Synthetic biology in chloroplasts

Dr Anil Day, University of Manchester

Dr Anil Day, University of Manchester

This week we spoke to Dr. Anil Day, a synthetic biologist at the University of Manchester who has developed an impressive array of tools and techniques to transform chloroplast genomes.

 

Could you begin by giving our readers a brief overview of synthetic biology?

Synthetic biology involves the application of engineering principles to biological systems. One approach to understanding a biological system is to break it down into smaller parts, which can be used to design new properties. These redesigned pieces can be reassembled into a new system, tested experimentally, and refined in an iterative process. Synthetic biology projects that are underway in our lab include designing plastids such as chloroplasts with new metabolic functions, and in the longer term the design and assembly of synthetic chloroplast genomes.

 

Anil Day examines transformed plants

Dr. Anil Day examines a cabinet of transformed plants. Credit: Dr. Anil Day.

Why do you use chloroplasts for synthetic biology systems?

Chloroplasts have a relatively small genome, coding for about 100 genes. Importantly, exogenous (foreign) genes coding for new functions can be precisely introduced into the chloroplast genome. All of the plastids within a plant contain the same genome so, once established, the user-designed reprogrammed plastids will be present throughout the plant. Chloroplasts can also produce very high levels of protein; researchers have achieved expression levels where over 70% of the total soluble protein in the leaves is the engineered protein. Expression in tomato fruit is also possible.

Multiple genes can be introduced into chloroplasts and expressed coordinately, allowing the metabolic engineering of more complex processes. The upper size limit for insertions is not known but is likely to be above the 50,000 nucleotide insertion achieved to date. Furthermore, chloroplasts and other plastids are important metabolic hubs and contain a wide variety of chemical substrates useful for metabolic engineering.

Plastids in plants

Plants have several types of plastids, including green photosynthetic chloroplasts, pigment-containing chromoplasts, and starch-containing amyloplasts. Credit: Dr. Anil Day.

 

Could you describe the current state of our ability to engineer chloroplasts?

Chloroplast engineering is routine in many labs around the globe. Although there are multiple chloroplasts in every cell, the process of converting all the chloroplasts to a single population of engineered genomes is not an issue. Most researchers use the tobacco plant because it is easily transformed, but other crops are amenable to transformation, including oilseed rape, soybean, tomato, and potato (cereals such as rice and wheat are more problematic). There has been progress with developing the inducible expression of exogenous genes in chloroplasts too.

 

What challenges/differences do you face when transforming chloroplast genomes when compared to the nuclear genome?

Typical genetic modification of the DNA in the nucleus is performed by introducing exogenous genes in T-DNA. T-DNA is transferred to the plant using the bacterium Agrobacterium tumefaciens, which is an efficient process, but the T-DNA integrates ‘randomly’ at many sites within chromosomes and different lines can have variable expression levels due to positional effects and gene silencing.

A. tumefaciens-mediated gene delivery systems do not work for chloroplast transformation. Most chloroplast transformation labs introduce genes into plastids by blasting cells with gold or tungsten particles coated with DNA. Because chloroplast genomes are present in multiple copies per cell, the process of converting all resident chloroplasts to the transgenic genome requires a continued period of selection. This means that the isolation of chloroplast transformants can take slightly longer than nuclear transformation. In our lab, we speed up this process by using restoration of photosynthesis to select chloroplasts with exogenous genes. Once plants with a uniform population of transgenic plastid genomes have been isolated, the transgenes are stable and inherited through the maternal line.

For the novice, I would say nuclear transformation using A. tumefaciens is easier to accomplish than chloroplast transformation.

 

Edited chloroplasts

A tobacco plant containing leaf areas with edited (pale green) and normal (darker green) chloroplasts. Credit: Dr. Anil Day.

Last year you reported that chloroplasts degrade in mature sperm cells just prior to fertilization. Could you elaborate on how this might be utilized in future crop breeding?

Chloroplasts are inherited from the female parent in wheat. This is useful because it restricts the pollen-mediated spread of chloroplast-localized transgenes into the environment. Previously, no-one had studied the mechanism of maternal chloroplast inheritance in wheat using modern cell biology tools. With our collaborators Lucia PrimavesiHuixia Wu, and Huw Jones at Rothamsted Research, we developed an efficient method to observe small non-green plastids in wheat pollen in real time. We found that the plastids were destroyed during the maturation of sperm cells, which explained the absence of paternal plastids in the offspring.

This discovery has applications in crop breeding. Anther culture is a powerful technique where new homozygous plants can be produced by doubling the chromosome numbers of haploid plants regenerated from pollen. This technique has been challenging in cereals, as chloroplast degradation in pollen leads to a high percentage of albino plants (in some cases 100% albinos). Understanding how to prevent the destruction of plastids in pollen sperm cells will improve this technique in cereals, which could speed up crop breeding in the future.

 

Selection of transformed plants

Transformed plantlets are selected by their ability to survive on a herbicide-containing agar plate, and can then be grown up into mature plants. Credit: Dr. Anil Day.

 What sorts of processes have you successfully transformed into chloroplasts, and what kinds of results have you achieved?

We have expressed a variety of exogenous genes in chloroplasts, from those conferring resistance to herbicides to vaccine epitopes and pharmaceutical proteins:

  • Plants expressing the bar gene in chloroplasts were resistant to the herbicide glufosinate (also known as phosphinothricin).
  • A chloroplast-expressed viral epitope was used to identify samples of human blood infected with the hepatitis C virus.
  • Human transforming growth factor 3 (hTGFβ3), a potential wound healing drug, accumulated to high concentrations in chloroplasts, and could be processed to a pure active form resembling clinical grade hTGFβ3.
  • In collaboration with Ray Dixon, Cheng Qi, and Mandy Dowson-Day at the John Innes Centre, we investigated the feasibility of introducing nitrogen-fixing genes into chloroplasts. This work was initiated in a unicellular green alga with the bacterial nifH gene.

 

What is the cutting edge of chloroplast transformation research?

Chloroplast genes are important for plant growth and development but they are difficult to improve by conventional breeding methods. We recently developed a method to edit plastid genomes, which allows beneficial single point mutations to be introduced into chloroplast genes. This is important because the resulting plants have an identical genome to the original cultivar apart the single base substitution, potentially leading to a new class of biotech crop.

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

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.

Sustainable, resilient, and nutritious food production with N8 AgriFood

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.

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

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.

 

RNA clay offers green alternative to plant pesticides

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.

Mother grain genome: insights into quinoa

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!

Drought-resistant grass to spur milk production

By Baraka Rateng’

Struggling East African dairy farmers could benefit from new varieties of high-quality, drought-resistant forage grass known as Brachiaria that boosts milk production by 40 per cent, a report says.

The forage grass could enable farmers to increase their incomes, according to experts at the Colombia-headquartered International Center for Tropical Agriculture (CIAT) – a CGIAR Research Center.

Steven Prager, a co-author of the report —  which was published last month — and a senior scientist in integrated modelling at the CIAT, says the report  was based on many years of forage research in Latin America and the Caribbean, and recent field trials in Kenya and Rwanda from 2011 to 2016.

According to Prager, the study demonstrates the high potential for improved forages in East Africa and high payoff for investment in improved forages.

“The results are based on multiple scenarios of an economic surplus model with inputs derived from a combination of databases, feedback from subject matter experts and a literature review,” he explains, adding that the economic analysis was carried out at CIAT headquarters with the support of tropical forage experts in East Africa.

Drought resistant grass
“The objective of this study was to understand the potential payoff for investment in action to improve dissemination and use of improved forages,” Prager tells SciDev.Net.

“The objective of this study was to understand the potential payoff for investment in action to improve dissemination and use of improved forages.”

Steven Prager, International Center for Tropical Agriculture (CIAT)

One of the big unknowns in the development and implementation of agricultural technology, according to Prager, is how many potential users are required to make it worthwhile to invest in the development and designation of different technologies.

Solomon Mwendia, a co-author of the report and forage agronomist at CIAT, Kenya, says the Brachiaria grass is climate-friendly and has high crude protein and less fiber, which leads to better use and digestion by cattle, in turn leading to less methane gas produced for each unit of livestock product such as milk or meat. Methane is one of the gases associated with global warming.

“This grass is relatively drought-tolerant compared to the Napier or elephant grass commonly used in East Africa. In addition, the grass can easily be conserved as hay for utilisation during forages scarcity or for sale,” Mwendia adds.

Smallholder dairy farming is important in East Africa for household nutrition and income. In Kenya, for instance, Mwendia says that milk production increased by 150 per cent between 2004 and 2012, from 197.3 million litres to 497.9 million litres.


East Africa cattle density 


The grass is native to Africa, according to Mwendia. It can grow in areas with up to 3,000 millimetres of rainfall and also withstand dry seasons of three to six months during which the leaf may remain green while other tropical species die. These conditions exist in other regions outside eastern Africa such as in Democratic Republic of Congo, Malawi, Zambia and Zimbabwe.

Sita Ghimire, a senior scientist at the Biosciences eastern and central Africa (BecA) Hub, who leads a research programme that focuses on Brachiaria, says 40 per cent increase in milk production is achievable in East Africa after feeding livestock with Brachiaria.


Livestock production in East Africa 


“Forage has been always a major challenge in livestock production in East Africa. It is mainly because of declining pastureland, frequent and prolonged drought and not many farmers conserve forage for dry season,” Ghimire says.

The major challenges for adoption of Brachiaria technology in East Africa are limited availability of seeds or  vegetative materials, lack of standardised agronomic practices for different production environments and lack of varieties that are well adapted to East African environment, Ghimire explains, citing other challenges such as pest and diseases, and low funding forage research and development.

This piece was produced by SciDev.Net’s Sub-Saharan Africa English desk.

References

Carlos González and others Improved forages and milk production in East Africa. A case study in the series: Economic foresight for understanding the role of investments in agriculture for the global food system (October 2016, Internacional de Agricultura Tropical [CIAT])

 

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Break down barriers between seed banks and field study

By Marie Haga , Ann Tutwiler

Food biodiversity needs both systems, just like pandas need zoos and bamboo forests, say Marie Haga and Ann Tutwiler.

The efforts of many organisations mean that most of us understand the importance of conserving the biodiversity of wild animals and their habitats.  But few of us think about food in the same way we think about pandas, even though the issues are much the same.

The effective and efficient conservation of agricultural biodiversity — the biodiversity that’s important for providing the food we eat — is vital to meeting the global challenges of food and nutritional security for an expanding world population under the threat of climate change, and growing pressures on land and water.

And as with pandas and other wild animals, conservation of agricultural biodiversity can and must be done both in the laboratory and in the field.

From pandas to seeds

If you had a choice, would you rather see a panda in a zoo, or in the bamboo forests of southern China?

For most of us, seeing wild and endangered animals in their own habitat and watching how they behave, adapt and survive in their natural surroundings would be the preferred choice. But, the role of zoos in conserving wild and endangered animals is equally important.

Many zoos are home to breeding programmes. These can help re-introduce animals into wild areas from which they have disappeared, and maintain the genetic diversity of small populations of threatened species.  Zoos that are well-run carry out vital conservation research and can increase public support for conservation. And the only chance that most of us (and our kids) will have to see a panda is in a zoo.

Much in the same way, and for several decades now, dedicated researchers around the world have invested a great deal of effort in collecting and storing the seeds of different varieties of crops in genebanks, for what’s called ex situ conservation. Their collective work has created a precious global collection of over seven million seed, tissue, and other samples in many global and national genebanks.

“The problem is that systems of in situ and ex situ conservation have been largely disconnected for some time. Some conservationists even see them as antagonistic.

And while devotees of one side argue with the other, the diversity that underpins the food we eat is lost both in genebanks and in farmers’ fields.”

Marie Haga and Ann Tutwiler

At the same time, some concerns that apply to zoos — that they cannot maintain the evolutionary dynamics which allow ‘wild’ animals to evolve and adapt, for example — also apply to seed banks.

Researchers are increasingly recognising that in situ conservation is also important: maintaining crop and livestock diversity in farmers’ fields and farms, gardens, orchards, and the natural landscapes in which these are embedded.

A call for collaboration

Ex situ and in situ conservation each has their benefits.

It is relatively cheap to maintain crop diversity in a genebank, where it is safe from the vagaries of changing climates, and is readily accessible for research and breeding. But crop diversity stored in genebank is less accessible to farmers, and is not exposed to changing environments — which means it does not evolve and adapt.

On the other hand, crop diversity in farmers’ fields and under other in situ conditions, continues to evolve and adapt as a result of natural and human selections.  As it evolves and adapts, this genetic diversity contributes directly to the resilience and sustainability of agricultural systems, as well as to farmers’ livelihoods and to their empowerment. But there’s a downside: it is more difficult for breeders to use in their crop improvement programmes.

This shouldn’t be about choosing one over the other — the world needs both conservation systems, with good communication channels and knowledge transfer between them. This will help to properly conserve the genepools of crops and make them available for use into the future, for food and nutritional security.

The problem is that systems of in situ and ex situ conservation have been largely disconnected for some time. Some conservationists even see them as antagonistic.

And while devotees of one side argue with the other, the diversity that underpins the food we eat is lost both in genebanks and in farmers’ fields.

Crop diversity in farmer’s fields continues to decline in many parts of the world, often driven by market forces beyond the control of farmers’ themselves. Diversity is also lost from genebanks — a shortage of funding and staff means collections are often poorly maintained.

But if we stop looking at these two forms of conservation as antagonistic but rather as complementary, attention can be focused on what matters most: how best to safeguard this diversity for the future.

First steps

The First International Agrobiodiversity Conference is an opportunity to begin anew. That’s why practitioners in all these fields, from all over the world, both industrialized and developing, and from both the formal and informal sector, are coming together in New Delhi, India this week.

This congress gives conservation and agro-biodiversity experts and policy makers the opportunity to start mapping out a future that breaks down barriers between the two approaches, integrating them to ensure global food and nutritional security.

Most importantly, this means helping politicians and the public understand that conserving the diversity of our food is just as important as conserving the diversity of wild animals.

The congress is a first step in the right direction.

Marie Haga is executive director of The Crop Trust, and Ann Tutwiler is director general of Bioversity International. Haga can be contacted on Twitter at @CropTrust, and Tutwiler at @AnnTutwiler

 

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Genome editing: an introduction to CRISPR/Cas9

Damiano Martignago

Dr Damiano Martignago, Rothamsted Research

This week’s blog post was written by Dr Damiano Martignago, a genome editing specialist at Rothamsted Research.

 

Genome editing technologies comprise a diverse set of molecular tools that allow the targeted modification of a DNA sequence within a genome. Unlike “traditional” breeding, genome editing does not rely on random DNA recombination; instead it allows the precise targeting of specific DNA sequences of interest. Genome editing approaches induce a double strand break (DSB) of the DNA molecule at specific sites, activating the cell’s DNA repair system. This process could be either error-prone, thus used by scientists to deactivate “undesired” genes, or error-free, enabling target DNA sequences to be “re-written” or the insertion of DNA fragments in a specific genomic position.

The most promising among the genome editing technologies, CRISPR/Cas9, was chosen as Science’s 2015 Breakthrough of the Year. Cas9 is an enzyme able to target a specific position of a genome thanks to a small RNA molecule called guide RNA (gRNA). gRNAs are easy to design and can be delivered to cells along with the gene encoding Cas9, or as a pre-assembled Cas9-gRNA protein-RNA complex. Once inside the cell, Cas9 cuts the target DNA sequence homologous to the gRNAs, producing DSBs.

CRISPR/Cas9

The guide RNA (sgRNA) directs Cas9 to a specific region of the genome, where it induces a double-strand break in the DNA. On the left, the break is repaired by non-homologous-end joining, which can result in insertion/deletion (indel) mutations. On the right, the homologous-directed recombination pathway creates precise changes using a supplied template DNA. Credit: Ran et al. (2013). Nature Protocols.

 

Genome editing in crops

Together with the increased data availability on crop genomes, genome editing techniques such as CRISPR are allowing scientists to carry out ambitious research on crop plants directly, building on the knowledge obtained during decades of investigation in model plants.

The concept of CRISPR was first tested in crops by generating cultivars that are resistant to herbicides, as this is an easy trait to screen for and identify. One of the first genome-edited crops, a herbicide-resistant oilseed rape produced by Cibus, has already been grown and harvested in the USA in 2015.

Wheat powdery mildew

Researchers used CRISPR to engineer a wheat variety resistant to powdery mildew (shown here), a major disease of this crop. Image credit: NY State IPM Program. Used under license: CC BY 2.0.

 

Using CRISPR, scientists from the Chinese Academy of Sciences produced a wheat variety resistant to powdery mildew, one of the major diseases in wheat. Similarly, another Chinese research group exploited CRISPR to produce a rice line with enhanced rice blast resistance that will help to reduce the amount of fungicides used in rice farming. CRISPR/Cas9 has also been already applied to maize, tomato, potato, orange, lettuce, soybean and other legumes.

Genome editing could also revolutionize the management of viral plant disease. The CRISPR/Cas9 system was originally discovered in bacteria, where it provided them with molecular immunity against viruses, but it can also be moved into plants. Scientists can transform plants to produce the Cas9 and gRNAs that target viral DNA, reducing virus accumulation; alternatively, they can suppress those plant genes that are hijacked by the virus to mediate its own diffusion in the plants. Since most plants are defenseless against viruses and there are no chemical controls available for plant viruses, the main method to stop the spread of these diseases is still the destruction of the infected plant. For the first time in history, scientists have an effective weapon to fight back against plant viruses.

Cassava brown streak disease

The cassava brown streak disease virus can destroy cassava crops, threatening the food security of the 300 million people who rely on this crop in Africa. Image credit: Katie Tomlinson (for more on this topic, read her blog here).

 

Genome editing will be particularly useful in the genetic improvement of many crops that are propagated mainly by vegetative reproduction, and so very difficult to improve by traditional breeding methods involving crossing (e.g. cassava, banana, grape, potato). For example, using TALENs, scientists from Cellectis edited a potato line to minimize the accumulation of reducing sugars that may be converted into acrylamide (a possible carcinogen) during cooking.

 

Concerns about off-targets

One of the hypothesized risks of using CRISPR/Cas9 is the potential targeting of undesired DNA regions, called off-targets. It is possible to limit the potential for off-targets by designing very specific gRNAs, and all of the work published so far either did not detect any off-targets or, if detected, they occurred at a very low frequency. The number of off-target mutations produced by CRISPR/Cas9 is therefore minimal, especially if compared with the widely accepted random mutagenesis of crops used in plant breeding since the 1950s.

 

GM or not-GM

Genome editing is interesting from a regulatory point of view too. After obtaining the desired heritable mutation using CRISPR/Cas9, it is possible to remove the CRISPR/Cas9 integrated vectors from the genome using simple genetic segregation, leaving no trace of the genome modification other than the mutation itself. This means that some countries (including the USA, Canada, and Argentina) consider the products of genome editing on a case-by-case basis, ruling that a crop is non-GM when it contains gene combinations that could have been obtained through crossing or random mutation. Many other countries are yet to issue an official statement on CRISPR, however.

Recently, scientists showed that is possible to edit the genome of plants without adding any foreign DNA and without the need for bacteria- or virus-mediated plant transformation. Instead, a pre-assembled Cas9-gRNA ribonucleoprotein (RNP) is delivered to plant cells in vitro, which can edit the desired region of the genome before being rapidly degraded by the plant endogenous proteases and nucleases. This non-GM approach can also reduce the potential of off-target editing, because of the minimal time that the RNP is present inside the cell before being degraded. RNP-based genome editing has been already applied to tobacco plants, rice, and lettuce, as well as very recently to maize.

In conclusion, genome editing techniques, and CRISPR/Cas9 in particular, offers scientists and plant breeders a flexible and relatively easy approach to accelerate breeding practices in a wide variety of crop species, providing another tool that we can use to improve food security in the future.
For more on CRISPR, check out this recent TED Talk from Ellen Jorgensen:


About the author

Dr Damiano Martignago is a plant molecular biologist who graduated from Padua University, Italy, with a degree in Food Biotechnology in 2009. He obtained his PhD in Biology at Roma Tre University in 2014. His experience with CRISPR/Cas9 began in the lab of Prof. Fabio Fornara (University of Milan), where he used CRISPR/Cas9 to target photoperiod genes of interest in rice and generate mutants that were not previously available. He recently moved to Rothamsted Research, UK, where he works as Genome Editing Specialist, transferring CRISPR/Cas9 technology to hexaploid bread wheat with the aim of improving the efficiency of genome editing in this crop. He is actively involved with AIRIcerca (International Association of Italian Scientists), disseminating and promoting scientific news.

Does Australia hold the key to food security?

This article is reposted from the Devex blog with kind permission from the author, Lisa Cornish.

CIAT research

Plant samples in the genebank at the International Center for Tropical Agriculture’s Genetic Resources Unit, at the institution’s headquarters in Colombia. Credit: Neil Palmer / CIAT. Used under license: CC BY-SA 2.0.

It was too dry in the Australian region of Wimmera to produce crops last summer. This year, floods are set to wipe out yields again. Like a number of other regions across the planet, climate change is starting to be felt.

“It’s like this every year somewhere,” said Sally Norton, head of the Australian Grains Genebank, which stores diverse genetic material for plant breeding and research.

For Norton and many of her colleagues in agricultural genetics, the picture is increasingly clear: The variety of crops used today are not able to withstand the changing conditions and changes expected in the future.

Australia’s biodiversity may offer some help, according to discussions at the recent International Genebank Managers Annual General Meeting held in Horsham, Victoria. The gathering, which brings together 11 countries, focused on how to better conserve seeds, build databases to manage collections, boost capacity across the world and fill gaps in genebanks.

Researchers are particularly interested in crop wilds, “the ancestors of our domesticated crops,” Marie Haga, executive director of the The Crop Trust, explained to Devex. Australia is one of the richest sources of these seeds. “It’s like the wolf being the ancestor to our domesticated dogs. Crop wild relatives have traits that we have lost in the domestication process — they might need less water, might live in unfriendly conditions, may be resistant to pests and diseases.”

As climate change continues to batter agricultural yields, crop wild relatives could provide resilience. The seeds give breeders and farmers new options of plant varieties with traits to withstand a variety of conditions based on the harsh climates they are found — drought, fire, flood, poor soil, high salinity.

For Haga, crop wild relatives are a solution for food security. “The challenge is that many of the varieties widely used in modern agriculture are very vulnerable, because we have been breeding on the same line and they are adapted to very specific environment,” Haga said. Varieties that flourish today, she said, could wither as the climate fluctuates.

“Utilization of the natural diversity of crops is key to the future,” she said. “The climate is rapidly changing and we need to feed a growing population with more nutritious food. It is very hard to see how we can do this unless we go back to the building blocks of agriculture.”

Norton agreed: “Crop wild relatives have an amazing adaptability to changing conditions,” she told Devex. “When we talk about food security, we are talking about getting varieties in farm paddocks that have greater resilience to extreme conditions. It may not be the highest yield, but you are going to get something from this crop.”

Why have they been overlooked?

Crop wild relatives have so far been underutilized in the research and breeding process of crops.

“We have this fabulous natural diversity out there including 125,000 varieties of wheat and 200,000 varieties of rice.” Haga said. “We have not at all unlocked the potential of these crops.”

One reason is a dearth of research. “Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives,” a 10-year project led by Haga to ensure long-term conservation of crop wild relatives, conducted a global survey of distribution and conservation and found that of 1,076 known wild relatives for 81 crops, more than 95 percent are insufficiently represented in genebanks and 29 percent are completely missing. They are missing purely due to the fact that they have yet to be collected.

“Genebank managers are generally open to include crop wild relatives in their collections.” Haga said. “It’s just quite simply that not enough work has been done in this area and the full potential is yet to be realized,” she said.

At the moment, seeds are being collected in 25 countries around the world as part of the crop wild relative project, but it is Australia that has been identified as one of the richest sources for crop wild relatives in the world. Because of the continent’s low population density and vast, undisturbed natural environment, a wide variety of species have been conserved, said Norton.

Australia holds significant diversity of wild relatives of rice, sorghum, pigeon pea, banana, sweet potato and eggplant currently missing from global collections, according to research by the Australian Seed Bank Partnership. Forty species have been prioritized for collection with high hopes that they will enable crops to withstand the harsh environmental conditions in which Australian species are found.

There are still many areas of Australia yet to be surveyed, and the full extent of its agricultural riches may yet to be tapped.

Australian researchers will play an important role in pre-breeding local species of wild relatives to improve their use in breeding programs. Crop wild relatives have historically been used in a variety of crops including synthetic wheat, but Australian native wild relatives have been harder to include in the breeding process.

“In the next 10 to 15 years it would be surprising if there is not something coming out that hasn’t got a component of Australian native wild relative in it,” Norton said who is currently involved in the collection of Australian crop wild relatives.

Collection of crop wild relatives is time sensitive

There is an urgency to collect crop wild relatives. Not only are wild species needed now to support changing environmental conditions affecting crops and farming, urbanization is putting crop wild relatives at risk of disappearing.

“We need to collect these sooner rather than later,” Norton told Devex. “Urbanization has a big impact on any native environment, let alone crop wild relatives. We know what species on our target list are more threatened than others — urbanization, flooding and fire are all risks to their security. We certainly have a priority list of species to collect and we need to make sure we target the ones that are under threat first.”

Once the varieties are conserved, breeders and farmers will need to be convinced to start using crop wild relatives. Many are already on board. “Most breeders understand these wild relatives have great potential,” Haga said.

Still, wild relatives can be difficult to work with and produce a lower yield. Haga expects there to be some reluctance, though limited.

“The understanding of the need is increasing and we feel very confident that this material will be used and some of them may be the game changer we are looking for,” she said.

The plans for crop wild relatives

Haga’s 10-year project on crop wild relatives is halfway complete. They are nearing the end of the collection phase and entering the pre-breeding process, before they are able to breed and deliver new species to farmers.

Australian support for the program includes an agreement for additional amount of $5 million. That comes on top of previous support of $21.2 million to the Crop Diversity Endowment Fund, which supports crop diversity globally and with a focus on the Indo-Pacific. Brazil, Chile, Germany, Japan, New Zealand, Norway, Switzerland and the United States are among other supporters of the endowment fund that hopes to reach $850 million. In Australia, further resources are still required to fund and support better seed collection at home.

Globally, plans for crop wild relatives includes raising greater awareness of their potential and importance.

“We have a big job to do to create awareness of the important of crop diversity generally and crop wild relatives specifically,” Haga said. “We have been speaking for years about biodiversity in birds and fish and a range of other animals, but we have talked very little about conserving the diversity of crops. I will fight for all types of diversity, but especially plants.”


 

This article is reposted from the Devex blog with kind permission from the author, Lisa Cornish.