivSeek brings together large-scale genotyping and phenotyping projects, computational and data standards projects with the genebanks and germplasm curators. The aim is to establish DivSeek as a hub to connect and promote interactions between these players and activities and to establish common state-of-the-art techniques for data collection, integration and sharing. This will improve the efficiency of each project by eliminating redundancy and increasing the availability of data to researchers around the world to address challenges in food and nutritional security, and to generate societal and economic benefit.
So, whilst I am here, I will be learning about how the APPF team collate and analyse their data and try and understand how the approaches here could be translated into solutions for the wider community. For example, the Zegami platform used in the high-throughput phenotyping Smarthouses™ at the Adelaide node is a useful visualisation tool that could benefit others.
Where else have you visited?
Whilst I am here in Australia I have been working with colleagues in Canberra including Prof Barry Pogson who is currently the chair of the Global Plant Council, Dr Xavier Sirault (APPF node based at CSIRO), Prof Justin Borevitz (APPF node based at ANU), and Dr Norman Warthmann. I will also be taking time to visit friends in Sydney and on the Central Coast.
Where do you see plant phenomics research in 5-10 years time?
High throughput and field based phenotyping has seen huge transformational change in the last decade and in the next 5-10 years I hope that it will start to become part of the everyday toolkit of plant science researchers in the way that genomics has.
If you could solve one plant science question what would it be?
I would actually like to try and solve a social/conceptual problem that effects science rather than an actual biological question and that is the sharing of data, information, knowledge and best practice. The sharing of scientific theories, including experimental data and observations has been a core concept of the scientific endeavour since the enlightenment. Sharing allows others to evaluate research (peer review), to identify errors, and allow ideas to be corroborated, invalidated and built upon. It also facilitates the transmission of concepts and theories to a wider audience and that will hopefully inspire others to get involved in science, contribute ideas and further our understanding of the world around us.
However, the current systems of reward and evaluation in science; lack of appropriate mechanisms, standard and infrastructures to easily share and access information; and in some cases the debilitating effects of ‘IP thickets’ can act as a barrier to ‘open science’. It is not all bad news. In the last decade a number of changes at the government, funder, publisher and institutional level have promoted and facilitated the concept of open science. However, if science is to be a truly open endeavour it will require a change in mind-set at many levels to migrate towards a culture where open data is the norm. Without this we will not be able to fully realise the investment in research, in terms of both finance provided and the time and intellectual contribution of the individual involved, and contribute to developing solutions that will help ameliorate current global problems.
When I am not working I am?
Walking the dog or gardening and generally enjoying the beauty of my home in South Wales in the UK.
If you could have one super power what would it be?
For my work it would probably be telepathy or omnilinguism, as most problems seems to arise from lack of understanding or miscommunication at some level, so these would be very helpful superpowers. From a personal perspective perhaps the ability to predict the future would be good.
Thanks again to the APPF for giving us permission to republish this blog post!
About the APPF
The APPF is a national facility, available to all Australian plant scientists, offering access to infrastructure that is not available at this scale or breadth in the public sectors anywhere else in the world. The APPF is based around automated image analysis of the phenotypic characteristics of extensive germplasm collections and large breeding, mapping and mutant populations. It exploits recent advances in robotics, imaging and computing to enable sensitive, high throughput analyses to be made of plant growth and function. New technologies are being developed to ensure that the APPF remains at the international forefront of plant science. Research networks and established pathways to market ensure outcomes are delivered for the long-term benefit for Australian scientists and primary producers.
When it comes to crop diseases, insects, viruses, and fungi may get the media limelight but in certain regions it is actually other plants which are a farmer’s greatest enemy. In sub-Saharan Africa, one weed in particular – Striga hermonthica – is an almost unstoppable scourge and one of the main limiting factors for food security.
Striga is a parasitic plant; it attaches to and feeds off a host plant. For most of us, parasitic plants are simply harmless curiosities. Over 4,000 plants are known to have adopted a parasitic mode of life, including the seasonal favorite mistletoe (a stem parasite of conifers) and Rafflesia arnoldii, nicknamed the “corpse flower” for its huge, smelly blooms. Although the latter produces the world’s largest flower, it has no true roots – only thread-like structures that infect tropical vines.
When parasitic plants infect food crops, they can turn very nasty indeed. Strigahermonthica is particularly notorious because it infects almost every cereal crop, including rice, maize, and sorghum. Striga is a hemiparasite, meaning that it mainly withdraws water from the host (parasitic plants can also be holoparasites, which withdraw both water and carbon sugars from the host). However, Striga also causes a severe stunting effect on the host crop (see Figure 1), reducing their yield to practically nothing. Little wonder then, that the common name for Striga is ‘witchweed’.
Figure 1:Striga-infected sorghum. Note the withered, shrunken appearance of the infected plants. Image credit: Joel Ransom.
Several features of the Striga lifecycle make it especially difficult to control. The seeds can remain dormant for decades and only germinate in response to signals produced by the host root (called strigolactones) (Figure 2). Once farmland becomes infested with Striga seed, it becomes virtually useless for crop production. Germination and attachment takes place underground, so the farmer can’t tell if the land is infected until the parasite sends up shoots (with ironically beautiful purple flowers). Some chemical treatments can be effective but these remain too expensive for the subsistence farmers who are mostly affected by the weed. Many resort to simply pulling the shoots out as they appear; a time-consuming and labor-intensive process. It is estimated that Striga spp. cause crop losses of around US $10 billion each year [1].
Certain crop cultivars and their wild relatives show natural resistance to Striga. Here at the University of Sheffield, our lab group (headed by Professor Julie Scholes) is working to identify resistance genes in rice and maize, with the eventual aim of breeding these into high-yielding cultivars. To do this, we grow the host plants in rhizotrons (root observation chambers) which allow us to observe the process of Striga attachment and infection (see Figure 3). Already this has been successful in identifying rice cultivars that have broad-spectrum resistance to Striga, and which are now being used by farmers across Africa.
Figure 2: Life cycle of Striga spp. A single plant produces up to 100,000 seeds, which can remain viable in the soil for 20 years. Following a warm, moist conditioning phase, parasite seeds become responsive to chemical cues produced by the roots of suitable hosts, which cause them to germinate and attach to the host root. The parasite then develops a haustorium: an absorptive organ which penetrates the root and connects to the xylem vessels in the host’s vascular system. This fuels the development of the Striga shoots, which eventually emerge above ground and flower. Figure from [2].
But many fundamental aspects of the infection process remain almost a complete mystery, particularly how the parasite overcomes the host’s intrinsic defense systems. It is possible that Striga deliberately triggers certain host signaling pathways; a strategy used by other root pathogens such as the fungus Fusarium oxysporum. This is the focus of my project: to identify the key defense pathways that determine the level of host resistance to Striga. It would be very difficult to investigate this in crop plants, which typically have incredibly large genomes, so my model organism is Arabidopsis thaliana, the workhorse of the plant science world, whose genome has been fully sequenced and mapped. Arabidopsis cannot be infected by Striga hermonthica but it is susceptible to the related species, Striga gesnerioides, which normally infects cowpea. I am currently working through a range of different Arabidopsis mutants, each affected in a certain defense pathway, to test whether these have an altered resistance to the parasite. Once I have an idea of which plant defense hormones may be involved (such as salicylic acid or jasmonic acid), I plant to test the expression of candidate genes to decipher what is happening at the molecular level.
Figure 3: One of my Arabidopsis plants growing in a rhizotron. Preconditioned Striga seeds were applied to the roots three weeks ago with a paintbrush. Those that successfully attached and infected the host have now developed into haustoria. The number of haustoria indicates the level of resistance in the host. Image credit: Caroline Wood.
It’s early days yet, but I am excited by the prospect of shedding light on how these devastating weeds are so effective in breaking into their hosts. Ultimately this could lead to new ways of ‘priming’ host plants so that they are armed and ready when Striga attacks. It’s an ambitious challenge, and one that will certainly keep me going for the remaining two years of my PhD!
You can follow my journey by reading my blog and keeping up with me on Twitter (@sciencedestiny).
References:
[1] Westwood, J. H. et al. (2010). The evolution of parasitism in plants. Trends in Plant Science, 15(4): 227-235.
[2] Scholes, J. D. and Press, M. C. (2008). Striga infestation of cereal crops – an unsolved problem in resource limited agriculture. Current Opinion in Plant Biology,11(2): 180-186.
For Africa to end chronic hunger, governments must invest in sustainable water supplies.
The fields are bare under the scorching sun and temperatures rise with every passing week. Any crops the extreme temperatures haven’t destroyed, the insect pests have, and for many farmers, there is nothing they can do. Now, news about hunger across Africa makes mass media headlines daily.
Globally, hunger levels are at their highest. In fact, according to the Famine Early Warning Systems Network, over 70 million people across 45 countries will require food emergency assistance in 2017, with Africa being home to three of the four countries deemed to face a critical risk of famine: Nigeria, South Sudan, Sudan and Yemen. African governments, non-governmental organisations (NGOs) and humanitarian relief agencies, including the United Nations World Food Programme, continue to launch short-term solutions such as food relief supplies to avert the situation. Kenya, for example, is handing cash transfers and food relief to its affected citizens. The UN World Food Programme is also distributing food to drought-stricken Somalia. And in Zambia, the government is employing every tool including its military to combat insect pest infestation.
But why are we here? What happened? Why is there such a large drought?
Reasons for chronic hunger
Many African smallholder farmers depend on rain-fed agriculture, and because last year’s rains were inadequate, many farmers never harvested any crops.
Indeed, failed rains across parts of the Horn of Africa have led to the current drought that is affecting Somalia, south-eastern Ethiopia and northern and eastern Kenya.
Then, even in the countries where adequate rains fell, many of the farmers had to farm on depleted soils, and consequently, the yields were lower. Degraded soils and dependence on rain-fed agriculture coupled with planting the wrong crop varieties are some of the fundamental problems that lead to poor harvests and then to hunger. Worsening the situation is the unpredictable climate. Given these fundamental and basic issues that fuel the hunger cycle in Africa, it naturally makes sense to tackle them.
It is not rocket science. Farming goes hand-in-hand with water. There can be no farming without it. While this seems easy to reason, there are few organisations working to make sure that African farmers and citizens have access to permanent water sources. Access to water sources all year round would ensure that farmers can farm year in and year out.
What African governments must do
African governments must, therefore, invest in ensuring that their citizens have access to water. Measures that can be implemented include drilling and rehabilitating boreholes, creating reservoirs and irrigation systems, constructing hand-pumps and implementing water harvesting schemes. Such measures would go a long way and ensure that countries continue to face the same problem both in the short and long term periods.
“If Africa wants to end the recurring droughts, hard decisions must be made.”
Esther Ngumbi, Auburn University in Alabama. United States
Of course it is understandable that it can be hard to choose long-term solutions such as ensuring that citizens have access to permanent water sources year round over investing in short-term solutions when there are people who need help now.
Acknowledging this dilemma, Mitiku Kassa, the Ethiopia’s commissioner for disaster risk management, is reported to have described how hard it was to direct even a fifth of his budget towards well drilling. But such decisions must be made. The Ethiopian government still made that tough decision and sunk hundreds of bore wells throughout the country.
There is a great need to ramp up water harvesting and conservation efforts across the African continent. African governments and other stakeholders need to increase investment in multiple water-storing techniques. Such techniques include rain and flood water harvesting and the construction of water storage ponds and dams. But there should be no need to reinvent the wheel.
Time to learn from others
African countries can learn from other countries. Countries in the developed world have sustained their agriculture efforts by either drilling water wells to ensure they have access to the water they need for farming or by investing in rain and flood water harvesting. In California, for example, there have been a rise in the number of wells being drilled by farmers who use well water for farming. In 2016 alone, farmers in the San Joaquin Valley dug about 2,500 wells, a number that was five times the annual average reported in the last 30 years.
Countries such as Bangladesh, China, India, Myanmar, Sri Lanka and Thailand have made progress and are working on pilot projects that capture, harvest and store flood water. Stored water is then available for use by communities when they need it the most. Harvesting and storing water and making it available for agriculture, especially during the dry seasons, will allow citizens and smallholder farmers to farm throughout the year. These would further improve the resilience of farmers to the unpredictability of climate change.
If Africa wants to end the recurring droughts, hard decisions must be made. By addressing the fundamental and basic issues of long-term availability of water for agriculture, African countries can once and for all end this never-ending cycle of hunger.
Esther Ngumbi is a postdoctoral researcher at the Department of Entomology and Plant Pathology at Auburn University in Alabama, United States. She serves as a 2015 Clinton Global University (CGI U) Mentor for Agriculture and is a 2015 New Voices Fellow at the Aspen Institute.
Could you begin by telling us a little about your research?
I am a plant physiologist specializing in seed biology. I have a long research record on various aspects of seeds, including the mechanisms and regulation of germination and dormancy, desiccation tolerance, as well as issues in seed technology. Being six years from retirement now, I decided to extend my desiccation tolerance studies from seeds to resurrection plants, which display vegetative desiccation tolerance. I strongly believe that unveiling of the mechanism of vegetative desiccation tolerance may help us create crops that are truly tolerant to severe drought, rather than (temporarily) resistant.
How did you become interested in this field of study, and how has your career progressed?
As with many things in life, it was coincidence. I majored in plant biochemistry and applied for a PhD position in seed biology. After obtaining the degree I was offered a tenure track position in seed physiology by the Laboratory of Plant Physiology at Wageningen University, where I still work as a faculty member. My career has progressed nicely and I am an authority in the field of seed science, editor-in-chief of the journal Seed Science Research, and will become the President of the International Society for Seed Science in September of this year.
I see my current work on vegetative desiccation tolerance as a highlight in my professional life. I have always been more interested in the desiccation tolerance of seeds until about five years ago, when my current collaborator Prof Jill Farrant of the University of Cape Town, South-Africa, made me enthusiastic about these wonderful resurrection plants. We started to work together and published our first study recently in Nature Plants.
In your recent paper, you sequenced the genome of the resurrection plant, Xerophyta viscosa, which can survive with less than a 5% relative water content. How is it possible for a plant to lose so much of its water and still survive?
These plants have a lot of characteristics that we’ve seen in seeds. They display protective desiccation tolerance mechanisms in their leaves, including anti-oxidants, protective proteins, and even dismantle their photosynthetic machinery during periods of drought. Even the cell wall structure and composition of resurrection plants resemble those of seeds. We are currently working on a paper describing the striking similarities between seeds and resurrection plants.
What was the most interesting discovery you made upon sequencing the genome of the resurrection plant?
First, the similarities between resurrection plants and seeds listed above were also apparent at the molecular level. For example, previous work suggested that the “ABI3 regulon”, consisting of about 100 genes regulated by the transcription factor ABI3, is specific to seeds, but we found that it is almost completely present (and active) in the leaves of Xerophyta viscosa too!
Secondly, we found “islands” or clusters of genes specific for desiccation tolerance that aren’t found in other species. Many of these regulate secondary metabolite pathways.
How challenging was it to sequence the genome of this plant? How did you overcome any difficulties?
It was very challenging. First, the species is an octoploid, meaning it has eight copies of each chromosome. This meant that we had to sequence its genome at very high coverage and employing the most advanced sequencing facilities, e.g. PacBio. Getting funding for this complex analysis was another challenge. We then took almost a year to assemble the genome and annotate it at the desired quality.
Xerophyta viscosa before and after the rains. Image credit: Prof. Henk Hilhorst.
You identified some of the most important genes involved in desiccation tolerance. Is it possible to translate this work into other species, such as crops that may be threatened by drought as the climate changes?
That will be our ultimate goal. It’s important to remember that desiccation-sensitive plants, including all our major crops, produce seeds that are desiccation tolerant. This implies that the information for desiccation tolerance is present in the genomes of these crops but that it is only turned on in the seeds. We are trying to determine how this is localized, in order to find a method to turn on the desiccation tolerance mechanism in vegetative parts of the (crop) plant too. In parallel we are expressing some of the key transcription factors from Xerophyta viscosa in some important crops to see how this affects them.
Are there any other interesting aspects of Xerophyta viscosa biology?
Contrary to plants that wilt and ultimately die because of (severe) drought, leaves of resurrection species do not show such stress-related senescence. This is related to the engagement of active anti-senescence genes during the drying of the leaves of resurrection species. We are currently investigating these senescence-related mechanisms too.
The rose of Jericho (Anastatica hierochuntica) is another resurrection plant. Image credit: FloraTrek. Used under license: CC BY-SA 3.0.
Do you expect to find that different types of desiccation-tolerant plants use the same subset of genes to survive drought, or could they have developed other pathways to resilience?
We expect that the core mechanism is very similar among the resurrection species but that each species may have adapted to its specific environment.
Funding permitting, we will sequence the genomes of at least another ten resurrection species to further clarify the various evolutionary pathways to desiccation tolerance and, importantly, to discriminate between species-specific and desiccation tolerance-specific genes.
What advice do you have for early career researchers?
Stick to what you believe in, even if you have to (temporarily) be involved in research that you appreciate less, e.g., because of better funding opportunities.
This post was written by Dr Colin Khoury. Colin studies diversity in the crops people grow and eat worldwide, and the implications of change in this diversity on human health and environmental sustainability. He is particularly interested in the wild relatives of crops. Colin is a research scientist at the International Center for Tropical Agriculture (CIAT), Colombia, and at the USDA National Laboratory for Genetic Resources Preservation in Fort Collins, Colorado.
New Changing Global Diet website explores changes in diets over the past 50 years in countries around the world.
One of the central concepts that unifies those concerned with biodiversity is the understanding that this diversity is being lost, piece by piece, to a greater or lesser degree, globally.
The same goes for the biodiversity of what we eat. Scientists and activists have worried about the loss of crops and their many traditional varieties for at least a hundred years, since botanist N. I. Vavilov traveled the world in search of plants useful for cultivation in his Russian homeland. He noticed that diversity was disappearing in the cradles of agriculture – places where crops had been cultivated continuously for thousands of years. The alarm sounded even louder 50 years ago, during the Green Revolution, when farmers in some of the most diverse regions of the world largely replaced their many locally adapted wheat, rice and other grain varieties with fewer, more uniform, higher yielding professionally bred varieties.
Cradles of agriculture: origins and primary regions of diversity of agricultural crops
(Click to magnify)
This is ironic, since modern productive crop varieties are bred by wisely mixing and matching diverse genetic resources. The disappearance of old varieties thus reduces the options available to plant breeders, including those working to produce more nutritious or resilient crops.
Being a food biodiversity scientist, I grew up (in the professional sense) with the loss of crop diversity looming over my head, providing both a raison d’être, and an urgency to my efforts. Somewhere along the line, I became interested in understanding its magnitude. That is, counting how many crops and how many varieties have been lost.
That’s where it started to become complicated, and also more interesting. Because, when I went looking for signs of the loss of specific crops, I couldn’t find any. Instead, I found evidence of massive global changes in our food diversity that left me worried, but at the same time hopeful.
A bit of background. Most of the numbers seen in the news on how much crop diversity has been lost go back to a handful of reports and books that reference a few studies: for example, the changing number of vegetable varieties for sale in the U.S. over time. The results are estimations for a few crops at local to national levels, but they somehow have been inflated to generalized statements about the global state of crop diversity, the most common of which being some variation of “75% of diversity in crops has been lost”.
Diverse produce, but is it all local? Image credit: Karyn Christner. Used under license: CC BY 2.0.
Putting true numbers on diversity loss turns out to be a complicated and contested business, with no shortage of strong opinions. One big part of the problem is that there aren’t many good ways to count the diversity that existed before it disappeared. Researchers have done some work to assess the changes in diversity in crop varieties of Green Revolution cereals, and to some degree on the genetic diversity within those varieties. The results indicate that, although diversity on farms decreased when farmers first replaced traditional varieties with modern types, the more recent trends are not so simple to decipher.
It was particularly surprising to me that very little work had been done to understand the changes in what is probably the simplest level to measure: the diversity of crop species in the human diet, that is, how successful is maize versus rice versus potato versus quinoa and so on. I realized that data on the contribution of crops to national food supplies were available for almost all countries worldwide via FAOSTAT, with information for every year since 1961. Perhaps these were the data that could show when a crop fell off the world map.
Fast forward through a couple of years of investigation. To my great surprise, I found that not a single crop was lost over the past 50 years! There was no evidence for extinction. What was going on?
It turns out that my failure to see any loss of crops was due to the lack of sufficient resolution in the FAO data. Only 52 meaningful crop species-specific commodities are measured and a number of these are general groupings such as “cereals, other”. Because of this lack of specificity, the data couldn’t comprehensively assess the crops that have been most vulnerable to changes in the global food system over the past 50 years. In FAO data, these plants are either thrown into the general categories or they aren’t measured at all, especially if they are produced only on a small scale, for local markets or in home gardens. This is, in itself, sign enough that they may be imperiled. We need better statistics about what people eat (and grow) around the world. But, enough is known to be confident that many locally relevant crops are in decline.
Over the past 50 years, almost all countries’ diets actually became more diverse, not less, for the crops that FAO statistics do report on. We found that traditional diets that were primarily based on singular staples a half century ago, for instance rice in Southeast Asia, had diversified over time to include other staples such as wheat and potatoes. The same was true for maize-based diets in Latin America, sorghum- and millet-based diets in sub-Saharan Africa, and so on.
Not that there weren’t plant winners and losers. Wheat, rice, and maize, the most dominant crops worldwide 50 years ago, became more important globally. Other crops emerged as widespread staples, particularly oilcrops such as soybean, palm oil, sunflower, and rapeseed oil. And, as the winners came to take more precedence in food supplies around the world, alternative staples such as sorghum, millets, rye, cassava, sweet potato, and yam were marginalized. They haven’t disappeared (at least not yet), but they have become less important to what is eaten every day.
As countries’ food supplies became more diverse in the winner crops reported by FAO, and the relative abundance of these crops within diets became more even, food supplies worldwide became much more similar, with an average decrease in variation between diets in different countries of 68.8% over the past 50 years!
This is why, although we could see no absolute loss in crops consumed over the past 50 years, I am concerned. For even in the relatively small list of crops reported in the FAO data, many of these foods are becoming marginalized, day by day, bite by bite. That doesn’t seem like a good thing for the long-term resilience of our agricultural areas, nor for human health, although it’s important to remember that such changes are the collateral damage resulting from the creation of highly productive mega-crop farming systems, which have increased the affordability of these foods worldwide, leading to less stunting and other effects of undernutrition worldwide. On the other hand, global dependence on a few select crops equates to expansive monocultures, with more lives riding on the outcome of the game of cat and mouse between pestilence and uniform varieties grown over large areas. Moreover, cheaply available macronutrients have contributed to the negative effects of the nutrition transition, including obesity, heart disease and diabetes.
So why then am I hopeful? Because the data, and some literature, and my own direct experience also indicate that diets in recent years, in some countries, are beginning to move in different directions, reducing the excessive use of animal products and other energy-dense and environmentally expensive foods, and becoming more diverse, particularly with regard to fruits and vegetables, and even healthy grains. What better evidence than quinoa, which was relatively unknown outside the Andes a couple of decades ago, and is now cultivated in 100 countries and consumed in even more?
When we published our findings of increasing homogeneity in global food supplies, we hadn’t yet found a good way to make the underlying national-level data readily visible to interested readers. This is why I’m tremendously excited to announce the publication of our new Changing Global Diet website, which provides interactive visuals for 152 countries over 50 years of change. We that hope you will enjoy your own investigations of dietary change over time. Perhaps you can tell us where you think the changing global diet is headed.
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 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.
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.
