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May 06
0

Choosing your growth media for plant science

By | Blog, Future Directions

Considering its weedy nature, Arabidopsis thaliana is a fussy little plant. This can be a pain – even tiny environmental fluctuations can have significant impacts on the physiology and development that many of us are investigating.

As silly as it sounds, my labmates and I have spent many months debating the best compost media to use when growing Arabidopsis for research. It began when our trusted compost supplier changed the formula of its peat-based compost, which stressed our plants and turned them a lovely shade of purple! The conversation has continued to develop as we learn about the different media used in other laboratories.

A new paper from Drake et al. at my university (University of Bristol, UK) has added a new depth to the debate, so I thought I’d bring it all to your attention and perhaps receive some other suggestions to consider!

 

Peat-based vs non-peat compost

Arabidopsis growth media

Arabidopsis growth on peat-based and peat-free growth media. Drake et al., 2016.

The experiment, led by Dr Antony Dodd, was designed to test whether peat-based composts could be replaced by alternatives in Arabidopsis research, in an attempt to reduce plant science’s use of unsustainable peat extraction. The researchers grew two ecotypes of Arabidopsis (Col-0 and Ler) on both autoclaved and non-autoclaved composts, including peat-based compost and some formed of coir, composted bark, wood-fiber, and a domestic compost.

In terms of reducing peat use, Arabidopsis unfortunately grew best on the peat-based growing media, although some vegetative traits were comparable in some peat-free composts.

 

Autoclaving compost

This study caught my eye for another reason, however. We always sterilize our compost before growing Arabidopsis to reduce its contamination by fungi and insect pests; however, after learning that manganese toxicity can become a problem, we no longer autoclave it. As you can see in Boyd’s 1971 paper, manganese is converted to a more bioavailable form during the autoclave process, which can be toxic to plants.

Interestingly, Drake et al.’s research revealed no differences in Arabidopsis growth on autoclaved vs. non-autoclaved media, but I expect that in other environmental conditions the elevated manganese availability could become a problem. They did find that the autoclaved soil actually had more issues with mildew and algae, possibly because the natural microbiota had been killed and the compost was therefore easier to colonize.

 

Insecticide treatment

One of the biggest issues our lab has with non-autoclaved soil is the presence of small insects, which can predate our precious plants. A potential alternative to autoclaving is to treat the media with insecticide, such as imidacloprid, a neonicotinoid. However, many labs have stopped using these pesticides; in 2010, Ford et al. showed that several neonicotinoids, including imidacloprid, induce salicylate-associated plant defense responses associated with enhanced stress tolerance, while in 2012, Cheng et al. found 225 genes were differentially expressed in rice plants treated with imidacloprid. In experiments designed to measure precise physiological responses, I’m not convinced that it’s a good idea to use these pesticides!

 

Potential alternatives

To avoid using autoclaves and insecticides, you could consider baking compost overnight at 60°C (140°F) to try and kill fungal spores and insects, freezing the media, and/or using biocontrols to tackle insect pests, such as nematodes or mites.

In the peat vs. non-peat debate, it looks as though peat-based media are still the frontrunners in terms of compost, but hydroponic systems are becoming more popular as a way of tightly controlling nutrient regimes and manipulating whole plants more easily. Check out this video from Associate Professor Matthew Gilliham (University of Adelaide, Australia) to learn more about the technique:

If you have any other suggestions, please leave a comment and share your methods and ideas!

Apr 28
0

Brexit and agriculture

By | Blog, Future Directions
Professor Wyn Grant

Professor Wyn Grant

In June 2016, the UK Government will hold a public referendum for the people to decide whether or not Britain should exit the European Union. This contentious issue, popularly known as “Brexit”, has even divided the governing political party, with key parliamentary figures standing on either side of the debate.

There are many complex political issues for the UK to consider ahead of this referendum. One of these issues is: “what would be the consequences for UK agriculture if Britain were to leave the EU?” Professor Wyn Grant, a member of the Farmer–Scientist Network in the UK, tells us about a new report asking this very question.

Brexit and agriculture

by Wyn Grant

The Farmer–Scientist Network was set up by the Yorkshire Agricultural Society (UK) to facilitate practical cooperation between farmers and academics on the challenges facing agriculture. The Network felt there was a need to produce an assessment of the possible consequences of Brexit for agriculture. A working party was established, made up of leading experts on the EU’s Common Agricultural Policy and farmer members. I chaired this working party, and we produced what we hope is a comprehensive report, available here: http://yas.co.uk/charitable-activities/farmer-scientist-network/brexit.

Brexit ReportIn producing the Brexit report, one of our objectives was to provide information that farmers and others concerned with agriculture could use to question politicians during the referendum campaign. We also felt that agriculture and food had not been given sufficient attention during the negotiations and subsequent discussions. Should Brexit occur, our report draws attention to the issues that would have to be considered in exit negotiations.

The ins and outs of leaving

When evaluating the implications of Brexit for agriculture, we expected there would be complexities and uncertainties, but these were, in fact, greater than we anticipated. One reason for this is that, although the Lisbon Treaty on which the EU is founded makes provision for Member States to leave the EU under ‘Article 50’, none have ever done so before. It is difficult to know in advance how Britain’s exit would proceed, but it would almost certainly be necessary to use the entire two-year negotiating window provided for in the Treaty. Another complication is that the UK Government has not undertaken any formal contingency planning for exit, so it is difficult to know what a future domestic agricultural policy would look like.

In the event of Brexit taking place, the Farmer–Scientist Network feels that an optimal arrangement for the UK would be to establish a free trade area with the rest of the EU, with tariff-free access for UK farm products to the internal market. However, we don’t think the EU would want to give too generous a deal for fear of encouraging other member states to think about the benefits of exit.

Subsidies

Currently, two ‘pillars’ of financial subsidy are awarded to stakeholders in EU agriculture. We believe that the existing ‘Pillar 1’ subsidies that are given to EU farmers would be vulnerable after Brexit. This is an important issue, as for many farmers these subsidies make the difference between making a profit and running at a loss. Supporters of Brexit argue that the savings made from contributions to the EU budget would more than allow for subsidies to continue to be paid at the existing level. However, this overlooks the fact that the UK Treasury has for a long time targeted these subsidies as “market distorting”, and in the current climate of austerity in the UK, they could be at risk of being phased out as a means to reduce public expenditure.

We did, however, think that the ‘Pillar 2’ subsidies directed at agri-environmental and rural development objectives would be continued in some form. This is in part because they are embedded in contracts that continue beyond 2020, and because they have a coalition of domestic support from outside the industry from environmental and conservation lobbies.

Regulation

Some farmers resent what they see as excessive regulation emanating from Brussels. However, we think it is unlikely that many of these controls would be dropped or relaxed following Brexit. There are good reasons for regulations covering such areas as water pollution, pesticide use and animal welfare that have nothing to do with membership of the EU. Domestic support for such regulations would continue from environmental, conservation, public health, animal welfare and consumer organisations.

Some farmers hope that plant protection products that have been banned under EU regulations could be used after Brexit. However, there would still be domestic pressure to regulate these products and manufacturers might be unwilling to produce them just for the UK market.

Negotiation and trade

The UK at present negotiates in the World Trade Organisation (WTO) as a part of an EU bloc which provides additional leverage against powerful countries such as the United States. The agreements that the EU has with ‘third’ countries (those outside of Europe) would have to be renegotiated on a single country basis. Supporters of Brexit are confident that this task could be completed within two years. However, given that the UK has relied on the negotiating resources of the European Commission, it does not have many international trade diplomats and the process could take considerably longer.

Migrant labour

The horticulture industry in the UK is substantially dependent on migrant labour from elsewhere in the EU. This could not easily be replaced with domestic labour. It would be necessary to try and negotiate a new version of the Seasonal Agricultural Workers Scheme (SAWS) – a scheme (redundant since 2013) that was established to allow migrant workers from certain countries outside of the EU to work in UK agriculture – to ensure that the sector would have the labour it needs to function.

Conclusions

Being part of a larger political community gives British farmers some political cover from countries where farming makes up a large share of GDP or has strong cultural roots. The Farmer–Scientist Network concluded that it was difficult to see Brexit as beneficial to UK agriculture. However, we also emphasised that there are broader considerations about UK membership that needed to be weighed in any voting decision.

 

Apr 22
0

Witty gene names

By | Blog, GPC Community

It is a well known fact that biologists are a clever bunch. Most of the time they’re out applying their intellect and tackling the world’s problems, but occasionally (probably at happy hour on a Friday evening) they sit around coming up with witty names for genes.

Drosophila (fruit fly) geneticists have some classics, including the tinman mutant (which lacks a heart), Smaug (represses the ‘dwarves’ – Nanos), and the tribbles mutant (which has out of control cell division – don’t add water!).

Don’t worry though – plant scientists have come up with some clever gene names of their own! I asked the #plantsci community on Twitter for their favorites:

The superman mutant in Arabidopsis lacks the female parts of the flower, replacing it with more stamens. Fairly funny on its own, but naming its suppressor KRYPTONITE was even better!   

Like the 1970s TV cop Kojak, the kojak mutant is completely (root) hairless! In contrast, the werewolf  mutant produces LOTS of root hairs.

kojak

The kojak mutant (B) is completely bald! Image credit: Favery et al., 2001 and Universal Television

 

Ah yes, we can partially blame GPC’s Ruth Bastow for this one as she was co-first author on the discovery paper! TIMING OF CAB EXPRESSION1 (TOC1) had been shown to be involved in the circadian clock, and when Ruth and her colleagues discovered a gene that appeared to regulate TOC1, they named it TIC for the clever TIC-TOC of the circadian clock, then fit the full name (TIME FOR COFFEE) around it! The official reason was, “We located TIC function to the mid to late subjective night, a phase at which any human activity often requires coffee”. Hmm!    

My thesis is on stomatal development, so these are close to my heart! The word ‘stoma’ is  ancient Greek for ‘mouth’, so lots of stomata genes are mouth-based puns!

Where does YODA fit into this, you ask? This gene is the (Jedi) master regulator of stomatal development, of course!

tmm

The too many mouths mutant produces too many stomata. Image credit: Guseman et al., 2010.

 

In the run-up to the Brexit referendum on the United Kingdom leaving the European Union, SCHENGEN is a topical choice! This gene is involved in establishing the Casparian Strip, a lignified type of cell wall located in the endodermis. The schengen mutants don’t form this barrier, so were named after the Schengen Agreement that ‘established a borderless area between European member states’.  

Lisa’s spot on with these. The pennywise mutation was discovered first, named after a band, then when a paralogous gene was identified by the same authors, they continued the finance theme with POUND-FOOLISH.

The armadillo mutant in Drosophila has abnormal segment development, which looks a little like the armor plating of an armadillo. This protein contains ‘Armadillo repeats’, which is actually found in a huge variety of species including plants. The ARABIDILLO genes in Arabidopsis promote lateral root development, while PHYSCODILLO genes affect early development in the moss Physcomitrella patens.

 

Thanks, Ian!

Thanks to everyone who participated in this list. If you have a favorite whimsical gene name that hasn’t been mentioned, let us know in the comment section!

Apr 15
0

Lessons from the oldest and most arid desert on Earth

By | Blog, Global Change, GPC Community
Atacama Desert

Image credit: Center for Genome Regulation

The Atacama Desert is a strip of land near 1000 km in length located in northern Chile. With an average yearly rainfall of just 15 mm (close to 0 in some locations) and high radiation levels, it is the driest desert in the world. Geological estimates suggest that the Atacama has remained hyperarid for at least eight million years. Standing in its midst, one may easily feel as though visiting a valley on Mars.

Despite these harsh environmental conditions, it is possible to find life in the Atacama. At the increased altitudes along the western slopes of the Andes precipitation is slightly increased, allowing plant life.

Convergent evolution

The driest and oldest desert in the world acts as a natural laboratory where for 150 million years plants adapted to and colonized this environment. These adaptations are likely present in multiple desert plant lineages, thus providing an evolutionary framework where these traits can be associated with a signature of convergent evolution.

Surviving a nitrogen-limited landscape

Plant in the Atacama Desert

Image credit: Center for Genome Regulation

The interplay of environmental conditions in the transect of the Atacama, ranging from 2500 to 4500 meters above sea level, results in three broad microclimates; Pre Puna, Puna, and High Steppe. These microclimates have different humidities, temperatures, levels of organic matter and even different pH levels, but share one common feature: low nitrogen levels.

To engineer crops with higher nitrogen use efficiency, it is very useful to first learn how plants adapt to growth in low nitrogen environments. Here the Atacama Desert enters into the game. Plants growing in the desert can survive 100-fold less nitrogen below optimum concentrations. Using phylogenetics it is possible to uncover novel genes and mechanisms related to adaptation to these extreme conditions, which have not been discovered through traditional genetic approaches.

Currently, nitrogen fertilizers are widely employed to increase crop yield. In 2008 100 million tons of this fertilizer were used and it is projected that for 2018 the demand for nitrogen will rise to 119 million tons. Regretfully, the production and over-usage of this type of fertilizer has an enormous impact in the environment and human health. Around 60% of the nitrogen introduced to the soil for agricultural purposes is leached and lost. Moreover, nitrogen runoffs to the water cause eutrophication in both freshwater and marine ecosystems, leading to algae and phytoplankton blooms, low levels of dissolved oxygen, and finally the migration or death of the present fauna, forming dead zones such as the one in the Gulf of Mexico.
 

Plants in the Atacama Desert

Image credit: Center for Genome Regulation

Nitrogen fertilizers are not the only major concern in modern agricultural procedures. The co-localization of drought and low nitrogen levels is especially detrimental for plant growth and development. We need to support not only the nutritional requirement of an expanding global population but also new energetic strategies based on production of biomass for biofuels on marginal nutrient poor soils. In order to increase crop yields while reducing the environmental impact of nitrogen fertilizers, it is necessary to develop new agricultural strategies and cutting edge technologies.

Learning from the desert

What if we could profit from the extraordinary plants that have had thousands of years to learn how to cope with nitrogen scarcity, drought and extreme radiation? Specifically, can we unravel the genes and mechanisms that allow them to survive in such a barren place?

Atacama Desert

Image credit: Center for Genome Regulation

Over the past three years our group has identified 62 different plant species that inhabit the Atacama Desert, and established a correlation between their habitat attributes and biological characteristics. Using tools such as whole transcriptome shotgun sequencing or RNA-Seq complemented with different bioinformatics approaches, we have identified over 896,000 proteins that are expressed in these conditions.

In this way we aim to learn which processes are highly utilized in these “extreme survivors” compared to similar species that are present in the deserts of California, where the climatic conditions are similar but there is no nitrogen scarcity. That is how we expect to find new mechanisms (or, more precisely, very old mechanisms) that enable plants to survive and grow efficiently in extreme environments.

 

Susana Cabello

Dr Susana Cabello

Written by Dr Susana Cabello, Center for Genome Regulation, Millennium Nucleus for Plant Systems and Synthetic Biology, Chile. Susana would like to acknowledge Maite Salazar & Rodrigo Gutierrez for their suggestions and edits.

Apr 11
0

A year at the Global Plant Council

By | ASPB, Blog, GPC Community

Last April I joined the Global Plant Council as a New Media Fellow along with Sarah Jose from the University of Bristol. The GPC is a small organization with a big remit: to bring together stakeholders in the plant and crop sciences from around the world! As New Media Fellows, Sarah and I have have assisted in raising the online profile of the GPC through various social media platforms. We wrote about our experiences in growing this blog and the GPC Twitter and Facebook accounts in the The Global Plant Council Guide to Social Media, which details our successes and difficulties in creating a more established online presence.

 

Why do it?

My wheat growing in Norfolk field trials. I have spent every summer for the past 3 years out here analysing photosynthesis and other possible contributors to crop yield

My wheat growing in Norfolk field trials. I have spent every summer for the past 3 years out here analysing photosynthesis and other possible contributors to crop yield

I chose to apply for the fellowship during the third year of my PhD. Around this time I had started to consider that perhaps a job in research wasn’t for me. It was therefore important to gain experience outside of my daily life in the lab and field, explore possible careers outside of academia and of course to add vital lines to my CV. I still loved science, and found my work interesting, so knew I wanted to stay close to the scientific community. Furthermore, I had always enjoyed being active on Twitter, and following scientific blogs, so the GPC fellowship sounded like the perfect opportunity!

 

The experience

I think I can speak for both Sarah and myself when I say that this fellowship has been one of the best things I’ve done during my PhD. Managing this blog for a year has allowed me to speak to researchers working on diverse aspects of the plant sciences from around the world. My speed and writing efficiency have improved no end, and I can now write a decent 1000 word post in under an hour! I discovered the best places to find freely available photos, and best way to present a WordPress article. Assisting with Twitter gave me an excuse to spend hours reading interesting articles on the web – basically paid procrastination – and I got to use my creativity to come up with new ways of engaging our community.

Next career move, camera woman?

Filming interviews at the Stress Resilience Forum. Next career move, camera woman?

Of course going to Brazil for the Stress Resilience Symposium, GPC AGM and IPMB was a highlight of my year. I got to present to the international community both about my own PhD research and the work of the GPC, Sarah and I became expert camera women while making the Stress Resilience videos, and I saw the backstage workings of a conference giving out Plantae badges on the ASPB stand at IPMB. It didn’t hurt that I got to see Iguassu Falls, drink more than a few caipirinhas and spend a sneaky week in Rio de Janeiro!

Helping out on the ASPB stand

Helping out on the ASPB stand with Sarah

 

Thank you

Working with the GPC team has been fantastic. I learnt a lot about how scientific societies are run and the work they do by talking to the representatives from member societies at the AGM. The executive board have been highly supportive of our activities throughout. Last but not least, the lovely GPC ladies, Ruth, Lisa and Sarah have been an amazing team to work with – I cannot thank you enough!

I have now handed in my PhD, left the GPC, and moved on to a new career outside of academic research. I’m going into a job focused on public engagement and widening access to higher education, and have no doubt my GPC experiences have helped me get there. My advice if you’re unsure about where you want to end up after your PhD? Say “yes” to all new opportunities as you never know where they will take you.

Thank you the GPC! Hopefully I’ll be back one day!

 

Thank you! It's been amazing!

Thank you! It’s been amazing!

Mar 10
2

The Secrets of Seagrass

By | Blog, Future Directions
Zosteramarina

Zostera marina. Public domain, via Wikimedia Commons.

It’s the ancient story of plant evolution: photosynthetic algae moved to damp places on land, eventually evolving more complex architecture, and spreading across almost all terrestrial habitats. To cope with the drier conditions, plants developed roots to absorb water, and vascular tissue to transport it; a waxy cuticle coating their surfaces to prevent evaporation; and microscopic pores called stomata that open to allow carbon dioxide to diffuse in for photosynthesis but close to prevent excessive water loss.

How, then, does eelgrass (Zostera marina) fit in to this tale? It’s a monocot descended from the flowering plants, but it has turned its back on dry land and returned to the sea; a rare feat that only appears to have happened on three occasions. The recent sequencing of the eelgrass genome has revealed several interesting insights into the dramatic genetic changes that have allowed it to adapt to what lead author Professor Jeanine Olsen described as, “arguably the most extreme adaptation a terrestrial (and even a freshwater) species can undergo.”

Sayonara to stomata

If you live in the sea, conserving water isn’t your main concern. Eelgrass was known to lack stomata, but genetic comparisons to other species, including its freshwater relative Spirodela polyrhiza, revealed the first surprise of the study: eelgrass has lost not only its stomata but also the genes involved in their development and patterning. “The genes have just gone, so there’s no way back to land for seagrass,” said Olsen.

A difference in defense

When angiosperms are attacked by herbivores or pathogens, their defense response typically involves the release of volatile secondary metabolites through their stomata. How can eelgrass release these compounds without stomata? The answer is: it doesn’t. The genome study found that eelgrass is missing crucial genes involved in making ethylene (an important hormone release in times of stress), as well as those responsible for producing non-metabolic terpenoids, which act to repel pests.

Selective pressures of the marine environment differ greatly from those of terrestrial habitats, so different pathways may be involved. Second, eelgrass has a wide repertoire of pathogen resistance genes, which suggests that it is exposed to a very different set of pathogens that may not respond to typical immune responses. Third, volatile secondary metabolites are often involved in attracting pollinators; this is not believed to be necessary in eelgrass, where submarine pollination occurs using the water itself.

Zostera marina. Public domain, CC0 1.0.

Zostera marina – National Museum of Nature and Science, Tokyo. Public domain, CC0 1.0, via WikiMedia Commons.

Changing the cell wall

Eelgrass is subject to extremely salty conditions, and it’s had to adapt to osmotic stress. Unlike typical plant cell walls, eelgrass has engineered its cell wall matrix to retain water in the cell wall, even during low tide. This involves depositing sulfated polysaccharides and low methylated pectins in the cell wall matrix, but until its genome was sequenced no-one knew exactly how. It turns out that eelgrass has rearranged its metabolic pathways: “They have re-engineered themselves,” Olsen explains.

Living with a lack of light

Some species of Zostera can grow in water 50m deep, where light levels are reduced and shifted into a narrow wavelength range; ultraviolet (UV), red and far-red light have particularly low penetration after the first 1–2m of seawater. In a classic eelgrass ‘use it or lose it’ response, it has lost the UVR8 gene, which is responsible for sensing and responding to UV damage, as well as the phytochromes associated with red and far-red receptors. It does, however, retain the photosynthetic machinery, including photosystems I and II.

Unravelling angiosperm evolution

The recent eelgrass publication has revealed how this plant has either lost or adapted typical angiosperm traits to suit its needs, by ditching its stomata, volatile secondary metabolites and certain light sensing genes, or by altering the structure and function of the cell wall. It also developed adaptations that enable gas exchange, help pollen stick to submerged stigmas, and promote nutrient uptake.

Could these adaptations be useful in crop breeding? While a lack of defense compounds would probably be a step backwards, it would be extremely useful to understand how eelgrass copes with biotic stresses without them. Removing light receptors would also be problematic, but could eelgrass help us to develop crops that can grow in shaded conditions, perhaps in intercropping systems? What can we learn from eelgrass’ nutrient uptake and salt-tolerant adaptations?

Now that we have seen some of the secrets of eelgrass, how can we best make use of them?

 

Read the paper: The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea (Open Access)

Read the editorial: Genomics: From sea to sea (paywall)

Read the press release: Genome of the flowering plant that returned to the sea

 

Feb 29
1

Plant Artificial Chromosome Technology

By | Blog, Future Directions

Established GM technologies are far from perfect

The first genetically modified (GM) crops were approved for commercial use in 1994, and GM crops are now grown on over 180 million hectares across 29 countries. The most used forms of genetic modification are systems that result in herbicide resistance or expression of the Bt toxin in maize and cotton to provide protection against pests such as the European corn borer. These systems both require few novel genes to be introduced to the plant, and allow more efficient use of herbicides and pesticides, both of which are harmful to the environment and human health. Current systems of genetic modification usually involve

Agrobacterium tumefaciens is used to genetically engineer plants in the lab. In nature this bacteria uses its ability to alter plant DNA to cause tumours.

Agrobacterium tumefaciens is used to genetically engineer plants in the lab. In nature this bacteria uses its ability to alter plant DNA to cause tumours. Image by Jacinta Lluch Valero used under Creative Commons 2.0.

the use of Agrobacterium vectors, direct transformation by DNA uptake into the plant protoplast, or bombardment with gold particles covered in DNA. However, current systems of transformation are far from perfect. Many beneficial traits such as disease resistance require stacking of multiple genes, something that is difficult with current transformation systems. Furthermore, it is essential that transgenes are positioned correctly within the host genome. Current systems of genetic modification can insert genes into the ‘wrong’ place, disrupting function of endogenous genes or having implications for down or upstream processes. An additional problem is that transfer of transgenes from one line to another requires several generations of backcrossing. However, the past two decades have seen great developments in microbiology. Many new tools and resources are now available that could greatly enhance the biotechnology of the future.

 

New technologies

Many new and emerging technologies are now available that could transform plant genetic engineering. For example, high throughput sequencing and the wide availability of bioinformatics tools now make identifying target genes and traits easier than ever. Technologies such as site-specific recombination (SSR) and genome editing allow specific regions of the genome to be precisely targeted in order to add or remove genes. Artificial chromosome technology is also part of this emerging group that could be of benefit to plant science. Synthetic chromosomes have already been used in yeast, and widely studied in mammalian systems due to their potential use in gene therapy. Although there have so far been no definitive examples in plants, work has been done in maize that shows the potential of the technology for use in GM crops.

 

Building an artificial chromosome

A minichromosomes is a small, synthetic chromosome with no genes of its own. It can be programmed to express any desirable DNA sequence that could encode for one, or a number, of genes. An ideal minichromosome would be small and only contain essential elements such as a centromere, telomeres and origin of replication. Once introduced into the plant the minichromosomes should be designed such that interference with host growth and development is minimal. A key requirement is that the chromosome is stable during both meiosis and mitosis. This would ensure introduced genes do not become disrupted or mutated during cell division and reproduction. Gene expression would therefore remain the same for many generations. Finally, the DNA sequence on the minichromosomes could be designed such that it is amenable to SSR or gene editing systems. This would allow re-design and addition of new traits further down the line.

 

Potential advantages of artificial chromosomes

Plant artificial chromosomes (PACs) have many advantages over traditional transformation systems. For example, to confer complex traits such as disease resistance and tolerance to abiotic stresses such as heat and drought, multiple genes are required. This is not easy with current methods of modification.

PACs could offer a new way to introduce beneficial traits to our crops plants and feed a growing population.

PACs could offer a new way to introduce beneficial traits to our crops plants and feed a growing population.Image by Seattle.Romer. Used under Creative Commons 2.0.

However, PACs allow an almost unlimited number of genes to be integrated into the host system. A further possibility that comes from being able to add multiple genes is the addition of new metabolic pathways into the plant. This could allow us to change the nutrients produced by a plant to benefit our diets. Additionally, in a contained environment, plants could be used as a cheap, sustainable way to produce pharmaceuticals. A second major benefit of PACs is that they avoid linkage drag. This is when a desirable gene is closely linked to a deleterious gene that acts to reduce plant fitness. Where this linkage is very tight even repeated backcrossing cannot separate out the genes. Design of new DNA sequences completely avoids this problem, and could allow us to select out detrimental traits from out crop plants.

 

Regulations for novel biotechnology

Emerging technologies pose new questions to policy makers regarding GM regulation. For example, the use of genome editing, whereby specific sites in the genome are targeted and modified, produces an end product with a phenotype almost identical to one that could be achieved through conventional breeding. This sets genome-edited crops apart from other transgene-containing GM material. For this reason many now argue that genome-edited crops ought not to come under current GM regulations. Much of this argument centres on whether or not to regulate the scientific technique used to produce a crop, or to regulate the end product in the field. For more information on genome editing including current regulations and consensus, see the links at the end of this article.

 

PACs pose a different set of problems entirely. Minichromosomes would be foreign bodies in the plant, and gene stacking within these introduces even more foreign genes than is possible with current technologies. This would require extensive assessment of both environmental and health effects prior to commercialization. Currently regulatory approval costs around $1-15 million per insertion into the genome. These heavy charges may discourage the further development of minichromosomes technology. However, with PACs it is possible that a particular package of genes could be assessed once, and then transferred into numerous cultivars. This would eliminate the requirement to individually engineer and test every cultivar, so perhaps saving time and money in the long term.

 

More information on genome editing:

Sense about science genome editing Q & A

The regulatory status of genome-edited crops

The Guardian article on genome editing regulation

A proposed regulatory network for genome edited crops in Nature

A recent workshop on the CRISPR-CAS system of genome editing was held in September 2015 by GARNet and OpenPlant at the John Innes Centre in Norwich, UK. You can read the full meeting report here.

 

 

 

 

 

 

 

 

 

 

 

Feb 22
0

Integrated Pest Management Systems

By | Blog, Future Directions

Herbivorous pests can devastate crops, with huge economic and social impacts that threaten global food security. In 2011 scientists warned that biological threats, including pests and pathogens, account for a 40% loss in global production and have the potential for even higher losses in the future.

A farmer sprays pesticides on her crop

A farmer sprays pesticides on her crop. From IFPRI – IMAGES. Used under Creative Commons 2.0.

In the 1950s and 1960s huge amounts of pesticides were being used in agriculture, with negative effects on both humans and ecology. Pests and pathogens were developing resistance to pesticides, and to counteract this chemical companies were developing ever stronger, more expensive chemicals.

Perry Adkisson and Ray Smith, both entomologists, noted the harmful effects on the economy and environment of the overuse of synthetic pesticides. Working together they identified practical approaches to pest control that minimized pesticide use. They developed and popularized integrated pest management (IPM) systems, for which they won the World Food prize in 1997.

 

“Integrated Pest Management (IPM) means the careful consideration of all available pest control techniques and subsequent integration of appropriate measures that discourage the development of pest populations and keep pesticides and other interventions to levels that are economically justified and reduce or minimize risks to human health and the environment. IPM emphasizes the growth of a healthy crop with the least possible disruption to agro-ecosystems and encourages natural pest control mechanisms.” FAO definition

 

What is IPM?

IPM is an approach to crop production that considers the whole ecosystem, integrating a number of management techniques, rather than focusing all resources on a single practice such as pesticide use. Adkisson and Smith identified a number of principals around which successful IPM should be based:

Firstly, crop varieties should be selected that are appropriate to the culture and local environment. This would ensure the crop species is already adapted to local conditions, and may have some defense mechanisms to protect itself from biotic and abiotic stresses.

Secondly, IPM is based around pest control rather than complete eradication. Therefore, maximum tolerable levels of the pest that still enable good crop yields should be identified and the pests should be allowed to survive at this threshold level, although allowing a number of pests to exist within the crop requires continual monitoring. Good knowledge of pest behavior and lifecycle enables the prediction of where more or less controls are required.

Finally, when choosing a method of control, both mechanical methods, such as traps or barriers, or appropriate biological control are preferential. However, pesticides can be integrated into the plan if necessary, providing use is responsible and not in excess of requirements. Some really cool practices are now emerging that can be used as part of an IPM system around the world.

 

Enhancing biological control

Simply reducing pesticide use can actually lead to increased yields, as farmers in Vietnam discovered when scientists convinced them to try it for themselves. Their nemesis, the brown planthopper (Nilaparvata lugens), is increasingly resistant to insecticides, with devastating outbreaks becoming more common. Rice farmers found that by stopping their typical regular insecticide sprays, the planthopper’s natural predators such as frogs, spiders, wasps and dragonflies were able to survive and remove the pests, giving farmers a 10% increase in harvest income. This improved biological control is a key component of IPM.

Brown Planthopper

The Brown Planthopper (Nilaparvata lumens) on a rice stem. From IRRI photos. Used under Creative Commons 2.0.

 

Push-pull technology

Push-pull agriculture has been very successful in Kenya, where stemborer moths can cause vast yield losses in maize with estimated economic impacts of up to US$ 40.8 million per year. Push-pull technology uses selected species as intercrops between the main crops of interest. Intercrops work in two ways, by pushing pests away from the economically valuable crop, and pulling them towards a less valuable intercrop. The stemborer moth push-pull system uses Desmodium (Desmodium uncinatum) to repel stemborer moths. Desmodium species are small flowering plants that produce secondary metabolites that repel insects. Moths are then attracted to the surrounding napier grass instead.

Aside from controlling the stemborer moth, this system has a number of additional benefits. Desmodium suppresses the growth of Striga grass (a devastating weed that you can read about here) via a number of mechanisms, primarily through interfering with root growth. Additionally, the intercrop species can be used for animal fodder and improve soil fertility. The multiple benefits and success of this system has meant push pull has now been adopted by over 80,000 small-holdings in Kenya and is being rolled out to Uganda, Tanzania and Ethiopia.

 

Stem borer larva feeding on a maize stem.

Stem borer larva feeding on a maize stem. From International Institute of Tropical Agriculture. Used under Creative Commons 2.0.

Abrasive weeding

Abrasive weeding is a relatively new technique that involves firing air-propelled grit at a crop to physically kill any weeds growing between crop rows. One issue with this method is that it indiscriminately damages the stem and leaf tissue of both crops and weeds, but grit applicator nozzles are available to more directly target the base of the stem to minimize collateral damage. A recent study found abrasive weed control reduced weed density by up to 80% in tomato and pepper fields, with 33-44% increases in yield.

Maize cob or walnut shells are currently the most frequently used grits, but the technique offers the exciting possibility of combining fertilization and weed control in one step, which could reduce time and cost to the farmer. For example, soybean meal is able to destroy plant tissues when fired from the gun, and has high nitrogen content that is released slowly into the soil over a period of at least three months, making it an ideal source of fertilizer.