Genetic Diversity in our Food Systems

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.

Providing For Our Brave New World

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.

Nanopores: Next, next generation sequencing

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

 

 

A Postcard From… The Argentinean Society of Plant Physiology (SAFV)

Professor Edith Taleisnik

This week Professor Edith Taleisnik describes the vision and activities of the Argentinean Society of Plant Physiology (SAFV), a Member Organization of the Global Plant Council dedicated to promoting collaboration in plant science within Argentina, across Latin America and beyond.

SAFV member Dr Constanza Carrera drinks mate, an infusion made from leaves of Ilex paraguariensis, which is very popular in Argentina, Uruguay and southern Brazil.

SAFV member Dr Constanza Carrera drinks mate, an infusion made from leaves of Ilex paraguariensis, which is very popular in Argentina, Uruguay and southern Brazil.

The Argentinean Society of Plant Physiology (Sociedad Argentina de Fisiologia Vegetal; SAFV) was founded in 1958 to nucleate researchers and teachers in plant physiology in Argentina. Since then the SAFV has maintained continuous activity in the country and the region, providing opportunities for the dissemination and exchange of information related to plant function. It has about 350 members, mostly from Argentina and also from neighboring Uruguay. The SAFV is linked with the Global Plant Council and many other important international plant science organizations.

Exchanging ideas in Argentina and beyond

29th SAFV meeting

The 29th SAFV meeting

One of the main objectives of the society is to organize meetings, which are held every two years. The last one was held in Mar del Plata, and was attended by nearly 600 people. The SAFV has close ties with the Brazilian Society of Plant Physiology (BSPP), so every other SAFV meeting is a joint Latin American event in association with the BSPP. These meetings provide a unique opportunity for scientists in the area to meet, analyze and exchange views on the future of this field, to plan for joint efforts and enterprises, to share personal experiences and contribute to a regional and global perspective of local endeavors.

The participation of students and young scientists in SAFV meetings is stimulated by invitations to deliver lectures and organize symposia, and by making available fellowships that cover travel and registration costs. In accordance with its mandate to promote and diffuse knowledge in plant science, the SAFV also organizes and sponsors courses and workshops.

Conversations with keynote speakers

Keynote speaker discussions at an SAFV meeting

Poster sessionPlant science, and plant physiology in particular, has experienced steady growth and development in Argentina, reflecting the importance of agriculture in its broadest sense; pastures and forests for the Argentine economy. Established groups all over the country produce novel data on various aspects of plant function and interaction with other organisms and the environment, which is particularly relevant to local and global crop production. The wide range of this work is reflected in the proceedings of the last plant physiology meeting.

Other Argentinian plant science societies

There are several other plant science societies in Argentina. Scientists working on botanical and morphological topics are affiliated to the Sociedad Argentina de Botánica (SAB). The focus of the members of the Asociación Argentina de Ecología (AsAE) is centered in environmental topics. A more recently formed society, the Asociación Argentina de Fitopatólgos (AAF), is dedicated to plant pathology, while the Sociedad Argentina de Investigación Bioquímica y Biología Molecular (SAIB) features a section specifically devoted to plant biochemistry and molecular biology. All of these societies hold periodical meetings, stimulate the work of young scientists through incentives and prizes, and publish journals (e.g. Ecología Austral) and books.

Get in touch

If you’d like to know more about the work of the SAFV, or how you can get involved with the society, have a look at their website, or get in touch via Facebook or Twitter (@fisiovegetal).


About the author

Edith TaleisnikProfessor Edith Taleisnik researches the physiology of plants under saline stress for the Argentinean National Scientific and Technical Research Council (CONICET), and is based at the Instituto de Fisiologia y Recursos Geneticos Vegetales  (IFRGV) CIAP, INTA, Argentina. Edith was the president of the SAFV from 2000 to 2004, and is now a member of the scientific committee.