Category Archives: Life

Evolution shaped the internal beauty of plants

Santa Cells

Image by Oliver Leroux.

As plants embraced the terrestrial lifestyle, they underwent a range of adaptations to increase their size and stature as well as to facilitate transport of water and/or solutes. These vegetative innovations, which include the development of vascular and mechanical tissues, increased the anatomical complexity of plants. Such specialization is reflected in the design of the cell walls which surround plant cells in each tissue and fulfill a wide range of roles that are fundamental to plant life. A recently published Special Issue of Annals of Botany features papers focusing on a diverse range of topics pertaining to cell wall diversity and evolution, as well as to cell wall biosynthesis and remodelling.

Plant microscopists take advantage of cell wall diversity and through combination of dyes with affinities for specific cell wall architectures and specialized optics one can display the beauty of the internal structure of plants. The Christmas-inspired image is composed of transverse sections of Equisetum arvense stem (eyes), Acorus calamus root (nose) and Apium graveolens petiole (mouth).

Editor’s Note: You can read Oliver Leroux’s review article Collenchyma: a versatile mechanical tissue with dynamic cell walls for free at Annals of Botany.

The Guardian tackles the ethics of rewilding

The Guardian posted an interesting article yesterday from Tori Herridge: Mammoths are a huge part of my life. But cloning them is wrong.

Mammoth

Mammoth of BC by Tyler Ingram / Flickr.

I’ll concede that a mammoth is not a plant, but part of what I found interesting is that Herridge points out that mammoths didn’t exist in isolation. She tackles the idea that mammoths could somehow be part of a plan to restore the arctic steppes, but she makes an important point:

There’s a reason the terms “de-extinction” and “rewilding” are so powerful and that’s because they imply a return to a time, a state of grace, a place that was somehow unspoiled. Cloning a mammoth offers us the hope of undoing the excesses of humanity, bringing back the creatures whose extinction we helped bring about.

I think the idea of turning back the clock, to a time when things are better, is a powerful image. However it isn’t practical. Herridge points out that the mammoth was part of a wider ecosystem of arctic steppe, and it’s not certain that the plants will naturally appear if you dump a load of mammoths in Siberia.

It’s not even purely about the plants. Looking this up I saw there was a lot about remediation in the Root Biology special issue of Annals of Botany (now free access). In particular, Interactions between exotic invasive plants and soil microbes in the rhizosphere suggest that ‘everything is not everywhere’ say Rout and Callaway. They’re talking about microbes in the context of invasive species, but I wonder what ten thousand years of change has done to the soil of the arctic.

We don’t have the plants, we may not have the right soils. We are going through a big extinction event. I’d love to see a mammoth, but sadly when you look at the social problems a mammoth would have, as well as the many conservation efforts competing for limited funding, I think Tori Herridge is right, and that she does a good job of explaining all the problems.

Is there a downside for plants when they can’t sense ‘up’?

Looking at a tree, it can be hard to visualise the sheer volume of water being drawn up from the roots to the canopy. That volume of was is massive, and puts cells under a lot of pressure, so lignin, the substance plants use to strengthen cell walls, is an important product. But what happens to lignin if you take gravity away? Growth and Lignification in Seedlings Exposed to Eight Days of Microgravity by Cowles et al. is a study that aims to find out.

The experiment on STS-3 was growing pine seedlings with mung beans and oat seeds. There were a couple of targets. One was to examine how gravity affected the production of lignin. The other was to test the PGU, the plant growth unit, that would be used in following missions.

Plant Growth Unit

From Cowles et al.

To see the effect of gravity a PGU with similar plants was kept on Earth, so the development of the plants could be compared.

Germination of the orbiting plants was much like the 1g plants. However, Cowles et al. point out that the seeds have to be prepared before launch, which gave them twelve hours on Earth to germinate. They found that the flying plants grew less, and in the case of the seeds, roots were growing ‘up’ as well as ‘down’. Some of the plants that grew in orbit also contained less lignin.

There have been plenty of papers that went on to cite this research, most recently Expression of stress-related genes in zebrawood (Astronium fraxinifolium, Anacardiaceae) seedlings following germination in microgravity by Inglis et al. in Genetics and Molecular Biology from this year.

Recently in Annals of Botany there’s been Xylem Development and Cell Wall Changes of Soybean Seedlings Grown in Space and in the opposite directon Hypergravity Stimulus Enhances Primary Xylem Development and Decreases Mechanical Properties of Secondary Cell Walls in Inflorescence Stems of Arabidopsis thaliana by Nakabayashi et al.

This is interesting that it still gets cited because the results weren’t all significant. While the mung beans had less lignin, the oat and pine seedlings didn’t have significantly less and the experiment was relatively small. However, this flight wasn’t just about the results, it also worked to establish a method. By laying out the experimental technique used to analyse the plant Cowles et al laid down a baseline for other researchers to compare and improve their techniques.

The basic question they studied remains important. Understanding the processes that produce lignin could help with technology on Earth. For example, it would be helpful in producing biofuel if there were less lignin in it to start with. Launching plants and growing them in space would be a spectacularly inefficient way to do that. However for small samples, it can be a useful way to isolate one variable and help figure out the mechanics of lignin production.

You can read more posts on papers from our spaceflight supplement by clicking the STS-3 tag.

Today’s Papers

Cowles J.R., Scheld H.W., Lemay R. & Peterson C. (1984). Growth and Lignification in Seedlings Exposed to Eight Days of Microgravity , Annals of Botany, 54 (supp3) 33-48. DOI:

Chapple C. & Rick Meilan (2007). Loosening lignin’s grip on biofuel production, Nature Biotechnology, 25 (7) 746-748. DOI: http://dx.doi.org/10.1038/nbt0707-746

de Micco V., J.-P. Joseleau & K. Ruel (2008). Xylem Development and Cell Wall Changes of Soybean Seedlings Grown in Space, Annals of Botany, 101 (5) 661-669. DOI: http://dx.doi.org/10.1093/aob/mcn001

Inglis P.W., Ciampi A.Y., Salomão A.N., Costa T.D.S.A. & Azevedo V.C.R. (2013). Expression of stress-related genes in zebrawood (Astronium fraxinifolium, Anacardiaceae) seedlings following germination in microgravity., Genetics and molecular biology, PMID: http://www.ncbi.nlm.nih.gov/pubmed/24688295

NAKABAYASHI I. (2006). Hypergravity Stimulus Enhances Primary Xylem Development and Decreases Mechanical Properties of Secondary Cell Walls in Inflorescence Stems of Arabidopsis thaliana, Annals of Botany, 97 (6) 1083-1090. DOI: http://dx.doi.org/10.1093/aob/mcl055

Crocus, saffron-omics and the highest value crop

Saffron, Crocus sativus and origin label

Saffron, Crocus sativus and a protected origin label

Saffron, the stigma of Crocus sativus, is the highest priced agricultural product (often €/$25 or £15 per gram) and a good example of a profitable crop with sustainability, cultural and social values, and high labour demand. I have been discussing –omics studies of the crop – the DNA, RNA, metabolites and secondary products – at the annual meeting of a European Science Foundation COST programme Saffronomics.

www.Saffronomics.org logo

www.Saffronomics.org logo

The ‘Action’ aims to coordinate research on Saffron-omics for crop improvement, traceability of the product, determination of authenticity, adulteration and origin to provide new insights that will lead a sound Saffron Bio-Economy. Despite the high price, the spice costs only a few pence/cents per portion, and adds enormously to the flavour and colour of many dishes. Biologically, saffron is the species Crocus sativus, as recognized by Linnaeus, and it is a sterile triploid with 2n=3x=24 chromosomes.

Audience for annual meeting

Audience for annual meeting

The programme of our Annual Meeting opened with the genomics sessions – the DNA, RNA, genetics and epigenetics. I don’t usually start reviews with, nor indeed include, my own talk, but here its content sets the scene for other work discussed at the meeting. I talked about the work of Nauf Alsayid, who shows the lack of any clear DNA differences between any accessions of saffron – whether from Kashmir, Greece, Italy, Spain, Holland or Iran. I cited a paper from 1900, itself reporting work back to 1844, where the French botanist Monsieur Paul Chappellier reported “for the Saffron, there is only known a single and unique species; for ages it has not produced a single variety”, writing that he was importing bulbs Naples, Athens, Austria, Spain, Cashmere and China (Chappellier P 1900. Creation of an improved variety of Crocus sativus. J. Royal Horticultural Society XXIV Hybrid Conference Report 275-277 – brilliant download, even available free for Kindle!). Plus ça change, plus c’est la même chose!

Highest quality Saffron from Thiercelin 1809

Highest quality Saffron from Thiercelin 1809

After my talk, Jean Marie Thiercelin, the seventh generation of the major saffron and spice company http://www.thiercelin1809.com told me that his grandfather knew Paul Chappellier, and he commented in the history of saffron production in France: Chappellier knew how to produce 10 to 15kg per ha before the First World War. After the war, saffron production stopped altogether in France, but it has restarted this century, with now some 137 growers on 37 ha but production of only some 5kg per ha.

Continuing with the talks, a DNA-sequence level study of saffron by Gerhardt Menzel with Thomas Schmidt (Dresden) analysed of several Gigabases of genomic survey sequence data, revealing about ten distinct tandemly repeated satellite DNA sequences that could be used to identify chromosomes in saffron by in situ hybridization. The species has a 78% repeat content in the DNA, with about 6% being the rDNA, and many different classes of transposons.

Giovanni Giuliano - High trhougput sequencing of saffron RNA and gene discovery

Giovanni Giuliano – High throughput sequencing of saffron RNA and gene discovery

Giovanni Giliano (with Sarah Frusciante, Italy) demonstrated the carotenoid cleavage dioxygenase from saffron stigmas catlayses the first step in saffron crocin biosynthesis, a clear example of the pathway to the critical secondary product giving saffron its value (http://www.pnas.org/content/111/33/12246.short).


Slivia Fluch - Saffronomics Genomics Working Group Leader

Slivia Fluch – Saffronomics Genomics Working Group Leader

Both Matteo Busconi and Silvia Fluch (Austria) discussed epigenetic differences detected from different saffron collections: important for both understanding the controls on gene expression and for determining the origin of samples. Each producing area seems to have distinct profiles. Caterina Villa (Porto) reported results from use of the plant ‘barcoding’ primers ITS and matK with high resolution DNA melting analysis for saffron authentication, and more detail about the chloroplast genomes was presented from Bahattin Tanyolac and his Turkish colleagues. Although wild species of crocus are of interest from several points of view, only one paper, from Joze Bavcon (Slovenia) discussed these in detail, with a report of the natural hybrid Crocus reticulatus x C. vernus.

Joze Bavcon Crocus of Slovenia Book Cover

Joze Bavcon Crocus of Slovenia Book Cover

The next group of talks discussed the saffron metabolome, the analysis of different constituents of Crocus. Crocus is one of the few species to have its own international standard (ISO3632: http://j.mp/isosaffron ), and both quality and purity are measured (including contamination with stamens and pollen, along with detection of adulteration. Several participants were involved in the formulation of the standard, and Gianluca Paredi reported improvements that need less than the ISO methods needing no less than 23g of stigmas! Natural colours from plants such as Buddliea, Calendula, Curcum, Gardenia, safflower (Carthamus Asteraceae), cochineal (from the insect) and turmeric are widely mixed with saffron.

Chair of the Saffronomics Action Professor Maria Tsimidou

Chair of the Saffronomics Action Professor Maria Tsimidou

The Saffronomics project leader, Maria Tsimidou (Greece), used the three ISO3632 peaks for saffron – colouring strength from crocins absorbing at a peak wavelength of 440nm, aroma from safranal at 330nm, and taste (flavour) from picrocrocin at 257 nm – for examination of quality and authenticity of commercial saffron samples. Of 16 samples, 3 were adulterated, and half of the pure samples were graded in ‘category I’. Another amazing figure quoted was the price of saffron in quantity: of 75 tonnes imported to one county, only 35% is priced at more than $500 per kg. Authentic saffron could not be produced for anywhere approaching $1000/kg (typically $10-$15000/kg), so all this bulk product is fraudulent. Technology sessions in the meeting covered alternative quantification approaches to spectroscopy: Laura Ruth Cagliani in Milan tested  different solvents for extraction for NMR-based metabolomic characterization of authentic saffron distributed within the COST partners as well as the NMR evidence of absence of plant adulteration in those saffron samples.

Moschos Polissiou Saffronomics

Moschos Polissiou Saffronomics

A leading group from Thessaloniki was able to detect adulteration with as little as 15% cochineal. EA Petrakis and Moschos Polissiou demonstrated how FT-IR spectroscopy is promising to quantify small amounts of adulterants in saffron – safflower, Gardenia and tumeric – where diffuse reflectance mode provides rapidity, ease of use and minimal sample preparation. Other important reports discussed aging effects on profile of secondary metabolites (Paraskevi Karastamati Greece) and detection of herbicide residues (Christina Mitsi).

H stable Isotope Map from http://www.earthmagazine.org/article/cold-case-files-forging-forensic-isoscapes

H stable Isotope Map from http://www.earthmagazine.org/article/cold-case-files-forging-forensic-isoscapes

Micha Horacek (Austria) presented new results looking at the ratios of stable isotopes in saffron, a technique increasingly used to determine the origin of all agricultural produce. He showed the impressive map of with the gradient of water (hydrogen and oxygen) isotope ratio from North to South and from East to West in Europe. He also showed the differences in nitrogen stable isotope ratios depending of fertilizer use, and sulphur which depends on the underlying geology. Current work with saffron shows considerable year-to-year variation in the position of accessions from different regions of Europe, but the data is still being collected. Soon Micha will be getting a sample of our own, Leicester-lab-produced, saffron to add to his map!

Our hosts at RIKILT, the Food Safety and Quality Institute, Wageningen University, have much advanced applied science on food quality. An eye-opening talk by John van Duynhoven told us about rehydration of freeze dried blanched carrot with dynamic assessment of water movement in samples with and without blanching, freeze drying at -28 and -150C. Another series of images showed water transport and the impact of pre-cooking of rice, using magnetic resonance imaging MRI as a functional measurement of rice cooking. The final section discussed why crackers don’t crack: vapour transport during shelf life of crackers! Modelling of the nature of water transport links processing & formulation to the structure and on to functional and storage implications.


Fran Azafran - a school book about saffron

Fran Azafran – a school book about saffron

For ESF – COST projects, dissemination and public understanding are important, and participants were treated to a preview of a series of six school books about Fran Azafran and Franny Azafran by Manuel Delgado from Cuenca, Spain. I look forward to seeing these in full, and hopefully to their availability in other languages too.


At the podium

At the podium

Like the best of the projects, I feel that saffron science has moved in the last decade, (including research in the consortia www.crocusbank.org and www.saffronomics.org) with notable fundamental, technical and applied outcomes of our research. We know about its relatives and genome structure, key genes, metabolic processes and the key secondary products, and even understand epigenetic control, corm growth and dormancy. After 4000 years of being sold fake saffron, the fraudsters know now that we can test for saffron purity and quality!

Marta Rodlan (Vice Chair of the Action), Jose Antonio Fernández Perez and Jean Marie Thiercelin: key people in saffronomics

Marta Rodlan (Vice Chair of the Action), Jose Antonio Fernández Perez and Jean Marie Thiercelin: key people in saffronomics

Saffronomics Meeting Book Cover

Saffronomics Meeting Book Cover

The Martian by Andy Weir

TheMartianA while back I asked for recommendations for science fiction reading involving botany. On our Facebook page Claire Soulsby suggested The Martian by Andy Weir. I’ve had a stroke of luck* and have been stuck in bed feeling sorry for myself. This has given me plenty of time to read it.

The story begins after a freak dust storm on Mars causes the Ares 3 team to abandon their mission, leaving behind their dead crew member, Mark Watney. Watney awakes to find himself alone with the habitat and no hope of rescue for years, and enough food for months. The challenge is to produce food, water and oxygen to keep him alive and then to establish contact with NASA to coördinate a rescue.

The key to survival is first botany. It’s Watney’s ability to grow food on Mars that keeps him alive long enough to get a fighting chance. As everybody knows Botanists are pretty much the closest thing we have to superhero geniuses, so Watney is able to engineer all the fixes he needs to make in the hab to make farming, and everything else he needs, happen.

The book reads like hard-SF for the most part. The science is plausible and by relying on near-future science it means that Weir puts his character in a believable danger. The start of the writing process was planning a hypothetical Mars mission, including contingency plans for what might go wrong. Then he realised the contingency plans would make the basis of a story.

Most of the story is told through log entries. This works to explain the problems and the solutions. It also gives a plausible reason for why the character comes across the way he does. I vaguely remember someone saying there are no characters in Shakespeare plays, just plot devices. In a similar way, I’m not sure there are many characters in this book. In a couple of other reviews, people think the characterisation is weak. Watney does things, but he’s not changed much by them. When the next problem comes along in the book, he simply settles down to solve it so while there are many problems, I don’t know if there are many setbacks or catastrophes. Watney’s job at times seems to be to set up the next problem.

Fortunately, the problems are interesting enough to pull the story along. It’s also a change to read something where not every scientific problem can be solved by basic physics.

There’s a video of a talk he gave at, including a reading of the first chapter.

*Not good luck. I tend to avoid that.

Other reviews

Developmental robustness and species diversity: A special issue of Annals of Botany open for submissions

Magnolia flowers

Flowers from the same Magnolia tree have different numbers of perianth organs, indicative of a low degree of robustness in perianth organ number determination.
Photos by Susanne Schilling.

J.B.S. Haldane is often quoted to have said that ‘God has an inordinate fondness for beetles’. Arguably, Haldane himself would not have accepted this as an explanation for the enormous number of beetle species – they make up some 25 – 30 % of all described animals. However, Haldane’s statement demonstrates that we still lack a satisfying explanation for an oddity in the tree of life: it is only a few taxa that contribute disproportionately strongly to species diversity, whereas other taxa contain relatively few species. This observation is by no means restricted to the animal kingdom; if Haldane would have been a botanist, he may have said that god (like most of us humans) has an inordinate fondness for flowering plants – these make up some 85 – 90 % of all described plant species. The question is obvious: Why are there so many flowering plant species but so few gymnosperm species? Likewise, one may ask: Why are there so many orchid, daisy and grass but so few early diverging angiosperm species? A number of explanations have been suggested over the years: the age of clades, evolutionary innovations and co-evolution may all well have contributed to the success (in terms of species number) of some taxa over others. But as obvious as some of these explanations might be for certain groups – for example, co-evolution with pollinators may well have accelerated the radiation of orchids – they fail to explain other cases of species diversity: co-evolution with pollinators can hardly explain why there are more than 10,000 species of mainly wind-pollinated grasses, for example.

However, one striking observation is that successful taxa appear to be morphologically rather uniform: all orchid flowers share a basic floral bauplan, the same applies to grasses or daisies (and also beetles have a highly standardized body plan). Highly standardized or uniform structures may be an indication for a high degree of developmental robustness. Thus, in contrast to what one may intuitively assume, robust developmental processes might facilitate rather than prevent the evolution of species diversity.

We started exploring the relationship between species diversity and developmental robustness on a symposium at the Euro Evo Devo 2014 conference in Vienna that was supported by the Annals of Botany. However, we are still far from understanding the relevance of robustness for species diversity. On account of this, a Special Issue on that topic will appear in the Annals of Botany. Authors already committed to contribute to this Special Issue are Peter Endress (Zürich), Angela Hay (Cologne), Matthew Wills (Bath), Koichi Fujimoto (Osaka), and Veronica Grieneisen (Norwich).

This is an open call for submission of manuscripts on developmental robustness, biodiversity and the relationship between the two for consideration for the Special Issue. We intend to have a mixture of papers treating the topic from the perspective of developmental genetics, evolutionary biology, plant morphology, paleobiology and systems biology. If you have a manuscript that you would like us to consider, please send an outline (Title, Authors and 250 to 500 words) until the end of 2014 to annalsbotany@le.ac.uk. If agreed, the full paper would need to be submitted by 31 March 2015, in order to enter the full review process.

Picture Perfect

Young Woman Taking Photos Of Sunflowers.

Are you a keen photographer? You are reading a botany blog, so we can speculate that you have at least a passing interest in plants! Over at photocrowd.com you can combine these two passions and throw in a little healthy creative competition, as they are currently running a photo contest to showcase your best images on the theme of ‘Seeds and fruit’ (entry closes Sept 19th 2014, midnight UK time, winners announced 25th September 2014).

Simply join photocrowd, and upload one or two images. By submitting your images into a contest you gain the right to see what other members have submitted on the same topic, and you can vote for your favourite images as part of the ‘Crowd vote’. You can choose to ‘love’, ‘like’ or ‘pass’ an image. The crowd votes are updated in real time, be warned – checking your current score and seeing what new images have been submitted can become a bit of an addiction! There is also an expert judge who choses their favourite image. In this contest the top voted pictures, as chosen by the crowd and expert, each win £50 of professional photo retouching.

Good luck!

This photo © Belahoche/BigStockPhoto.

Domestication – rabbits now catching up with plants

Wild rabbits: how do their genomes differ from domesticated rabbits?

Wild rabbits: how do their genomes differ from domesticated rabbits?

Domestication of species is critical for our farming and own nutrition, as well as being important for retrospective studies of evolutionary genetics and future applications in animal and plant breeding. The genes involved in the first stages of domestication in plants are relatively clear: a single, tasty, energy-rich, product over-produced with a high proportion easily harvested, quick and easy establishment when planted, and disease resistance (free: Special Issue Preface and full issue of Annals of Botany). It has been less clear what is needed from a newly domesticated animal: many are multi-purpose (wool, leather, milk, meat, draught/traction, as well as companions and guarding), but why haven’t more animals been domesticated? What traits are being selected? (In particular, not one of the nearly 1000 sub-Saharan vegetarian mammal species has been domesticated.) Remarkably, most of our current crop plants and animals were domesticated in a relatively short period about 10,000 years ago, so, particularly for animals, finding near-relatives for genetic studies has been difficult.

A new paper from Miguel Carneiro Porto, Portugal, and colleagues from Sweden and the US in Science this week (Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication – Carneiro et al. p. 1074; 29 August, on the Science website) uses genomic analysis of DNA in domestic and wild rabbit with whole-genome DNA sequencing information. They address some of the key questions about animal domestication. Another summary of the paper is given by Penny Sarchet in New Scientist today. Rabbit domestication is recent – only in the last 1400 years; wild populations exist for comparison, and there are multiple selected breeds, so it is a good system to work with compared to other animals. I met first Miguel Carneiro when he talked about a related paper at a meeting in Portugal in 2010 (2011 Mol Biol Evol, The Genetic Structure of Domestic Rabbits Carneiro et al.), but have not had other contact with him, although we have continuing collaboration with a nearby lab Prof Raquel Chaves at Vila Real, Portugal, on bovid genome structure and evolution.

Domesticated rabbits - friendly and little fear

Domesticated rabbits – friendly and little fear

Key points for me from the rabbit paper are that they found about 100 regions that were selected to be different and showed evidence for selective sweeps (genomic regions of reduced variation and segregation distortion or linkage disequilibrium) in the domesticated compared to wild rabbits. This means that many genes were selected simultaneously (new result) so domestication was difficult and involved only a dozen to a thousand individuals (those latter data are in the 2011 Mol Biol Evol paper) with the appropriate combination of genes. This high number also explains why domestication loci have been hard to find in animals – it is too many to study with crosses and genetic analysis, only with genome sequencing (a new result). The second really interesting new point is which genes are in these regions: they find genes affecting brain development and sensory organs are strongly over-represented in these regions. In other words, selection during domestication might have focused on tameness and lack of fear: as a farmer, you neither want the animal to hurt you, nor for the animal to die from stress. Secondarily, an animal uses a lot of energy and time to keep a look-out and flee – energy that humans would rather went into meat and milk! It is notable that gene loss is not significant during evolution: most of the changes are due to gene allele polymorphisms.

A wild rabbit on guard, using lots of energy and sensory perception. These genes are selected in domesticated rabbits.

A wild rabbit on guard, using lots of energy and sensory perception. Carneiro et al. 2014 show these genes are selected in domesticated rabbits.

I do mention sensory perception, ‘friendliness’ and fear in my lectures on animal domestication – zebras kill more people in zoos than any other animal because they bite and hold on to their keeper, while deer panic and have heart attacks or break a leg. But until now there have been minimal real data about the changes in this group of genes – I think this paper is a first. (I once heard a talk about reduced brain size in farmed trout fish, but forgot the author and never found a reference.) Given the large number of loci, possible introgression and crosses to wild rabbits every few dozen generations (although this was not noted in the study and should have been evident), and large regions around genes affected by the genomic sweep that include non-coding polymorphisms, the results make a lot of sense. They also explain why previous studies have had difficulty in showing genetic signatures of domestication in farmed animals – lots of loci, too long periods to study, more difficult population structures without wild relatives.

I did contact Miguel Carneiro about the introgression question: he replied “there is good solid data that domestic rabbits when released in the wild and in the native range (Iberia and France) are very unlikely to survive the first couple of days due to predation pressure, indicating that introgression in this direction is difficult.” So indeed, the reduced sensory perception and reduced fear response has an immediate and large consequence. He comments that the reverse of wild introgression into domestics is likely to have happened, but the genetic bottleneck signature in domestic rabbits perhaps suggests that this is not so frequent.

Lack of segregation of characters in crosses to look at rabbit (or indeed other animals,where wild x domestic crosses are possible) domestication characters suggests many genes are involved (unlike the small number of genes controlling, say, coat colour in rabbits, or growth-related genes like broiler vs egg-laying chickens). I would speculate that many different monasteries in France in the middle ages tried to keep wild rabbits, eventually with a few finding rare rabbits with a suitable combination of characters which were then progenitors to the current domestic breeds.

A cow tooth found in a milking parlour: cows loose their own milk teeth in their second lactation. Humans selected early breeding but not loss of other juvenile characters.

A cow tooth found in a milking parlour: cows loose their own milk teeth in their second lactation. Humans selected early breeding but not loss of other juvenile characters. Wild relatives would have their first calf years later.

The genomic loci give many suggestions where we should look to improve rabbits. I have blogged about the possible importance of aquaculture and fish or crustaceans as a part of improving agricultural sustainability already, but introduction of rabbits as a more exploited source of animal protein also has potential: they (or at least their bacterial gut microbiome) means they digest grasses and fibres. Thus, like cows but unlike pigs or chickens, they can use agricultural products that do not compete with human food uses. Since rabbit domestication is so recent, we can also anticipate what ‘second stage’ domestication traits we should be looking for – rather as we suggested earlier this year should be done in proso millet, Panicum miliaceum, which was domesticated in the first wave but has since declined in relative importance despite having extremely high water efficiency.

What wasn’t found in the the genes associated with rabbit domestication was remarkable. There is no mention of disease-resistance loci and nor of reproduction or breeding-related genes – I would expect these to be over-represented in selected regions (both of which are important traits for domestication of both plants and animals). Disease and reproduction are very important in other domestic animals: high population densities mean diseases spread quickly, while we need fast and easy breeding with no photoperiodic breeding response (not least so we can have eggs and milk all through the year and don’t need to keep cattle until they are 4 or 5 years old before breeding). It is possible these are single-gene loci which would be found but not necessarily stand-out in a genome-wide analysis. Or maybe these are characters where wild rabbits already have the domestication-required genes: they live in large inter-connected colonies (not unlike a farm already) and of course are a byword for reproductive success!

The ultimate friendly, domesticated rabbit

The ultimate friendly, domesticated rabbit.

Another summary of the rabbit genomics of domestication paper is given by Penny Sarchet in New Scientist.

Science 29 August 2014:
Vol. 345 no. 6200 pp. 1074-1079
DOI: 10.1126/science.1253714

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication

Miguel Carneiro, Carl-Johan Rubin, Federica Di Palma, Frank W. Albert, Jessica Alföldi, Alvaro Martinez Barrio, Gerli Pielberg, Nima Rafati, Shumaila Sayyab, Jason Turner-Maier, Shady Younis, Sandra Afonso, Bronwen Aken, Joel M. Alves, Daniel Barrell, Gerard Bolet, Samuel Boucher, Hernán A. Burbano, Rita Campos, Jean L. Chang, Veronique Duranthon, Luca Fontanesi, Hervé Garreau, David Heiman, Jeremy Johnson, Rose G. Mage, Ze Peng, Guillaume Queney, Claire Rogel-Gaillard, Magali Ruffier, Steve Searle, Rafael Villafuerte, Anqi Xiong, Sarah Young, Karin Forsberg-Nilsson, Jeffrey M. Good, Eric S. Lander, Nuno Ferrand, Kerstin Lindblad-Toh, Leif Andersson

ABSTRACT
The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small number of fixed (or nearly fixed) single-nucleotide polymorphisms (SNPs) for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved noncoding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that because of a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few domestication loci.

Stevia hits the mainstream with ‘Life’

Last year Aurélien Azam blogged about Stevia in his post, Can we find all the tastes we like in the Wild? He mentions Stevia in it and if you don’t remember it, then Coca Cola will try to change that. Stevia is the plant behind the new Coke variety, Life.

Coca Cola Life and Death

The marketing department at Coca Cola are about to discover that if the green bottle is called ‘Life’ there’s an obvious name for the red bottle.

Stevia rebaudiana leaves are complicated sugar factories. Initially they import carbohydrates, but as leaf area increases photosynthesis means they start producing more sugars to supply the rest of the plant. The key chemicals are Steviol glycosides. These are, for the same concentration, around 300 times more sweet than sugar. The exciting feature is that human body cannot produce any calories from these sugars. For marketing, it’s the fact that it’s a plant that’s the chemical factory that’s news. If it’s made in a plant then you can label it: From Natural Sources.

But this is one of those situations where natural is probably not a synonym for good.

Stevia growing naturally in Paraguay. #156515950 / gettyimages.com

Abdel-Rahman et al. (2011) report on Stevia, among other natural products in Toxological Sciences, and note that in aqueous, crude or partially purified form Stevia can be bad news for rats. One side-effect can be reduced fertility in female rats. It’s always best to be wary from directly applying animal tests to humans, but they also note that the Guarani Indians of Paraguay would make something a bit like a tea from the Stevia leaves. They used it as an oral contraceptive.

For this reason it’s a relief that the sweetener isn’t natural, but a highly processed form of Stevia. But how does it taste?

I set up a comparison taste test with Coca Cola Life (green bottle) and the Cola Cola from the red bottle – which for ease of labelling we’ll call Death. I also added Coke Zero as a third option. All bottles were chilled and the opened with ice added. I then ignored protests from the tasters that they weren’t that thirsty.

The taste test followed a predictable pattern.

After glass 1 Zero: “Hmm.”
After glass 2 Death: “That’s definitely the full-fat Coke and the first is Stevia.”
After glass 3 Life: “Euww! No, that’s Stevia isn’t it?”

Stevia has a distinctive taste, and one that’s unexpected in Coke. Success will depend on how much the public develop a taste for it.

If it does succeed, the payoff could be big. As well as the battle against obesity, Stevia-derived sweeteners promise other benefits including fighting diabetes, high-blood pressure and tooth decay. However for now if it’s a choice between liberty from health issues or Death, a good chunk of the public will opt for Death.