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Nov 17
0

Stress Resilience: Call for papers for a JXB Special Issue!

By | Blog, GPC Community, Scientific Meetings, SEB

GPC banner Without linkFollowing the recent Stress Resilience Symposium and Discussion Forum that we co-hosted in Brazil last month with the Society for Experimental Biology, we are pleased to announce a call for papers for a forthcoming Special Issue of the SEB’s Journal of Experimental Botany.

Achieving food security in a changing and unpredictable climate urgently requires a better understanding of the mechanisms by which plants interact with and respond to their environments. This special issue will bring together a collection of papers highlighting the best current research in stress resilience contributing to global efforts to develop crops and cropping systems that are better able to deal with fluctuating and stressful environmental conditions.

Proposals are invited for the submission of new and innovative research papers that contribute to this goal (submission before the end of January 2016 will guarantee inclusion in the special issue pending positive peer review). Confirmed contributors already include: Andrew Borrell (University of Queensland, Australia), Elizabete Carmo-Silva (Lancaster University, UK), Scott Chapman (CSIRO, Australia), Bill Davies (GPC President and Lancaster University, UK), Lyza Maron (Cornell University, USA), Jianbo Shen (China Agricultural University), and Roberto Tuberosa (University of Bologna, Italy).

If you would like to contribute a paper, please email a title and short abstract to Mary Traynor: m.traynor@lancaster.ac.uk.

Oct 28
0

Taking Care of Wildlings

By | Blog, Future Directions

By Hannes Dempewolf

We at the Global Crop Diversity Trust care about wildlings! No, not the people beyond The Wall, but the wild cousins of our domesticated crops. By collecting, conserving and using wild crop relatives, we hope to be able to adapt agriculture to climate change. This project is funded by the Government of Norway, in partnership with the Millennium Seed Bank at Kew in the UK, and many national and international research institutes around the world.

The first step of this project was to map and analyze the distribution patterns of hundreds of crop wild relatives. Next, we identified global priorities for collecting, and are now providing support to our national partners to collect these wild species and use them in pre-breeding efforts. An example of a crop we have already started pre-breeding is eggplant (aubergine). This crop, important in developing countries, has many wild relatives, which we are using to develop varieties that can better withstand abiotic stresses and variable environments.

More recently we have started a discussion with the crop science community on how best to share our data and information about these species, and genetic resources more generally. This discourse that was at the heart of what has now become the DivSeek Initiative, a Global Plant Council initiative that you can read more about in this GPC blog post by Gurdev Khush.

Why should you care?

Good question. I couldn’t possibly answer it better than Sandy Knapp, one of the Project’s recent reviewers, who speaks in the video below.

One of the great leaders in the field, Jack Harlan, also recognized their immense value: “When the crop you live by is threatened you will turn to any source of relief you can find. In most cases, it is the wild relatives that salvage the situation, and we can point very specifically to several examples in which genes from wild relatives stand between man and starvation or economic ruin.”

Oryza

Wild rice, Oryza officinalis, is being used to adapt commercial rice cultivars to climate change. Photo credit: IRRI photos, used under Creative Commons License 2.0

Crop wild relatives have indeed been used for many decades to improve crops and their value is well recognized by breeders. This is increasingly true also for abiotic stress tolerances, particularly relevant if we care about adapting our agricultural systems to climate change. One such example is the use of a wild rice (Oryza officinalis) to change the flowering time of the rice cultivar Koshihikari (Oryza sativa) to avoid the hottest part of the day.

Share the care

Fostering the community of those who care about crop wild relatives is an important objective of the project. We make sure that all the germplasm collected by partners is accessible to the global community for research and breeding, within the framework of the International Treaty on Plant Genetic Resources for Food and Agriculture (the ‘Plant Treaty’). The project invests into building capacity into collecting: it’s not as simple a process as it may sound. The following shows the training in collection in Uganda:

We also put a heavy emphasis on technology transfer and the development of lasting partnerships in all of the pre-breeding projects we support.

The only way we can safeguard and reap the benefits of the genetic diversity of crop wild relatives over the long term is by supporting a vibrant, committed community.  We hope you agree, and encourage you to get in touch via cropwildrelatives@croptrust.org.

To find out more about the Crop Trust and how you can take action to help conserve crop diversity for food security, please visit our webpage. For more information about the Crop Wild Relatives project, please visit www.cwrdiversity.org.

 

Oct 21
0

Biofortification

By | Blog, GPC Community

Approaches to biofortification

Biofortification is the improvement of the nutritional value of our crops through both traditional breeding and genetic engineering. Alongside DivSeek and Stress Resilience, biofortification is one of the Global Plant Council’s three main initiatives and will be central to addressing many of the challenges facing world health. However, biofortification doesn’t always involve changing our crops in some way. Often the nutrients we are lacking are present in pre-existing crops. We can biofortify our diets simply by identifying what’s missing and altering our life style accordingly.

Tackling undernourishment

The share

The share (%) of undernourished people per country. From: Max Roser (2015) -‘Hunger and Undernourishment’. Published online at www.OurWorldInData.org

More often that not we intuitively link biofortification with tackling undernourishment in the developing world, and indeed improvements in the diets of deprived communities would be of enormous benefit to global health.

To do this, a key challenge is to increase the nutrient content of staple food crops such as rice in Asia and maize in sub-Saharan Africa. We need to do this in a sustainable and affordable way; ensuring foods are accessible to those who need it. Alongside the fortification of staple crops we need to identify economical crop species that will grow in harsh environments and provide nutrients currently absent from the diet.

Addressing obesity

It is easy to forget that malnutrition is also a problem in developed countries. Worldwide, at least 2.8 million people per year die from obesity-related illnesses, and in 2011 more than 40 million children under the age of five were overweight. Obesity and related health problems such as diabetes, heart disease and certain cancers, place enormous strain on health services, and are partly a function of poor diet lacking in fibre and key phytonutrients. Addressing this is as important as tackling undernourishment, and many of the same principles apply.

Simple lifestyle changes, such as encouraging the consumption of more fruits and vegetables, are clearly a priority. In addition to this dietary change, if we are going to biofortify foods, there should be an emphasis on crops that are already widely consumed.

Purple tomatoes

Professor Cathie Martin

Professor Cathie Martin works at the John Innes Centre researching the link  between diet and health, and how crops could be fortified to improve our diets and global health.

Tomatoes, are one crop plant already eaten widely in the West, commonly found in fast and convenience foods. For this reason they became the focus of the work of Professor Cathie Martin at the John Innes Centre in Norwich, UK. Cathie’s lab has developed a genetically modified tomato that is rich in anthocyanins, making them purple in colour. Anthocyanins are an important dietary component that can have numerous health benefits, including a potentially significant role in the prevention of diseases such as cancer and diabetes. They are the compounds that give some foods, such as blueberries or eggplant, their distinctive blue or purple colouring. Consuming higher quantities could be highly beneficial to health.

“We focused on anthocyanins because of their huge potential health benefits. Pre-clinical studies show that introducing our purple tomatoes into the diet could be an incredibly effective way to protect against diseases such as cancer. Our next steps will be to confirm these findings in human trials,” says Cathie.

However, naturally occurring tomato varieties containing anthocyanins already exist. Wouldn’t it be better to increase consumption of these rather than creating new ones?

“Indeed purple tomatoes do occur naturally. However, these have anthocyanins only in the skin, in quantities too small to make a significant impact on health. Our genetically modified tomatoes have anthocyanins in all tissues,” explains Cathie.

Since developing the purple tomatoes, Cathie, in collaboration with Professor Jonathan Jones, has set up Norfolk Plant Sciences, the UK’s first GM crop company. However, resistance and uncertainty in Europe surrounding GM technology means that progress has been slow.

“The company was founded in 2007 and we are currently working towards the approval of our purple tomato juice in the USA. Producing just the juice rather than the entire fruit means there are no seeds in the final product. This eliminates environmental challenges without compromising health benefits. If the juice proves successful in the USA we may then work towards approval in the UK and Europe.”

It’s not all about Genetic Modification

Of course if we want to make drastic changes to our foods, such as increase anthocyanins in our tomatoes or carotenoids in our rice, GM technology will be a necessity. However, we can go some way to biofortifying our diets without the use of GM.

Golden rice

Golden rice, shown on the left, is a biofortified crop that accumulates high quantities of provitamin A in the grain. This could help tackle Vitamin A Deficiency in developing countries, from which 500,000 children become blind every year, and nine million will die of malnutrition. Photo credit: IRRI photos used under Creative Commons 2.0

Primarily we really need to focus on changing diet and lifestyle. Promoting plants rich in the nutritional components we need is essential, in addition to encouraging traditional diets such as the Mediterranean diet rich in fish, fruits and vegetables. However, changing people’s behavior and relationship with food is a huge challenge. Cathie cites the UK 5-A-Day governmental campaign as an example.

“This campaign was aimed at encouraging people to eat five portions of fruit or vegetables a day. At the end of this 25-year campaign only 3% more of the UK population was getting their five a day.”

In addition to dietary change, we could biofortify our crops through traditional breeding. For example, one answer to increasing anthocyanins in the diet could be red wheat. Red wheat is rich in anthocyanins, and furthermore less susceptible to pre-harvest sprouting, which causes large crop losses every year for farmers. However, we have so far resisted selecting for this trait in wheat breeding programs as it is not considered esthetically pleasing. To improve our diets we may need to change our expectations of what we want our plates to look like.

Next steps

Plant scientists alone cannot tackle biofortification of our diets! Cathie believes the key to a healthier future is interdisciplinary research:

“Everyone needs to come together: nutritionists, epidemiologists, plant breeders, and plant scientists. However, with such a diverse group of people it is hard to reach agreement on the next steps, and equally as difficult to secure funding for research projects. We really need to promote collaboration and interaction between all groups in order to move forwards.”

Oct 15
0

Women in Plant Science, Part II

By | Blog, GPC Community, Interviews

Tuesday 13th October was Ada Lovelace Day, an international celebration of women in science, technology, engineering and maths (STEM) in honor of Ada Lovelace, the first computer programmer.

To highlight the achievements of women in STEM we’ve spoken to female plant scientists around the world about their careers and experiences. Read on for Part II of the series (for Part I, click here):

 

Professor Kalunde Sibuga

Professor Kalunde Sibuga

Professor Kalunde Sibuga

Sokoine University of Agriculture, Tanzania

What are you working on?

I have always been interested in working with farmers who have limited resources and coming up with production technologies that can help reduce their workload (particularly for women) and dependence on purchased inputs such as fertilizers, herbicides and other pesticides. These interests led to a research career focusing on weed management and agronomy of legumes, vegetable crops and cereals.

 

Have you ever faced any specific challenges as a female scientist in Tanzania?

Not particularly, because policies in Tanzania encourage girls to go to school and do whatever they are able to do. Women in science in my country are not targeted for discrimination, but until recently, certain sections of science such as engineering were considered a male domain. The government aims for gender equality and funds various projects to encourage girls to take science subjects, which have assisted in increasing enrolment of girls in universities.

 

What are your hopes and goals for the future?

I have always believed that whatever we do, our aim should be to increase productivity, reduce drudgery and increase household income. This can only be achieved if governments, particularly African governments, would take a serious look at mechanization, timely delivery of inputs, marketing, and value addition aspects. Our work in agronomy is of no great benefit if the other components are not properly and appropriately addressed.

Weed Science and Management are not as well staffed as other branches of crop protection such as entomology and plant pathology. My goals for the future are therefore to continue to train and encourage young scientists to engage in weed research.

 

 

Associate Professor Siobhan Brady

Associate Professor Siobhan Brady

Associate Professor Siobhan Brady

University of California, Davis, USA

Could you give a brief overview of your research into root development?

My lab explores the development of root cell types, and the gene regulatory mechanisms and networks that are responsible for producing them. We are also interested in how different species and stresses have different networks in order to adapt to different environments. We love to utilize genome-scale data and systems approaches to understand how these systems are organized.

 

Have you faced any specific challenges as a woman in science?

Yes. Finding the right time to have a baby is one example. I ended up having my first child five months into my position as a PI and the experience was one of the most challenging in my life. I was trying to find my feet being a new mum at the same time as being a new lab leader, writing grants and teaching. I even felt “guilty” (purely self-imposed) for starting my position by having a baby and felt that I had so much to prove by being able to get this position at a time when getting faculty positions was incredibly challenging. I went back to work full time after six weeks. Nursing, working, and travelling was very hard, but I made it. I had the support of my partner and of an incredibly wonderful lab and colleagues. Looking back in fact, I wish I’d opened up to them a little more.

I now have two beautiful boys. I have had to cut some of my work responsibilities (for instance, picking and choosing which weekly meetings are really the most important to attend). It has changed our lives, but learning to be flexible (not always easy for me!) and finding the unique advantages in each challenge that faces us has been a tremendous learning experience.

 

What would you say is the general experience of women in science in the US?

So much better than it once was. When I started in science I knew of very few female faculty members with children. Now there are many more incredible mentors who have families, are very successful and maintain a good work-life balance.

That being said, given the current funding situation in the US and the general economy there are fewer and fewer faculty jobs available. Many graduate students and postdocs have presented their concerns to me that raising a family and having a successful career are inherently incompatible in this era – that is, that you will always be so busy that something will fail.

It is hard to figure out when to have children. If you have a grant, there is no allowance for your graduate students or postdocs to take leave, but you are mandated to take some leave (as you should be). This is a real challenge, both for PIs and for students/postdocs, as there is really only a limited amount of time to get a project done and to have a mother stay with an infant. I don’t know of a good way to handle this other than to always have open communication with people in your group and to let them know (if a PI) that you support them in their life goals, no matter what they are, while encouraging them to be the best they can be.

 

What are your goals for the future?

Raise happy, well-adjusted children, continue to train amazing scientists, learn different fields of research and ask new and creative biological questions. And of course, publish well and get funded sufficiently so that our work can make a difference in science and the world in general!

 

 

Thank you to both Professor Kalunde Sibuga and Associate Professor Siobhan Brady for taking the time to discuss their experiences with us.

Please leave a comment below and describe any challenges or opportunities you have observed for women in science in your country!

 

Oct 13
0

Women in Plant Science, Part I

By | Blog, GPC Community, Scandinavian Plant Physiology Society

Today is Ada Lovelace Day, an international celebration of women in science, technology, engineering and maths (STEM) in honor of Ada Lovelace, the first computer programmer.

To highlight the achievements of women in STEM we’ve spoken to female plant scientists around the world about their careers and experiences. Read on for the first of two posts:

Associate Prof Lum Fontem

Associate Professor Lum Fontem

 

Associate Professor Lum A. Fontem

University of Buea, Cameroon, and Women Representative of the African Crop Science Society.

 

Could you give a brief overview of your research?

I have always had the desire to carry out research that is oriented towards solving the problems of resource-poor farmers, which led me towards my areas of interest; weed science, agronomy, management of post-harvest losses and phytoremediation. I work with many crops, including cereals, legumes, vegetables, roots and tubers.

The major output of my work has been the adoption of technologies that have led to  an improvement of livelihoods, food security and increased household incomes.

 

Have you faced any challenges as a woman in science?

Occasionally I face the challenges that women go through because of their gender, but I have always stood my ground. My parents encouraged me to go to school and provided for my needs, and I won awards, all of which helped me to sail through smoothly.

 

What would you say is the general experience of women in science in Cameroon?

In Cameroon, the policy of gender equality has received a strong impetus from government and women are encouraged in the area of science, however there are still domains that women still have to break through.

 

What are your goals for the future?

I hope to train more weed scientists that can respond to the multifarious challenges of food production.

 

 

Professor Cornelia Spetea Wiklund

Professor Cornelia Spetea Wiklund

Professor Cornelia Spetea Wiklund

University of Gothenburg, Sweden, and Council Member of the Scandinavian Plant Physiology Society.

 

What is the subject of your research?

My research focuses on the solute transport network from the thylakoid membrane of Arabidopsis thaliana. We also study the impact of mycorrhiza symbiosis on photosynthesis in the model legume Medicago truncatula.

 

How has your career progressed?

My PhD at the University of Szeged, Hungary, and postdoc at Stockholm University, Sweden, focused on the proteolytic mechanisms in thylakoid membranes during light stress. I moved to Linköping University, Sweden, where I got funding from the Swedish Research Council to build my own research group working on my current areas of interest. I have been a Professor of Plant Cell Physiology at the University of Gothenburg for the past 4.5 years.

 

Have you dealt with any specific challenges as a woman in science?

Of course. I gave birth to two children in my first years as group leader. The major challenge was how to manage my group and raise the children at the same time, even though my husband took over quite a lot of the family responsibilities. On one hand, I have become a very good ‘manager’ of my time, but on the other, I have missed a lot of my children’s development. Another challenge was to learn to understand how my male colleagues think and undertake management in science.

 

How does Sweden help women in science to succeed?

Sweden, as other Scandinavian countries, is known for a generous parental leave system, which allows the father to be at home for at least 60 out of 480 days. Day care is heavily subsidized by the state and accepts children over a year old.  These advantages allow many female scientists in Sweden to have children during their PhD or later on in their career. However, the ‘price’ may be that the young female group leaders with small children at home experience delays in their career development as compared with male colleagues of similar age.

A survey at my institution in Gothenburg revealed additional causes for delayed career success, such as poor networking and visibility of young females in various scientific forums. Remarkably, according to the same survey, there is not much difference in career development between senior male and female scientists.

 

What do you hope to achieve in the future?

I will continue my research on the regulation of photosynthesis since I find it fascinating and because I believe this can bring solutions to many of the problems with crop productivity within the context of increasing human population and depleted resources. I also aim to spend more time with my children at least in the coming five years, before they leave home to continue their studies.

 

Thank you to both Associate Professor Lum Fontem and Professor Cornelia Spetea Wiklund for taking the time to discuss their experiences with us.

Please leave a comment below and describe any challenges or opportunities you have observed for women in science in your country!

Sep 24
0

Genetic Diversity in our Food Systems

By | Blog, Future Directions
Gurdev Khush at IRRI

Gurdev Khush at IRRI. Photo credit: IRRI photos. Reproduced under a Creative Commons license 2.0. 

This week’s blog post has been written by agronomist and geneticist Gurdev Khush. Gurdev had a major role to play in the Green Revolution, and while working at the International Rice Research Institute (IRRI) developed more than 300 rice varieties, one of which (IR36) became the most widely planted variety of rice. The impact and significance of his work has been recognized by numerous awards including the World Food Prize in 1996, the Wolf Prize in Agriculture in 2000, the Golden Sickle Award in 2007, and in 1987 the Japan Prize.

Our civilization developed with the domestication of plants for food, fiber and shelter about 10,000 years ago. Since then we have made constant improvements to these domesticated plants based on genetic diversity. It is the conservation, evaluation and utilization of this genetic diversity that will be essential for further improvements in our food crops and world food security.

Gene banks conserve biodiversity

The first important step in conserving biodiversity was the establishment of a gene bank by Nikolai Vavilov at the Leningrad Seedbank in Russia during the 1920s. In subsequent years more gene banks were created in developed countries, and the Green Revolution provided major impetus for the establishment of gene banks in developing countries. The first gene bank for the conservation of rice germplasm was organized after IRRI was established in the Philippines in 1960. Other rice growing countries followed suit and now most of them have their own gene banks.

The IRRI gene bank has over 120,000 entries

IRRI medium term seed store

The medium term storage unit of the IRRI seed bank. Photo credit: IRRI photos. Reproduced under a Creative Commons license 2.0.

The IRRI gene bank has progressively grown from a few thousand entries in 1962 to over 120,000 entries today, including accessions of all the wild species. The germplasm is stored under two-temperature and humidity regimes. The medium term store keeps seeds at 4ºC and a relative humidity of 35% for 30–40 years, while in the longer term store, maintained at –10ºC and a relative humidity of 20%, seeds are expected to remain viable for 100 years.

IRRI accessions are evaluated for morphological traits, grain quality characteristics, disease and insect resistance, and for tolerance to abiotic stresses such as drought, floods, problem soils and adverse temperatures. These are all important characteristics in terms of breeding resilient and high yielding rice varieties for the future.

Selection of new rice varieties

Numerous landraces have been utilized for breeding high yielding rice varieties. The first high yielding variety, IR8, was developed from a cross between two landraces, one from Indonesia and the other from China. Another variety, IR64, is one of the most widely grown rice varieties, and has 19 landraces and one wild species in its ancestry.

IR64

Rice variety IR64, one of the most widely grown rice varieties. Photo credit: IRRI photos. Used under Creative Commons license 2.0.

Ensuring future food security

Gene banks have played an important role in world food security. However, as the population grows there are now even bigger challenges for meeting demand. Climate change and increased competition for land and water resources further magnify the problem. We need to breed climate resilient crop varieties with higher productivity, durable resistance to diseases and insects, and tolerance to abiotic stresses. Success will depend upon the continuous availability of genetic diversity; we must redouble our efforts to unlock the variability currently preserved in our gene banks.

Diversity Seek Initiative

Establishment of the Diversity Seek Initiative (DivSeek) and the proposed Digital Seed Bank, under the auspices of the Global Plant Council, is a welcome development.

The aim of DivSeek is to develop a unified, coordinated and cohesive information management platform to provide easy access to genotypic and phenotypic data on germplasm preserved in gene banks. It is an international effort to bring together gene bank curators, plant breeders and biological researchers. To begin with, the project will develop standards and generate genotypic, transcriptome and phenotypic information for cassava, rice and wheat diversity. This will form the foundation of the Digital Seed Bank, a novel type of database containing standardized and integrated molecular information on crop diversity. The information from this database will be publicly available, and will be of enormous scientific and practical value. It has the potential to significantly increase our understanding of the molecular basis of crop diversity, and its application in breeding programs.

If your organization is interested in joining DivSeek, information can be found here. Alternatively, sign up to the mailing list to keep up to date with the initiative.

Sep 17
0

Providing For Our Brave New World

By | Blog, Future Directions
The Journal of Experimental Botany (JXB) published a special issue in June entitled ‘Breeding plants to cope with future climate change’

The Journal of Experimental Botany (JXB) published a special issue in June entitled ‘Breeding plants to cope with future climate change’

By Jonathan Ingram

The Journal of Experimental Botany (JXB) recently published a special issue entitled ‘Breeding plants to cope with future climate change’.

More often than not, climate change discussions are focused on debating the degree of change we are likely to experience, unpredictable weather scenarios, and politics. However, regardless of the hows and whys, it is now an undeniable fact that the climate will change in some way.

This JXB special issue focuses on the necessary and cutting edge research needed to breed plants that can cope under new conditions, which is essential for continued production of food and resources in the future.

The breadth of research required to address this problem is wide. The 12 reviews included in the issue cover aspects such as research planning and putting together integrated research programs, and more specific topics, such as the use of traditional landraces in breeding programs. Alongside these reviews, original research addresses some of the key questions using novel techniques and methodology. Critically, the research presented comes from a diversity of labs around the world, from European wheat fields to upland rice in Brazil. Taking a global view is essential in our adaptation to climate change.

Avoiding starvation

Why release this special issue now?

Quite simply, the consequences of an inadequate response to climate change are stark for the human population. In fact, as previously discussed on the Global Plant Council blog, changing climate and extreme weather events are already having an impact on food production. For example, drought in Australia (2007), Russia (2010) and South-East China (2013) all resulted in steep increases in food prices. However, a positive side effect of this was to put food security at the top of the global agenda.

A farm in China during drought. Reduced food production can cause steep rises in food prices leading to socio-economic problems. Photo credit: Bert van Dijk used under Creative Commons License 2.0

A farm in China during drought. Reduced food production can cause steep rises in food prices leading to socio-economic problems.
Photo credit: Bert van Dijk used under Creative Commons License 2.0

Moving forwards, researchers and breeders alike will have to change their fundamental approach to developing novel varieties of crops. In the past, breeders have been highly succesful in increasing yields to feed a growing population. However, we now need to adapt to a rapidly changing and unpredictable environment.

Dr Bryan McKersie sums this up in his contribution to the special issue. He commented: “Current plant breeding methods use large populations and rigorous selection in field environments, but the future environment is different and does not exist yet. Lessons learned from the Green Revolution and development of genetically engineered crops suggest that a new interdisciplinary research plan is needed to achieve food security.”

Driving up yields

So which traits should we be studying to increase resilience to climate change in our crops?

A potentially important characteristic brought to the foreground by Dr Karine Chenu and colleagues (University of Queensland, Australia) is susceptibility to frost damage. Although seemingly counterintuitive at first, the changing climate could result in greater frost exposure at key phases of the crop lifecycle. Warmer temperatures, or clear and cool nights during a drought, would allow vulnerable tissue to emerge earlier in the spring (Gu et al., 2008; Zheng et al., 2012). A late frost could then be incredibly destructive to our agricultural systems, causing losses of up to 85% (Paulsen and Heyne, 1983; Boer et al., 1993).

As explained by Dr Chenu, “Finding frost tolerant lines would thus help to deal with frost damage but also with losses due to extreme heat and drought – as they could be avoided by earlier sowings”.

The authors conclude that a “national yield advantage of up to 20% could result from the breeding of frost tolerant lines if useful genetic variation can be found”. The impact of this for future agriculture is incredibly exciting.

This study is just one illustration of the importance of thinking outside the box and investigating a wide range of traits when looking to adapt crops to climate change.

You can find the full Breeding plants to cope with future climate change Special Issue of Journal of Experimental Botany here. Much of the research in the issue is freely available (open access).

Journal of Experimental Botany publishes an exciting mix of research, review and comment on fundamental questions of broad interest in plant science. Regular special issues highlight key areas.

References

Association of Applied Biologists. 2014. Breeding plants to cope with future climate change. Newsletter of the Association of Applied Biologists 81, Spring/Summer 2014.

Boer R, Campbell LC, Fletcher DJ. 1993. Characteristics of frost in a major wheat-growing region of Australia. Australian Journal of Agricultural Research 44, 1731–1743.

Gu L, Hanson PJ, Post WM et al. 2008. The 2007 Eastern US spring freeze: increased cold damage in a warming world? BioScience 58, 253–262.

Paulsen GM, Heyne EG. 1983. Grain production of winter wheat after spring freeze injury. Agronomy Journal 75, 705–707.

Zheng BY, Chenu K, Dreccer MF, Chapman SC. 2012. Breeding for the future: what are the potential impacts of future frost and heat events on sowing and flowering time requirements for Australian bread wheat (Triticum aestivum) varieties? Global Change Biology 18, 2899–2914.

Sep 10
0

Nanopores: Next, next generation sequencing

By | Blog, Future Directions

Do you have a genome sequencer in your pocket or are you just happy to see me?

By Nikolai Adamski

On September 4 I attended an event sponsored by Oxford Nanopore Technologies (ONT) at Norwich Research Park, UK, which focused on nanopore technologies. This new technology has been dubbed ‘Next, next-generation sequencing’, and could have really exciting implications for the future of genome sequencing.

ONT has developed a pocked-sized genome sequencing device called the MinION that can sequence genomes in real time. Thanks to recent pop culture this generates visions of cuddly yellow creatures with an overly developed desire to serve super-villains. However, a MinION is actually a new genome sequencing device. To help confused readers, the figure below should help clarify the issue once and for all (Figure 1).

Figure 1: Demonstrating the difference between the pop culture Minion on the left and the genome sequencing MinION on the right.

Figure 1: Demonstrating the difference between the pop culture Minion on the left and the genome sequencing MinION on the right.

The striking thing about the MinION is its size. Sequencing machines these days vary in size from something that sits on a desktop, to something that fills half a student’s room. The MinION however, fits in the palm of your hand. This is possible thanks to highly miniaturized electronics.

So how does it work?

At the core of the MinION are two biological components: the nanopore protein, which gives the company its name, and a motor protein. The nanopore protein sits on top of an artificial layer and acts a microscopic sluice gate that controls how much of the sample solution passes through it into the lower layer. The sample solution contains DNA, but also ions that pass through the nanopore, thus creating a measurable electrical current. If a big molecule like a strand of DNA passes through the nanopore, the flow of ions is perturbed, which results in a change in the electrical current. These changes are recorded and interpreted to give the sequence of said DNA molecule.

Meanwhile, the motor protein sticks to a DNA molecule, attaches itself to the top of the nanopore, and feeds the DNA through the nanopore as a single strand at a certain speed. This process is similar to a ratchet. Each MinION device has thousands of nanopores allowing for as many molecules to pass through and be sequenced in real time. This is nicely illustrated in a video made by ONT, which you can see here which is well worth a watch!

The sequence data are sent to a cloud server in real time, where they are transformed and analyzed and the final data sent back to the user. This eliminates the need for an expensive computer infrastructure as well as the need for extensive training in bioinformatics.

Limitations of the technology

So far so good, but there are still some issues with the MinION system. One of these is the average length of the DNA molecules that can be sequenced. In theory, the MinION system is able to sequence DNA molecules of any length, although the data from users at last week’s event suggests that, at the moment, the average length of sequence obtained is around 6,000 base pairs (bp). This is still a great value, but there is room for improvement. Another issue is the amount of data generated by a single MinION run, which according to user experience is generally around 1Gb, approximately 200 times the size of the gut bacterium E. coli. Both of these issues can be easily remedied by running several MinION sequencers with the same sample.

A larger problem is the matter of sequencing accuracy, which is now somewhere around 90%, although it can be as low as 75%. This can in part be compensated for by the sheer amount of data generated. However, it would require a lot of sequencing to make up for these mistakes, and is a critical point that needs to be addressed by ONT in the future.

Current applications

The MinION system has been and is being used worldwide for a number of different applications. Scientists and medical doctors have used the MinION to monitor strains of the Ebola virus in different patients. Thanks to the real time sequencing data and cloud-based data analysis, patients could be screened within a few days as opposed to weeks. Another interesting example of the usefulness of the MinION system was when scientists travelled to the Tanzanian jungle to assess the biodiversity of frogs in the region.

There are many more fascinating applications for the MinION sequencer. Scientists who are interested can join the MinION Access Programme (MAP) to become part of the research and development community.

I very much enjoyed the ONT event and I am hopeful and curious about what the next few years will bring in terms of innovation and development.

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About the Author:

nikolaiadamskiNikolai Adamski is a postdoctoral scientist working at the John Innes Centre in Norwich, UK, in the group of Cristobal Uauy. He studies yield and yield-related traits in wheat, trying to identify the underlying genes to understand the control and regulation of these traits.

 

You can follow him on Twitter @NikolaiAdamski