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crop science Archives - Page 3 of 5 - The Global Plant Council

Apr 13
1

Roots of a second green revolution

By | Blog, Research

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.

Apr 06
0

Creole maize reveals adaptation secrets

By | Blog, Future Directions

By Lucina Melesio

[MEXICO CITY] An international team of scientists identified a hundred genes that influence adaptation to the latitude, altitude, growing season and flowering time of nearly 4,500 native maize varieties in Mexico and in almost all Latin American and Caribbean countries.

Creole — or native — varieties of maize are derived from improvements made over thousands of years by local farmers, and contain genes that help them adapt to different environments.

“We are now using this analysis to find other genes that are of vital importance to breeders, such as those resistant to extreme heat, frost or drought — environmental conditions associated with climate change and that could affect maize production.”

Sarah Hearne, CIMMYT

“Latin American breeders will be able to use these results to identify native varieties that could contribute to improved adaptation”, Edward Buckler, a Cornell University researcher and co-author of the study published in Nature Genetics (February 6), told SciDev.Net.

The information on the genetic markers described in the study will be available online, said Sarah Hearne, a researcher at the International Maize and Wheat Improvement Center (CIMMYT) and co-author of the study. “Meanwhile, any breeder can contact us to request information”, she said.

“We are now using this analysis to find other genes that are of vital importance to breeders, such as those resistant to extreme heat, frost or drought — environmental conditions associated with climate change and that could affect maize production”, Hearne said.

Maize ears from CIMMYT’s collection, showing a wide variety of colors and shapes. CIMMYT’s germplasm bank contains about 28,000 unique samples of cultivated maize and its wild relatives, teosinte and Tripsacum. These include about 26,000 samples of farmer landraces—traditional, locally-adapted varieties that are rich in diversity. The bank both conserves this diversity and makes it available as a resource for breeding.
Photo credit: Xochiquetzal Fonseca/CIMMYT.

Studying native maize varieties is extremely difficult because of their genetic variation. Although domesticated, they are wilder than commercial varieties.

For this study, the researchers cultivated hybrid creole varieties in various environments in Latin America and identified regions of the genome that control growth rates. They looked into where the varieties came from and what genetic features contributed to their growth in that environment.

 In comments to SciDev.Net, James Holland, a researcher at North Carolina State University, Jeffrey Ross-Ibarra, a researcher at the University of California Davis, and Rodomiro Ortiz, a researcher at the Swedish University of Agricultural Sciences — who did not participate in the study — commended the magnitude of the study and the original method developed by the researchers to access the rich set of genetic information about native maize varieties.

Hearne added that the research team has initiated a “pre-breeding” programme with a small group of breeders in Mexico. As part of that programme, CIMMYT delivers to breeders materials from its germplasm bank of Creole maize; it also provides molecular information the breeders can use to generate new varieties.

This piece was produced by SciDev.Net’s Latin America and Carribean edition.

This article was originally published on SciDev.Net. Read the original article.

Mar 31
0

Global Plant Council stress resilience commentaries published in Food and Energy Security

By | Blog, Scientific Meetings, SEB

In October 2015, researchers from around the world came together in Iguassu Falls, Brazil, for the Stress Resilience Symposium, organized by the Global Plant Council and the Society for Experimental Biology (SEB), to discuss the current research efforts in developing plants resistant to the changing climate. (See our blog by GPC’s Lisa Martin for more on this meeting!)

Building on the success of the meeting, the Global Plant Council team and attendees compiled a set of papers to provide a powerful call to action for stress resilience scientists around the world to come together to tackle some of the biggest challenges we will face in the future. These four papers were published in the Open Access journal Food and Energy Security alongside an editorial about the Global Plant Council.

In the editorial, the Global Plant Council team (Lisa Martin, Sarah Jose, and Ruth Bastow) introduce readers to the Global Plant Council mission, and describe the Stress Resilience initiative, the meeting, and introduce the papers that came from it.

In the first of the commentaries, Matthew Gilliham (University of Adelaide), Scott Chapman (CSIRO), Lisa Martin, Sarah Jose, and Ruth Bastow discuss ‘The case for evidence-based policy to support stress-resilient cropping systems‘, commenting on the important relationships between research and policy and how each must influence the other.

Global Plant Council President Bill Davies (Lancaster University) and CIMMYT‘s Jean-Marcel Ribaut outline the ways in which research can be translated into locally adapted agricultural best practices in their article, ‘Stress resilience in crop plants: strategic thinking to address local food production problems‘.

In the next paper, ‘Harnessing diversity from ecosystems to crops to genes‘, Vicky Buchanan-Wollaston (University of Warwick), Zoe Wilson (University of Nottingham), François Tardieu (INRA), Jim Beynon (University of Warwick), and Katherine Denby (University of York) describe the challenges that must be overcome to promote effective and efficient international research collaboration to develop new solutions and stress resilience plants to enhance food security in the future.

University of Queensland‘s Andrew Borrell and CIMMYT‘s Matthew Reynolds discuss how best to bring together researchers from different disciplines, highlighting great examples of this in their paper, ‘Integrating islands of knowledge for greater synergy and efficiency in crop research‘.

In all of these papers, the authors suggest practical short- and long-term action steps and highlight ways in which the Global Plant Council could help to bring researchers together to coordinate these changes most effectively.

Read the papers in Food and Energy Security here.

Mar 14
0

Lentils under the lens: Improving genetic diversity for sustainable food security

By | Blog, Research

This week’s post comes to us from Crystal Chan, project manager of the Application of Genomic Innovation in the Lentil Economy project led by Dr. Kirstin Bett at the Department of Plant Sciences, University of Saskatchewan.

 

Could you begin with a brief introduction to your research?

Our research focuses on the smart use of diverse genetic materials and wild relatives in the lentil (Lens culinaris) breeding program.

Canada has become the world’s largest producer and exporter of lentils in recent years. Lentils are an introduced species to the northern hemisphere and, until recently, our breeding program at the University of Saskatchewan involved just a handful of germplasms adapted to our climatic condition. With dedicated breeding efforts we have achieved noteworthy genetic gains in the past decade, but we are missing out on the vast genetic diversity available within the Lens genus. This is a major dilemma faced by all plant breeders: do we want consistency (sacrificing genetic diversity and reducing genetic gains over time) or diversity (sacrificing some important fixed traits and spending lots of time and resources in “backcrossing/rescue efforts”)?

 

In our current research, we use genomic tools to understand the genetic variability found in different lentil genotypes and the basis of what makes lentils grow well in different global environments (North America vs. Mediterranean countries vs. South Asian countries). We will then develop molecular breeding tools that breeders can use to improve the diversity and productivity of Canadian lentils while maintaining their adaptation to the northern temperate climate.

 

What first led you to this research topic?

Dr. Albert (Bert) Vandenberg, professor and lentil breeder at the University of Saskatchewan, noticed one of the wild lentil species was resistant to several diseases that devastate the cultivated lentil. After years of dedicated breeding effort, he was able to transfer the resistance traits to the cultivated lentil, but it took a lot of time and resources. We began looking into other beneficial traits and became fascinated with the domestication and adaptation aspects of lentil – after all lentil is one of the oldest cultivated crops, domesticated by man around 11,000 BC! With the rapid advance in genomic technology, we can start to better understand the biology and develop tools to harness these valuable genetic resources.

 

You have been involved in the development of tools that assist researchers to build databases of genomics and genetics data. Could you tell us more about projects such as Tripal?

Over the past six years, Lacey Sanderson (bioinformaticist in our group) has developed a database for our pulse research program at the University (Knowpulse, http://knowpulse.usask.ca/portal/). The database is specifically designed to present data that is relevant to breeders, as our group has a strong focus on variety development for the Canadian pulse crop industry. Knowpulse houses genotypic information from past and on-going lentil genomics projects, and includes tools for looking up genotypes as well as comparing the current genome assembly (currently v1.2) and other sequenced legume genomes. The tools are being developed in Tripal, an open-source toolkit that provides an interface between the data and a Drupal web content management system, in collaboration with colleagues at Washington State University.

 

At the moment we are developing new functionalities that will allow us to store and present germplasm information as well as phenotypic data. We are also working with our colleagues at Washington State University (under the “Tripal Gateway Project” funded by the National Science Foundation) to enhance interconnectivity between Knowpulse and other legume databases, such as the Legume Information Service (LIS) and Soybase, to facilitate comparative genomic studies.

How challenging are pulse genomes to assemble? How closely related are the various crops?

We had the fortune to lead the lentil genome sequencing initiative thanks to the support from producer groups and governments across the globe.  The lentil genome is really challenging to assemble! We see nice synteny between lentil and the model legume, medicago, however the lentil genome is much bigger. We see a significant increase in genome size between chickpea and beans versus lentil (and pea for that matter), yet we have evidence to show that genome duplication is not the cause of the size increase. There are a lot of very long repetitive elements sprinkled around the genome, which makes its sequencing and proper assembly very challenging. Not to mention understanding the role of these long repetitive elements in biological functions…

 

What insights into crop domestication have you gained from these genomes?

That’s what we are working on right now under the AGILE (“Application of Genomics to Innovation in the Lentil Economy”) project. Stay tuned!

 

Do you work with breeders to develop new cultivars? What sorts of traits are most important? 

Breeding is at the core of our work – both Kirstin and Bert are breeders (Kirstin has an active dry bean breeding program when she’s not busy with genomic research). All our research aims to feed information to the breeders so that they can make better crossing and selection decisions. Our work in herbicide tolerance has led to the development and implementation of a molecular marker to screen for herbicide resistance. With that marker we save time (skipping a crossing cycle) and forego the herbicide spraying test for all of our early materials.

Disease resistance and drought tolerance are also important for the growers. Visual quality (seed shape, size, color) are very important too as our customers are very picky as to what sort of lentils they like to buy/eat.

What does the future of legume/lentil agriculture hold?

Lentils have been a staple food in many countries for centuries and have been gaining popularity in North America in recent years as people are looking for plant-based protein sources. Lentils are high in fibre, protein, and complex carbohydrates, while low in fat and calories, and have a low glycemic index. They are suitable for vegetarian/vegan, gluten-free, diabetic, and heart-smart diets. Lentils also provide essential micronutrients such as iron, zinc and folates. Lentils are widely recognized as nutrient-dense food that could serve as part of the solution to combat global food and nutritional insecurity.

In modern agriculture, adding lentil or other leguminous crops in the crop rotation helps improve soil structure, soil quality, and biotic diversity, as well as enhancing soil fertility through their ability to fix nitrogen. Because pulse crops require little to no nitrogen fertilizer, they use half of the non-renewable energy inputs of other crops, reducing greenhouse gas emissions.

2016 was marked by the United Nations as the International Year of Pulses, which was great as many people have become more aware of the benefits of pulse crops on the plate and in the field.

 

Follow us on twitter (@Wildlentils) for research updates!

 

All images are credited to Mr Derek Wright.

Mar 07
0

Sustainable, resilient, and nutritious food production with N8 AgriFood

By | Blog, Future Directions

This week we spoke with Dr Sally Howlett, a Knowledge Exchange Fellow with the N8 AgriFood Programme. (More on Sally at the end).

Sally, what is the N8 AgriFood Programme? When and why was it established?

The N8 Research Partnership is a collaboration of the eight most research-intensive universities in the North of England, namely Durham, Lancaster, Leeds, Liverpool, Manchester, Newcastle, Sheffield, and York. It is a not-for-profit organization with the aim of bringing together research, industry and society in joint initiatives. These partners have a strong track record of working together on large-scale, collaborative research projects, one of which is the N8 AgriFood Programme. This £16M multi-disciplinary initiative is funded by the N8 partners and HEFCE (The Higher Education Funding Council for England), and was launched in 2015 to address three key global challenges in Food Security: sustainable food production, resilient food supply chains, and improved nutrition and consumer behavior.

How does plant science research fit into the N8 AgriFood Programme?

There is a strong motivation to ‘think interdisciplinary’ when it comes to developing projects for the N8 AgriFood Programme; therefore, whilst the most obvious home for plant science may be within the theme of sustainable food production, e.g. crop improvement, we see no boundaries when it comes to integrating fundamental research in plant science with applications in all three of our research themes. The testing of research ideas in the ‘real world’ is supported by the five University farms within the N8, which include arable and livestock holdings.

We are launching a Crop Innovation Pipeline to assist with the translation of research into practical applications, with the first event taking place in Newcastle on 2nd-3rd May 2017. It is an opportunity for scientists from academia and industry and representatives from the farming community to discuss their ideas for the implementation of plant biology research into on-farm crop improvement strategies.

How is the work split between the different institutions? How is such a large-scale initiative managed?

Whilst there are many areas of shared expertise between the eight partner institutions, each also has its own areas of specialism within the agri-food arena. The strength of the N8 AgriFood Programme is in working collaboratively to identify complementary strengths and grow those areas in a synergistic way. In this way, we are collectively able to tackle research projects that would not be possible for a single university alone. Pump-priming funds are available at a local and strategic level to support this kick-starting of new multi-institution projects. The Programme itself is led out of the University of York, and each University has its own N8 AgriFood Chair in complementary areas across the Programme. Having both inward- and outward-facing roles, they work with the Knowledge Exchange Fellows and the Programme Lead for each theme to ensure activities at their own institute are connected with what is going on in the wider N8.

What does your work as a Knowledge Exchange Fellow entail?

As a Knowledge Exchange Fellow within the N8 AgriFood Programme, my initial contact with people usually begins with the question ‘What on earth does a Knowledge Exchange Fellow do?’ – and it can be quite difficult to answer! Although some form of knowledge transfer activity has been a defined output of research projects for some time now, knowledge exchange as an ongoing two-way dialogue between researchers and external stakeholders to enable a co-creation process has been less common until recently. Hence dedicated Knowledge Exchange Fellows with academic training are a relatively ‘new’, but growing, phenomenon.

My role is best described as acting as a bridge between the research community and non-academics with a vested interest in developing or using the findings of the research process. It is key to have a good understanding of the perspectives of all parties involved and be able to translate this into the appropriate language for a particular sector. Each of the N8 institutes has appointed Knowledge Exchange Fellow(s), and we work as a cohort to keep abreast of the latest developments in our fields in order to support the development of relationships and innovative projects. In such a huge undertaking, the phrase ‘there is strength in numbers’ is certainly apposite!

 

How does N8 AgriFood interact with companies?

N8 Agrifood engages with UK-based companies in many ways, including individual face-to-face meetings, attending and hosting networking events, participating in national exhibitions, and holding business-facing conferences. We also run a series of Industry Innovation Forums on various topics throughout the year. These provide a unique opportunity to discuss key challenges, identify problems and deliver new insights into innovation for agri-food, matching practical and technical industry challenges with the best research capabilities of the N8 universities.

 

How does N8 Agrifood interact with farmers?

As the engine of the agri-food industry, the views and collective experience of the farming community are vitally important in shaping the direction and content of the projects we develop. Co-hosting events with programs such as the ADAS Yield Enhancement Network (YEN), which involves over 100 farms, is one way that we connect with the sector. We are also working with agricultural societies to promote what we are doing and engage directly with their networks of farming members, e.g. the Yorkshire Agricultural Society’s Farmer Scientist Network. Last year we gave a series of seminars at the Great Yorkshire Show and are keen to encourage further collaboration with practicing farmers and growers across the UK.

 

Does N8 AgriFood collaborate with other research institutes around the world?

The N8 AgriFood Programme has strong international connections and actively welcomes working with international research institutes. Given the interconnectedness of our global food system, we feel that it is vital to link with overseas partners and that real impact can be had by bringing together top researchers from other countries to work together on problems. The value of N8 AgriFood as a one-stop shop is that we represent a large breadth and depth of expertise under a single umbrella, which greatly facilitates collaborating and finding suitable collaboration partners. Our pump-priming funds are a way for researchers to initiate new international partnerships, and we are also working to build links with global research organizations who have shared interests. For example, we recently visited Brazil and China to explore specific opportunities for collaboration and leveraging of research expertise and facilities, and are currently organizing a workshop in Argentina in March.

 

Where can readers get more information?

If you’d like to find out more, please visit our website: http://n8agrifood.ac.uk/, or consider attending one of our upcoming events:

 

All images are credited to the N8 Agrifood Programme.

Dr Sally Howlett is a Knowledge Exchange Fellow with the N8 AgriFood Programme. Her research background is in sustainable crop production and plant pest management.  After working on the control of invertebrate crop pests in New Zealand for several years, she returned to on-farm research in the UK and extended her focus to include the crops themselves taking a whole-systems view and comparing performance under conventional, organic and agroforestry management approaches. Sally’s role within N8 AgriFood provides a great opportunity to use her experience of agriculture and working with different actors across the sector to engage with external stakeholders, co-producing ideas and multi-disciplinary projects with applications throughout the agrifood chain.

Feb 24
0

Chickpea innovation: Revisiting the origins of crops to solve the challenges of modern agriculture

By | Blog, Future Directions
Doug Cook

Professor Doug Cook

This post was written by Professor Doug Cook (University of California, Davis), the Director of the Feed the Future Innovation Lab for Climate Resilient Chickpea. His current research spans both model and crop legume systems from a cellular to an ecosystem scale. 

 

The origins of modern human society derive, in large part, from the transition to an agrarian lifestyle that occurred in parallel at multiple locations around the world, including ~10,000 years ago in Mesopotamia*. Early agriculturalists wrought a revolution that would define human trajectory to the current day, domesticating wild plant and animal species into crops and livestock. The wild progenitors of chickpea, for example, were among a handful of Mesopotamian neo-crops, brought from hilly slopes into more fertile and cultivable plains and river valleys. In doing so, these farmers selected a small number of useful traits largely based on natural mutations that made wild forms amenable to agriculture, such as the consistency of flowering, upright growth, and seeds that remained attached to plants rather than dispersing.

Chickpea innovation

Doug Cook collecting chickpeas

Collecting wild chickpea plants, soil, and seed in southeastern Turkey. Image credit: Chickpea Innovation lab.

An unintended consequence of crop domestication was the loss of the vast majority of genetic diversity found in the wild populations. The Feed the Future Innovation Lab for Climate Resilient Chickpea at the University of California, Davis (Chickpea Innovation Lab) documented a ~95% loss of genetic variation from wild species to modern elite varieties. This reduction in genetic variation constrains our ability to adapt the chickpea crop to the range of challenges facing modern agriculture.

The Chickpea Innovation Lab is re-awakening the untapped potential of wild chickpea and directing that potential to solve global problems in agriculture, especially in the developing world.  Combining longstanding practices in ecology with the remarkable power of genomics and sophisticated computational methods, we have spanned the gap from the wild systems to cultivated crops. Beginning with the analysis of ~2,000 wild genomes, the simple technology of genetic crosses applied at massive scale has delivered a large and representative suite of wild variation into agricultural germplasm. These traits are now being actively used for phenotyping and breeding in the U.S., India, Ethiopia and Turkey, and our team is currently prospecting for tolerance to drought, heat and cold; increased pest and disease resistance; improved seed nutritional content; nitrogen fixation; plant architecture; and yield.

Characterizing wild germplasm

Sultan Mohammed Yimer

Visiting Ethiopian student, Sultan Mohammed Yimer investigating disease resistance in wild chickpea. Image credit: Chickpea Innovation lab.

Along the way, the Chickpea Innovation Lab has deposited wild germplasm into the multi-lateral system, providing open access to a treasure trove of genetic variation. The Chickpea Innovation Lab derives support from numerous sponsors whose funds enable the collection, characterization, and utilization of this vital germplasm resource.

International research

A unique strength of the lab is that our diverse sponsorship permits activities ranging from fundamental scientific investigation to applied agricultural research and product development.

An additional objective of the Lab is to train and educate students in the developing world. Towards that end, 18 international and nine domestic students, postdoctoral scientists and visiting faculty have received training in disciplines ranging from computational biology, plant pathology and entomology, to agricultural microbiology, and molecular genetics and breeding.

Chickpea breeding

Harvesting progeny derived by crossing wild and cultivated chickpea plants in Davis, California. Image credit: Chickpea Innovation lab.

* Mesopotamia, literally “between the rivers”, is the region of modern day southeastern Turkey, bounded by the Tigris and Euphrates rivers.

 

Feb 16
0

RNA clay offers green alternative to plant pesticides

By | Blog, Future Directions

By Neena Bhandari

A nano-sized bio-degradable clay-comprising double stranded ribonucleic acid (dsRNA) could offer a cost-effective, clean and green alternative to chemical-based plant pesticides.

Australian researchers from the University of Queensland have successfully used a gene-silencing spray, named BioClay, a combination of biomolecules and clay, to protect tobacco plants from a virus for 20 days with a single application. Their study has been published in Nature Plants.

“When BioClay is sprayed onto a plant, the virus-specific dsRNA is slowly released from the clay nanosheets into the plant. This activates a pathway in the plant that is a natural defence mechanism. The dsRNA is chopped up into small bits of RNA by enzymes of this pathway. These small bits attack the virus when it infects the plant without altering the plant genome,” explains lead researcher, Neena Mitter.

“Even with current pesticides, we lose up to 40 per cent of our crop productivity because of pests and pathogens. We are hoping that having BioClay in the mix as an environmentally friendly, sustainable crop protection measure will reduce crop losses,” Mitter adds.

“The clay-based delivery technology could represent a positive inflection point in the progress towards commercialisation of topical RNAi. This is a non-GM, environmentally benign and very specific technology.”

 John Killmer, APSE

While chemical-based pesticides kill the targeted insect, they can also affect a range of other insects that are beneficial. Mitter says, “BioClay is specific and it only kills the pathogen being targeted. Currently farmers use insecticides to kill the vector that comes with the viruses, but with BioClay we can target the virus itself.”

BioClay field trials may begin in Australia by year-end. “The first test will be on a virus that infects vegetable crops — capsicum, tomato, chilli,” Mitter tells SciDev.Net.

Farmers can use the existing equipment to deliver BioClay and the researchers are hopeful that it will be a commercially viable product for farmers everywhere. The clay component is cheap to make, but not the RNA.

Several companies like APSE, a US based startup, are working on the mass production of RNAs. APSE is developing RNA manufacturing technology for RNA interference (RNAi) or gene silencing applications.

“Our technology for RNA production should be ready in 2-3 years. We are targeting US$2 per gram,” APSE’s John Killmer tells SciDev.Net.

Killmer says, “The clay-based delivery technology could represent a positive inflection point in the progress towards commercialisation of topical RNAi. This is a non-GM, environmentally benign and very specific technology.”

RNAi technology is being used by many in the agriculture industry including the biotech firm Monsanto. The company’s BioDirect technology is focused on applications of RNAi directly onto the leaves of a plant.

Monsanto’s spokesperson John Combest tells SciDev.Net, “As insects develop resistance to certain classes of pesticides, giving farmers another option to control these pests is critical. The idea is not to replace any given system of farming, whether modern GM systems or others — it’s to provide farmers with products that can complement or replace agricultural chemical products.”

This piece was produced by SciDev.Net’s Asia & Pacific desk.

 

This article was originally published on SciDev.Net. Read the original article.

Feb 09
0

Mother grain genome: insights into quinoa

By | Blog, KAUST, Research

Sales of quinoa (Chenopodium quinoa) have exploded in the last decade, with prices more than tripling between 2008 and 2014. The popularity of this pseudocereal comes from its highly nutritious seeds, which resemble grains and contain a good balance of protein, vitamins, and minerals. The nourishing nature of quinoa meant it was prized by the Incas, who called it the “Mother grain”.

Quinoa

Quinoa is a popular ‘grain’, but it is more closely related to spinach and beetroot than cereals like wheat or barley. Image credit: Flickr user. Used under license: CC BY 2.0.

Quinoa is native to the Andes of South America, where it thrives in a range of conditions from coastal regions to alpine regions of up to 4000 m above sea level. Its resilience and nutritious seeds means that quinoa has been identified as a key crop for enhancing food security, but there are currently very few breeding programs targeting this species.

The challenge of improving the efficiency and sustainability of quinoa production has so far been restricted by the lack of a reference genome. This week, a team of researchers led by Professor Mark Tester (King Abdullah University of Science & Technology; KAUST) addressed this issue, publishing a high-quality genome sequence for quinoa in Nature. They compared the genome with that of related species to characterize the evolution and domestication of the crop, and investigated the genetic diversity of economically important traits.

 

The evolution of quinoa

Tester and colleagues used an array of genomics techniques to assemble 1.39 Gb of the estimated 1.45-1.50 Gb full length of quinoa’s genome. Quinoa is a tetraploid, meaning it has four copies of each chromosome. The researchers shed light on the evolutionary history of this crop by sequencing descendants of the two diploid species (each containing two sets of chromosomes) that hybridized to generate quinoa; kañiwa (Chenopodium pallidicaule) and Swedish goosefoot (Chenopodium suecicum). Comparing these sequences to quinoa and other relatives, the team showed that the hybridization event likely occurred between 3.3 and 6.3 million years ago. A comparison with other closely related Chenopodium species also suggested that, contrary to previous predictions, quinoa may have been domesticated twice, both in highland and coastal environments.

Quinoa field

Quinoa field. Image credit: LID. Used under license: CC BY-SA 2.0.

 

Washing away quinoa’s bitter taste

Quinoa seeds are coated with soap-like chemicals called saponins, which have a bitter taste that deters herbivores. Saponins can disrupt the cell membranes of red blood cells, so they have to be removed before human consumption, but this process is costly, so quinoa breeders are always looking for varieties that produce lower levels of saponins.

Sweet (low-saponin) quinoa strains do occur naturally, but the genes that regulate this phenotype were previously unknown. Tester and colleagues investigated sweet and bitter quinoa strains and discovered that a single gene (TRITERPENE SAPONIN BIOSYNTHESIS ACTIVATING REGULATOR-LIKE 1 [TSARL1]) controls the amount of saponins produced in the seeds. The low-saponin quinoa strains contained mutations in TSARL1 that prevented it from functioning properly. This is a key target for the improvement of quinoa in the future, although farmers will have to find new ways to protect their crops from birds and other seed predators!

Quinoa flowers

Quinoa flowers. Image credit: Alan Cann. Used under license: CC BY-SA 2.0.

 

Quality quinoa

The high-quality reference genome for quinoa generated by Tester and colleagues is likely to be vital for allowing many exciting improvements in the future. Breeders hoping to improve the yield, ease of harvest, stress tolerance, and saponin content of quinoa can develop genetic markers to speed up breeding for these key traits, improving the productivity of quinoa varieties and enhancing future food security.

 

Read the paper in Nature: Jarvis et al., 2017. The genome of Chenopodium quinoa. Nature. DOI: 10.1038/nature21370

Thank you to Professor Mark Tester (KAUST) for providing information used in this post!

Feb 01
0

The future of phenotyping

By | Blog, Future Directions, Research

This week’s post was written by Dr Kasra Sabermanesh, Rothamsted Research.

I am a post-doctoral research scientist within Rothamsted Research’s BBSRC-funded 20:20 Wheat® program, which aims to provide the knowledge base and tools to increase the UK wheat yield potential from 8.4 to 20 tons of wheat per hectare within the next 20 years. Field phenotyping is one component of this program and facilitates the non-destructive monitoring of field-grown crops. Traditional methods of field phenotyping require huge human effort, which consequently limits the accuracy, frequency, and number of different measurements that can be taken at one time. Fortunately, Rothamsted has an exciting solution to this problem.

The Field Scanalyzer

Kasra Sabermanesh

Dr Kasra Sabermanesh shows off the Field Scanalyzer. Image credit: Rothamsted Research

Our field phenotyping platform, the Field Scanalyzer (constructed by LemnaTec GmbH and being further developed by ourselves), supports a motorized measuring platform with multiple sensors that can be accurately positioned anywhere within a dedicated field. The sensor array comprises a high-definition RGB camera, two hyperspectral cameras, a thermal infrared camera, a system for imaging chlorophyll fluorescence and twin scanning lasers for 3D information capture. Together, these sensors generate a wealth of data about crop growth, architecture, performance, and health. The Field Scanalyzer operates autonomously and in high-throughput, meaning it can take a lot of non-destructive measurements without human supervision, throughout the crops lifecycle, with high-accuracy and reproducibility. (You can read more about the Field Scanalyzer in our recent paper: http://www.publish.csiro.au/FP/pdf/FP16163).

We are currently using the Field Scanalyzer to identify new characteristics of crops that relate to performance, as well as identifying new genetic diversity for existing traits. Outputs from either of these research components can be delivered to breeders. We are screening approximately 400 wheat varieties, but also imaging some oilseed rape and oat plants.

Rothamsted Research

The scanalyzer. Image credit: Rothamsted Research

The big data problem

The Field Scanalyzer at Rothamsted is a world first, so we initially had to develop all the necessary image acquisition protocols and image processing tools, in order to exploit its full capabilities. A number of image processing tools are available; however, they are not suitable for field-grown crops, as they were not developed for complex canopies consisting of hundreds of plants in highly dynamic ambient conditions. The platform can generate up to 100 TB data with a year’s continuous operation (using all of the sensors). That’s why I work with two other post-docs to develop robust computer vision tools to automate the way we extracting quantitative image datasets. We are also validating the accuracy of the values extracted from our images by comparing them with measurements obtained manually.

Approximately 1.5 years have passed since we first began operating the Field Scanalyzer, and we have now optimized all of our image acquisition protocols and have collected a full seasonal dataset. With the good quality images stored in our database, we have developed some robust tools to automatically extract the information about some key growth stages (ear emergence and flowering), as well as quantifying height and the number of some plant organs. We are still just scraping the surface though, and have a list of traits for which we want to develop computer vision tools, in order to automatically analyze them.

Take to the skies: Drones for data collection

Some of my colleagues work with drones (UAVs) to capture information about crop height, plant density (Normalized Difference Vegetation Index), and canopy temperature from large-scale field trials containing 5000 plots. They also fly the UAVs over our Field Scanalyzer site, so we can compare data collected from the higher flying UAV with those collected from the Field Scanalyzer at close proximity. The way we see it, UAVs can image large fields in a very short time (15 min), so if we notice something interesting using the UAV at the large plot-scale, we can put the material under the Field Scanalyzer for high-resolution phenotyping. On the other hand, with the Field Scanalyzer, once we gain a better understanding of which trait/s we need to focus on, when we should be looking at them, and exactly which sensor/s are required to quantify the trait, we can deploy drones with the necessary sensors (once the sensors are portable enough) to collect this information at field-scale and at the appropriate time.

Drones at Rothamsted

Taking to the skies: Drones are used for large-scale phenotyping at Rothamsted. Credit: Rothamsted Research.

The future of phenotyping

I envision that the future of phenotyping technology will focus on reducing the cost and size of cameras/sensors, ultimately increasing their portability and accessibility. This will result in more sophisticated cameras being attached to UAVs (as many of sensors we currently use far out-weigh a UAV’s payload). Parallel to this, research efforts are focusing on developing image processing systems that efficiently extract quantitative information about the crops from acquired images. Together, phenotyping systems such as low-flying UAVs that generate easily interpreted data outputs could be developed, which may be more widely adopted by breeders and farmers to get a deeper insight into their crop’s health and performance.

Jan 05
0

2016 Plant Science Round Up

By | Blog, Research

Another fantastic year of discovery is over – read on for our 2016 plant science top picks!

January

Zostera marina

A Zostera marina meadow in the Archipelago Sea, southwest Finland. Image credit: Christoffer Boström (Olsen et al., 2016. Nature).

The year began with the publication of the fascinating eelgrass (Zostera marina) genome by an international team of researchers. This marine monocot descended from land-dwelling ancestors, but went through a dramatic adaptation to life in the ocean, in what the lead author Professor Jeanine Olsen described as, “arguably the most extreme adaptation a terrestrial… species can undergo”.

One of the most interesting revelations was that eelgrass cannot make stomatal pores because it has completely lost the genes responsible for regulating their development. It also ditched genes involved in perceiving UV light, which does not penetrate well through its deep water habitat.

Read the paper in Nature: The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea.

BLOG: You can find out more about the secrets of seagrass in our blog post.

 

February 

Plants are known to form new organs throughout their lifecycle, but it was not previously clear how they organized their cell development to form the right shapes. In February, researchers in Germany used an exciting new type of high-resolution fluorescence microscope to observe every individual cell in a developing lateral root, following the complex arrangement of their cell division over time.

Using this new four-dimensional cell lineage map of lateral root development in combination with computer modelling, the team revealed that, while the contribution of each cell is not pre-determined, the cells self-organize to regulate the overall development of the root in a predictable manner.

Watch the mesmerizing cell division in lateral root development in the video below, which accompanied the paper:


Read the paper in Current Biology: Rules and self-organizing properties of post-embryonic plant organ cell division patterns.

 

March

In March, a Spanish team of researchers revealed how the anti-wilting molecular machinery involved in preserving cell turgor assembles in response to drought. They found that a family of small proteins, the CARs, act in clusters to guide proteins to the cell membrane, in what author Dr. Pedro Luis Rodriguez described as “a kind of landing strip, acting as molecular antennas that call out to other proteins as and when necessary to orchestrate the required cellular response”.

Read the paper in PNAS: Calcium-dependent oligomerization of CAR proteins at cell membrane modulates ABA signaling.

*If you’d like to read more about stress resilience in plants, check out the meeting report from the Stress Resilience Forum run by the GPC in coalition with the Society for Experimental Biology.*

 

April

Arbuscular mycorrhizal fungi.

This plant root is infected with arbuscular mycorrhizal fungi. Image credit: University of Zurich.

In April, we received an amazing insight into the ‘decision-making ability’ of plants when a Swiss team discovered that plants can punish mutualist fungi that try to cheat them. In a clever experiment, the researchers provided a plant with two mutualistic partners; a ‘generous’ fungus that provides the plant with a lot of phosphates in return for carbohydrates, and a ‘meaner’ fungus that attempts to reduce the amount of phosphate it ‘pays’. They revealed that the plants can starve the meaner fungus, providing fewer carbohydrates until it pays its phosphate bill.

Author Professor Andres Wiemsken explains: “The plant exploits the competitive situation of the two fungi in a targeted manner, triggering what is essentially a market-based process determined by cost and performance”.

Read the paper in Ecology Letters: Options of partners improve carbon for phosphorus trade in the arbuscular mycorrhizal mutualism.

 

May

The transition of ancient plants from water onto land was one of the most important events in our planet’s evolution, but required a massive change in plant biology. Suddenly plants risked drying out, so had to develop new ways to survive drought.

In May, an international team discovered a key gene in moss (Physcomitrella patens) that allows it to tolerate dehydration. This gene, ANR, was an ancient adaptation of an algal gene that allowed the early plants to respond to the drought-signaling hormone ABA. Its evolution is still a mystery, though, as author Dr. Sean Stevenson explains: “What’s interesting is that aquatic algae can’t respond to ABA: the next challenge is to discover how this hormone signaling process arose.”

Read the paper in The Plant Cell: Genetic analysis of Physcomitrella patens identifies ABSCISIC ACID NON-RESPONSIVE, a regulator of ABA responses unique to basal land plants and required for desiccation tolerance.

 

June

Knoblauch with phloem

Professor Michael Knoblauch shows off a microscope image of phloem tubes. Image credit: Washington State University.

Sometimes revisiting old ideas can pay off, as a US team revealed in June. In 1930, Ernst Münch hypothesized that transport through the phloem sieve tubes in the plant vascular tissue is driven by pressure gradients, but no-one really knew how this would account for the massive pressure required to move nutrients through something as large as a tree.

Professor Michael Knoblauch and colleagues spent decades devising new methods to investigate pressures and flow within phloem without disrupting the system. He eventually developed a suite of techniques, including a picogauge with the help of his son, Jan, to measure tiny pressure differences in the plants. They found that plants can alter the shape of their phloem vessels to change the pressure within them, allowing them to transport sugars over varying distances, which provided strong support for Münch flow.

Read the paper in eLife: Testing the Münch hypothesis of long distance phloem transport in plants.

BLOG: We featured similar work (including an amazing video of the wound response in sieve tubes) by Knoblauch’s collaborator, Dr. Winfried Peters, on the blog – read it here!

 

July

Ancient barley grain

Preserved remains of rope, seeds, reeds and pellets (left), and a desiccated barley grain (right) found at Yoram Cave in the Judean Desert. Credit: Uri Davidovich and Ehud Weiss.

In July, an international and highly multidisciplinary team published the genome of 6,000-year-old barley grains excavated from a cave in Israel, the oldest plant genome reconstructed to date. The grains were visually and genetically very similar to modern barley, showing that this crop was domesticated very early on in our agricultural history. With more analysis ongoing, author Dr. Verena Schünemann predicts that “DNA-analysis of archaeological remains of prehistoric plants will provide us with novel insights into the origin, domestication and spread of crop plants”.

Read the paper in Nature Genetics: Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley.

BLOG: We interviewed Dr. Nils Stein about this fascinating work on the blog – click here to read more!

 

August

Another exciting cereal paper was published in August, when an Australian team revealed that C4 photosynthesis occurs in wheat seeds. Like many important crops, wheat leaves perform C3 photosynthesis, which is a less efficient process, so many researchers are attempting to engineer the complex C4 photosynthesis pathway into C3 crops.

This discovery was completely unexpected, as throughout its evolution wheat has been a C3 plant. Author Professor Robert Henry suggested: “One theory is that as [atmospheric] carbon dioxide began to decline, [wheat’s] seeds evolved a C4 pathway to capture more sunlight to convert to energy.”

Read the paper in Scientific Reports: New evidence for grain specific C4 photosynthesis in wheat.

 

September

CRISPR lunch

Professor Stefan Jansson cooks up “Tagliatelle with CRISPRy fried vegetables”. Image credit: Stefan Jansson.

September marked an historic event. Professor Stefan Jansson cooked up the world’s first CRISPR meal, tagliatelle with CRISPRy fried vegetables (genome-edited cabbage). Jansson has paved the way for CRISPR in Europe; while the EU is yet to make a decision about how CRISPR-edited plants will be regulated, Jansson successfully convinced the Swedish Board of Agriculture to rule that plants edited in a manner that could have been achieved by traditional breeding (i.e. the deletion or minor mutation of a gene, but not the insertion of a gene from another species) cannot be treated as a GMO.

Read more in the Umeå University press release: Umeå researcher served a world first (?) CRISPR meal.

BLOG: We interviewed Professor Stefan Jansson about his prominent role in the CRISPR/GM debate earlier in 2016 – check out his post here.

*You may also be interested in the upcoming meeting, ‘New Breeding Technologies in the Plant Sciences’, which will be held at the University of Gothenburg, Sweden, on 7-8 July 2017. The workshop has been organized by Professor Jansson, along with the GPC’s Executive Director Ruth Bastow and Professor Barry Pogson (Australian National University/GPC Chair). For more info, click here.*

 

October

Phytochromes help plants detect day length by sensing differences in red and far-red light, but a UK-Germany research collaboration revealed that these receptors switch roles at night to become thermometers, helping plants to respond to seasonal changes in temperature.

Dr Philip Wigge explains: “Just as mercury rises in a thermometer, the rate at which phytochromes revert to their inactive state during the night is a direct measure of temperature. The lower the temperature, the slower phytochromes revert to inactivity, so the molecules spend more time in their active, growth-suppressing state. This is why plants are slower to grow in winter”.

Read the paper in Science: Phytochromes function as thermosensors in Arabidopsis.

 

November

Ginkgo

A fossil ginkgo (Ginkgo biloba) leaf with its modern counterpart. Image credit: Gigascience.

In November, a Chinese team published the genome of Ginkgo biloba¸ the oldest extant tree species. Its large (10.6 Gb) genome has previously impeded our understanding of this living fossil, but researchers will now be able to investigate its ~42,000 genes to understand its interesting characteristics, such as resistance to stress and dioecious reproduction, and how it remained almost unchanged in the 270 million years it has existed.

Author Professor Yunpeng Zhao said, “Such a genome fills a major phylogenetic gap of land plants, and provides key genetic resources to address evolutionary questions [such as the] phylogenetic relationships of gymnosperm lineages, [and the] evolution of genome and genes in land plants”.

Read the paper in GigaScience: Draft genome of the living fossil Ginkgo biloba.

 

December

The year ended with another fascinating discovery from a Danish team, who used fluorescent tags and microscopy to confirm the existence of metabolons, clusters of metabolic enzymes that have never been detected in cells before. These metabolons can assemble rapidly in response to a stimulus, working as a metabolic production line to efficiently produce the required compounds. Scientists have been looking for metabolons for 40 years, and this discovery could be crucial for improving our ability to harness the production power of plants.

Read the paper in Science: Characterization of a dynamic metabolon producing the defense compound dhurrin in sorghum.

 

Another amazing year of science! We’re looking forward to seeing what 2017 will bring!

 

P.S. Check out 2015 Plant Science Round Up to see last year’s top picks!