Monthly Archives: September 2011

Food Crisis in 2050?

Wheat Ears Anthesis

Wheat Ears Anthesis by Pat Heslop-Harrison

A realistic scenario, if the production of major crops does not increase significantly. Estimated 9 billion people will need 70% more food than today. In June 2011, The G20 Agriculture Ministers agreed on an “Action plan on food price volatility and agriculture”. As a first step of the G20 Action, an International Research Initiative for Wheat Improvement (IRIWI) has been launched in Paris on September 15, 2011. This initiative should pave the way to similar initiatives for other crops.

Wheat is the most widely grown crop worldwide and provides 20% of all calories and 20% of all protein. Despite the importance of wheat for food security, its production has not met demand in 6 of the last 10 years. The yields are stagnating and the investment in wheat research and development is disproportionally low. The first aims of IRIWI will be targeted towards generating and sharing tools, methods and results that will enable breeders to take full advantage of genomics assisted approaches.

A publicly available high quality annotated sequence of the wheat genome is one of the much needed resources. In order to tackle the huge and polyploid genome of 17Gb, the International Wheat Genome Sequencing Consortium (IWGSC) adopted the chromosome strategy, which relies on the ability to dissect the genome to 42 small parts represented by individual chromosome arms. These are physically mapped and sequenced. The strategy facilitates division of labor and international collaboration.

On our Scoop It between September 21st and September 30th

These are links from our Scoop It page between September 21st and September 30th:

How to Grow a Beautiful But Deadly Garden

From hemlock through castor bean to nightshade and monkshood … while “most of the plants you’d find in a garden are harmless beauties, not all are so innocent and a few can even be downright deadly. But some gardeners prefer to grow on the wild side, cultivating botanical killers that can be as beautiful as they are lethal.
From rat-eating carnivores to toxin-producing plants tapped by KGB assassins, these are some of the strangest and most deadly botanicals

Read more:

Flowers bloom for a second time

UK plants are flowering for a second time this year because of the unseasonably warm weather. With temperatures soaring, plants such as foxglove and cowslip, which usually flower in the spring, are in full bloom six to eight months early. Cold nights experienced across the UK in August are thought to have led to the early onset of autumn colours. This warmer spell now has plants acting like it is spring.

Affable Nerds and Second Bananas: What Science Communicators Can Learn From Top Gear

“Why has academia largely ignored one of the world’s most popular technology programmes – and what does the show tell us about the effective communication of complex ideas?”

A review of a scholarly paper on what we as scientists can learn from Top Gear about presentation of technical material …

Starting and Maintaining Your First Laboratory An Essential Checklist

Valuable points and pointers about starting a new lab in this three-part series. Make sure you learn these skills as a PhD student or post-doc!


Running your own lab is an exciting venture filled with success, discovery, and the opportunity to pursue novel research. With such excitement comes great responsibility, whether in the form of mentoring graduate students, helping postdocs find jobs, publishing a steady stream of research, and securing tenure at your university or research institute. In addition, the combined logistics of managing startup (and additional grant) funding, ordering supplies and setting up a functional lab, not to mention relocating and finding housing, can be very overwhelming and stressful, to the point of impeding productivity. But it doesn’t have to be.

Money for shiny new rope?

Thoughtful comments on what research is needed to support farming in Africa. Exactly how useful is a genome to the typical farmer?

The Story of Agriculture and the Green Economy

The future of our world depends on addressing global challenges now. We need to create sustainable livelihoods, feed a growing population and safeguard the environment. Agriculture accounts for 37% of employment, but 97% of these live in developing countries. We must increase productivity and reduce wait, increasing quality and biodiversity.

Plant bends to bury its own seeds

A new plant that “bends down” to deposit its seeds has been discovered in the Atlantic forest in the state of Bahia, northeastern Brazil. The new species has been named Spigelia genuflexa after its unusual adaptation. After fruits are formed, the fruiting branches bend down, depositing the capsules of seeds on the ground and sometimes burying them in the soft cover of moss

Smithsonian magazine: Maize geneticist Barbara McClintock is a female scientist you should know

Barbara McClincock determined that genes could move within and between chromosomes by observing the patterns of coloration of maize kernels over generations of plants. The finding didn’t fit in with conventional thinking on genetics, however, and was largely ignored; McClintock began studying the origins of maize in South America. But after improved molecular techniques that became available in the 1970s and early 1980s confirmed her theory and these “jumping genes” were found in microorganisms, insects and humans, McClintock was awarded a Lasker Prize in 1981 and Nobel Prize in 1983.


Link via American Society of Plant Biologists


Plant biodiversity theory debunked

Why are some environments teeming with different plant species whereas others support only a few? Light, not productivity, may control species richness.

Search for ‘lost apples’ widens

A search of a variety of apple first grown in the Highlands has widened out into an effort to trace four other ‘lost’ types.


Free—open access paper: Phylogeny and divergence times inferred from rps16 sequence data analyses for Tricyrtis (Liliaceae), an endemic genus of north-east Asia

The rate of molecular evolution of Tricyrtis plant groups as a model system was estimated. The outcome further highlights the importance of conserving biodiversity in a rapidly changing Earth environment. This phylogenetic analyses of Tricyrtis with its high endemism in north-east Asia sheds light on processes of speciation processes.


Affable Nerds and Second Bananas: What Science Communicators Can Learn From Top Gear

Via Scoop.itmolcyt

“Why has academia largely ignored one of the world’s most popular technology programmes – and what does the show tell us about the effective communication of complex ideas?”   A review of a scholarly paper on what we as scientists can learn from Top Gear about presentation of technical material …  
Show original

Autumn Clean

I’ve been tidying up my online presence, RSS feeds and so on for the new academic year. I’ll be moving my life sciences posts to a professional account on Google Plus, In some ways this is the wrong way round as my PhD is not in Botany, but it helps dealing with students. Another AoB Blog contributor on Google Plus is Alan Cann, who is a lot more active there than me.

One of the things I noticed is linkrot in my RSS feed. I’ve only just caught up with moving Google Reader to look to follow the Phytofactor who is now at

Another useful thing is that I now get timely reminders of other use posts like Introduction to R Statistical Software: Application to Plant BReeding on the Plant and Crop Science Blog. Francisco Fuentes has posted a video on the stats package by Dr. Heather Merk.

Free—open access paper: Co-ordinated changes in storage proteins during development and germination of elite seeds of Pongamia pinnata, a versatile biodiesel legume

Seeds of Pongamia pinnata used as feedstock for biodiesel production and the protein-rich residue is fed to farm animals. This paper describes seed development and early germination in terms of phenology, protein and reserve accumulation and utilization. The findings will underpin rapid and successful exploitation of this promising energy and animal feed crop.

Italian Genetics Societies in Assisi: staple foods and orphan crops via epigenomics and systems biology

Joint meeting of the Italian Genetics Societies Assisi

Joint meeting of the Italian Genetics Societies Assisi

Italian genetic research is in good health: this week I’m at a meeting held in the Cittadella in Assisi with about 500 people and 300 posters. The conferees reflect my own research interest with respect to species: about 80% of the work was on plants, and 80% of that work on crops, making a good start. The posters were all in English, as were the slides, but almost all the talks were in Italian, proving an unusual challenge. Nevertheless, my command of Italian is improving, and I am now fluent with Italian phrases such as “loss of function mutanti” and “next generation sequencing risultati”.

The three Genetics Societies in Italy – AGI, SIBV and SIGA  – put together a programme that nicely flagged the research going on in the country with strong international-level programmes. It was great that many of the top geneticists took part in the meeting, including Roberto Tuberosa, Michele Morgante, Antonio Blanco, Giovanni Giuliano, Roberto Papa or Mariano Rocci, to name just a few from my area. Even better, many only played a supporting role to key laboratory members who showed their own dedication and hard work in their results! This was much appreciated by the strong student representation, many of whom presented their first work at this meeting with its informal and supportive ethos. Not least because of my general familiarity with the work presented and its background (making the language of presentation less of a problem for me), it was particularly valuable to hear the Italian students and post-docs focusing on their contributions to major European and international projects, whether in whole genome sequencing, annotation and functional analysis, or in crop physiology, or animal genetics. The Organizers juggled the difficulty of breadth of coverage with keeping the meeting short and focussed nicely, with plenary and mostly only two parallel sessions. Major sessions were on topical issues such as epigenetics and epigenomics, then genome plasticity, moving on to systems biology. Sadly though, despite coverage of so many crops of special importance in Italy and the involvement of the agricultural genetics society, I failed to notice substantial contributions to discussions or presentations from breeders or seed organizations, the end users of so much of the research discussed.

Thunderstoms, here approaching Assisi, kept us in the conference centre

Thunderstoms, here approaching Assisi, kept us in the conference centre

At a couple of recent conferences, I have helped writing a slightly more balanced report of many talks through Twitter. I’m not going to give any overview of the meeting here – the abstracts are of course helpful – but I can just point to a few pieces of work which I will certainly be discussing with my lab. Next week. It was very exciting to hear and consider the consequences of modern genetic work for the crops of particular importance in Italy: a systematic analysis of transcriptomics through three wine vintages in three different regions, all with same grape variety, Corvina, demonstrated how modern biology is addressing long-standing questions about genotype x environment interactions, agronomy and food production (Dal Santo et al.). Genes involved in transcriptome plasticity can be assigned to vineyards with different agronomic classes and plastic transcriptional drifts impacted metabolic rearrangements depending on microenvironment and growing conditions.

Pre-breakfast viewing avoids the crowds at the posters

Pre-breakfast viewing avoids the crowds at the posters

Several posters addressed the genetics and diversity of Tuber magnatum, the white truffle, and one was even using mitochondrial DNA fingerprinting to identify the oils in paints used by the Renaissance artists of Italy. The next area of genetics research – integrating systems – was well-covered, with A Vigilante showing network analysis approaches for identifying gene associations or functions, and understanding consequences of genome duplication.

I was really pleased to have been part of this meeting, and to have so many valuable discussions. I have a substantial list of people where I want to continue discussions – ranging from needs for cytogenetic textbooks, to systems biology, to alien gene transfer. I hope some of the discussions we had will lead to visits to my lab for periods of joint research too. Of course, the beautiful environment of the Cittadella in Assisi was ideal for the meeting. We could mediate on the impact of genetics in the shadow of St Francis and world’s finest renaissance frescoes, in a small enough venue (the conference represented nearly 15% of the total population of the town) that demanding meditation (translating words of the Cittadella website) was in the framework of informal discussions of molecular genetics.

Back to reality: 77 hours without e-mails and 248 new ones!

Back to reality: 77 hours without e-mails and 248 new ones!


Free—open access paper: A platform for efficient genotyping in Musa using microsatellite markers

Establishment of a standardized platform for genotyping banana (Musa spp.) using a set of previously published SSR markers is described in this free—open access paper. The platform will serve a broad Musa research and breeding community and support the conservation and use of genetic diversity.

Plant versus Bee Power

Coming up in October we have a paper, ‘Flower power: its association with bee power and floral functional morphology in papilionate legumes‘ by Silvina A. Córdoba and Andrea A. Cocucci, in the journal. The paper examines if there’s any correlation between the strength of flowers and the strength of bees. Are they in an evolutionary struggle over access to flowers or is there no connection? More importantly how do you measure the strength of bees? Do you get them to bench-press tiny weights? Here’s a better way.

It turns out a bee has to be a complete wimp to be shut out of a flower. Bees don’t need their strength to enter, but the researchers find that flower shape may be significant.

On our Scoop It between September 3rd and September 17th

These are links from our Scoop It page between September 3rd and September 17th:

Man-in-a-box lives off plants

In the 1770s, Joseph Priestly put a mouse in a jar with some plants. It lived for several days, much longer than one without plants. He recognised that plants were allowing us to breathe, and called them 'lungs'. He recognised they were taking something in and giving something out that we needed.

Peruvian Cacao Collection Trip Yields Treasures

A stand of very old trees, in an unexpected location, has yielded a coveted type of cacao tree. Usually, cacao trees are found along rivers, but these gems were found at a higher altitude than normal, and in Peru instead of Ecuador or Venezuela.
Collection expeditions in 2008 and 2009 through the Amazon Basin of Peru uncovered the exceptional find, along with other distinctive new populations of cacao. (Link pointed out by Rodomiro Ortiz)

US plant scientists seek united front

The perennial grass Miscanthus × giganteus has all the makings of a biofuel superstar. It grows rapidly, converts sunlight into biomass ten times more efficiently than the average plant and has little need for fertilizer. But M. × giganteus is a headache in the lab. Researchers hope that the first ever summit to map the future of US plant science will change that, by encouraging researchers to tackle the genomic wilderness of emerging biofuel crops in a more systematic way.

Timeline for evolution of wheat from the origin of plants – Annual Wheat Newsletter.

A timeline of wheat evolution:

Bread wheat originated 8 thousand years ago (TYA). The wheat ancestors separated from rye 7 million years ago. This timeline from Byrne and Gornicki in the new Annual Wheat Newsletter (AWN) shows the key steps in wheat's origin from the earliest land plant fossils of 420 million years ago.

Evolution of Fruit Shape in Tomato « Biofortified

Someday you’ll be able to use CAD software to draw up what you want a plant to look like and the software (containing detailed growth models) will tell you what genetic constructs you need to bring it into the world…

But for now we barely understand how natural morphological variation is controlled. So I was excited to see this paper out of the van der Knaap and Francis labs. In it, they review some of the known levers by which tomato plants control fruit shape and investigate their historical appearance.

FAO: Global hunger declining but still unacceptably high

Interactive hunger map and >Policy Brief: click on the timeline or select a country for national data. At close to one billion, the number of undernourished people in the world remains unacceptably high in 2010 despite an expected decline – the first in 15 years. The recent increase in food prices, if it persists, will create additional obstacles in the fight to further reduce hunger. The number is higher than before the food and economic crises of 2008-2009 and higher than the level that existed when world leaders agreed to reduce the number of hungry by half at the World Food Summit in 1996.


Alien worms ‘threat to forests’

Alien earthworms can alter the carbon and nitrogen cycles in woodland, as well as undermine native plant species, a study suggests.

Encyclopedia of Life catalogues more than one-third of Earth’s species

The Encyclopedia of Life (EoL), a free and collaborative website, said on Monday it now has pages for each of 750,000 species, meaning more than one-third of all the planet's 1.9m species are now covered.

Jennifer Preece, dean of the College of Information Studies at the University of Maryland said, "There are many online sites dedicated to specific groups of species such as insects, birds or mammals. Not since Noah, however, has there been an effort like this to bring all the world's species together."

The site uses content from 180 partners to bring together images, videos and scientific information, including 35m pages of scanned literature created by the Biodiversity Heritage Library. The new site allows members to create their own collection of species.

Manipulating plants’ circadian clock may make all-season crops possible

Researchers have identified a key genetic gear that keeps the circadian clock of plants ticking. "Farmers are limited by the seasons, but by understanding the circadian rhythm of plants, which controls basic functions such as photosynthesis and flowering, we might be able to engineer plants that can grow in different seasons and places than is currently possible"

Counting chickens

THE world’s average stock of chickens is almost 19 billion, or three per person, according to statistics from the UN’s Food and Agriculture Organisation. Cattle are the next most populous breed of farm animal at 1.4 billion, with sheep and pigs not far behind at around 1 billion. China’s vast appetite helps make it the world leader in the number of chickens, pigs and sheep,