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.

Sesquiterpene lactones and herbivore resistance

Sesquiterpene lactones and herbivore resistance

Sesquiterpene lactones and herbivore resistance

Stereochemical variation is common in plant secondary metabolites, but its importance in mediating plant–herbivore interactions has received little attention. Ahern and Whitney  use common garden experiments with common cocklebur, Xanthium strumarium (Asteraceae), to examine relationships between stereochemical variation in sesquiterpene lactones, herbivore damage and plant fitness. They find that the stereochemistry of sesquiterpene lactone ring junctions helps explain variation in plant herbivore resistance, in turn influencing plant fitness. Their results indicate that subtle differences in stereochemistry may be a major, yet under-appreciated, determinant of the protective role of secondary metabolites.

The trees have it…

Image: Stefan Laube/Wikimedia Commons.

Image: Stefan Laube/Wikimedia Commons.

Trees, those magnificent, organic, large – sometimes huge – woody constructions continue to fascinate and inspire all who stop, stand and stare up (and up, and up…) at them. So here’s a selection of tree-based items to maintain – or maybe even initiate? – the phenomenon of arborifascination. But first a question: why did the three-toed sloth come down from the trees?

Answer: to defecate! Sloths are considered to be amongst the most, well, er, slothful of animals that, anecdotally, spend most of their time in trees, doing ‘not a lot’, apart from eating tree leaves [they are arboreal herbivores, after all; Tree Use No. (TUN) 1]. However, not only is this descent to the ground energy-consuming, it also exposes the sloth to potential predators; so why would they risk it? Work by Jonathan Pauli et al. may have the answer to this otherwise inexplicable behaviour. Three-toed sloths* harbour moths, inorganic nitrogen (N) and algae (e.g. green algae Trichophilus spp.) within their fur. The lipid-rich algae are eaten by the sloths and presumably supplement their diet of leaves. By leaving the tree for defecation, the fur-residing moths are transported to their oviposition (egg-laying) sites in sloth dung, which subsequently facilitates further moth colonisation of sloth fur. Since those moths are ‘portals for nutrients’, levels of inorganic N (potentially from moth excreta) in sloth fur increase, which in turn fuels algal growth. As the researchers conclude, ‘these linked mutualisms between moths, sloths and algae appear to aid the sloth in overcoming a highly constrained lifestyle’. Wow! I will never look at a three-toed sloth in quite the same way again.

Also challenging perceived wisdom is work by Marc Ancrenaz et al. Traditionally, orangutans (the world’s largest arboreal mammal) are assumed to be obligate arborealists, swinging seemingly effortlessly from tree to tree (TUN 2) as they navigate their lofty aerial neighbourhood. However, observations of terrestrial activity by these primates in the wild begs the question, why? Hitherto this activity was considered to be a response to habitat disturbance, but Ancrenaz et al. found no difference in instances of this behaviour in disturbed versus non-disturbed areas. They therefore propose that terrestrial locomotion is part of the Bornean orangutan’s natural behavioural repertoire and may increase their ability to cope with at least smaller-scale forest fragmentation, and to cross moderately open spaces in mosaic landscapes. So, it seems that even orangutans can have a bit too much of the ‘high life’ at times.

Finally, a terrestrial–aquatic organism that’s going up in the world. Reviewing evidence of tree-climbing activity in extant crocodilians (crocodiles and alligators), Vladimir Dinets et al. suggest it is much more widespread than previously considered and ‘might have multiple functions’, e.g. as an alternative site for thermoregulation (TUN 4), or increased detectability of prey (TUN 5). So, there you have it, ‘tons’ of alternative tree uses! Trees, helping to make the world an even more amazing place.

 

* Two-toed sloths don’t go in for this more energetic activity – and have lower densities of moths, lower N levels and reduced algal biomass in their fur…

Pollination by sexual deception in Pterostylis

Pollination by sexual deception in Pterostylis

Pollination by sexual deception in Pterostylis

Pterostylis is an Australasian terrestrial orchid genus of more than 400 species, most of which use a motile, touch-sensitive labellum to trap dipteran pollinators. The mode of attraction, however, is uncertain. Phillips et al. find that a single species of male gnat (Mycetophilidae) visits and pollinates the rewardless flowers of P. sanguinea, and that the gnats often show probing copulatory behaviour on the labellum, leading to its triggering and the temporary entrapment of the gnat in the flower. Pollen deposition and removal occurs as the gnat escapes from the flower via the reproductive structures. The labellum is the sole source of the chemical attractant involved. It is predicted that sexual deception will be widespread in the genus, although the diversity of floral forms suggests that other mechanisms may also operate.

Hydraulic integration in tree root vessels

Hydraulic integration in tree root vessels

Hydraulic integration in tree root vessels

Plants can adapt to their environment by varying the hydraulic integration of their xylem network. While much is known about xylem organization in aerial parts, roots have been less well studied. Johnson et al. measure xylem embolism resistance and connectivity in roots of two co-occurring tree species in a semi-arid habitat, Quercus fusiformis and Sideroxylon lanuginosum.They find that Quercus vessels are primarily solitary, while Sideroxylon xylem is highly connected, leading to resistant and vulnerable xylem networks, respectively. Pit membrane thickness plays less of a role in embolism resistance than expected, suggesting that xylem organization is an important trait that has yet to be fully explored.

The controversial origin of the coconut

Lagoons, coral atolls and coconut palm dispersal (Viewpoint)

Lagoons, coral atolls and coconut palm dispersal (Viewpoint)

When coconut palms are the subject of a scientific report, the introductory paragraphs can mention only a few of the multiple uses that make this pan-tropical crop invaluable to thousands of smallholder farmers. A comment on the beauty and familiar appearance of coconut palms is hard to resist, and may be illustrated by a picture showing the graceful stems, supporting a crown of fronds, curving over a tropical lagoon, into which the ripe fruit can fall and float. The difficulty of dealing with a long-lived monocotyledon of unknown origin that cannot be vegetatively propagated may also be mentioned.

The original home of the coconut palm, Cocos nucifera, and the extent of its natural dispersal are not known. Proponents of a South American origin must explain why it is not indigenous there and why it shows greatest diversity in southern Asia. Conversely, proponents of an Asian origin must explain why there are no Asian Cocoseae and why the closest botanical relative to Cocos is in South America. Both hypotheses share the common problems of how, when, where and in what directions long-distance dispersal occurred.

 

Harries, H.C., & Clement, C.R. (2013) Long-distance dispersal of the coconut palm by migration within the coral atoll ecosystem. Annals of Botany, 113 (4): 565-570. doi: 10.1093/aob/mct293

 

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.

A better understanding of wheat gluten

Effects of nitrogen on ω-gliadins in wheat grain

Effects of nitrogen on ω-gliadins in wheat grain

Wheat is the most important food crop in the temperate world, being used to produce bread, pasta, noodles and a range of other baked goods and foods. The ability to produce this wide range of products is largely determined by the grain storage proteins (prolamins), which form a viscoelastic network, called gluten, in dough formed from wheat flour. The classification into gliadins and glutenins has proved to be remarkably durable, but does not reflect the true molecular and evolutionary relationships of the proteins.

The ω-gliadin storage proteins of wheat are of interest in relation to their impact on grain processing properties and their role in food allergy, particularly the ω-5 sub-group and wheat-dependent exercise-induced anaphylaxis. The ω-gliadins are also known to be responsive to nitrogen application. A recent study published in Annals of Botany compares the effects of cultivar and nitrogen availability on the synthesis and deposition of ω-gliadins in wheat grown under field conditions in the UK, including temporal and spatial analyses at the protein and transcript levels.

The results show that wheat ω-gliadins vary in amount and composition between cultivars, and in their response to nitrogen supply. Their spatial distribution is also affected by nitrogen supply, being most highly concentrated in the sub-aleurone cells of the starchy endosperm under higher nitrogen availability.

 

Wan, Y., Gritsch, C.S., Hawkesford, M.J., & Shewry, P.R. (2014) Effects of nitrogen nutrition on the synthesis and deposition of the ω-gliadins of wheat. Annals of Botany, 113(4), 607-615. doi: 10.1093/aob/mct291

A new website introducing genetic engineering

The Journey of a Gene is a new website at UNL-Nebraska that teaches the basics of genetic engineering. There’s a combination of videos, some from YouTube and some specifically made as well as some interactive sections.

The video above, explaining what a gene is, is an example of what they’re bringing in. Later they explain the role of promoters and coding and you get elements like the video below explaining how to use the interactive elements.

I tend to be wary of websites a teaching tools by themselves. There are very few good ones. However, I don’t know if they have some sort of special unit at UNL, but this is the second time I’ve found useful interactive animations produced there. They also do some handy astronomy tools. As one of AoB Blog’s non-botanists, I found the videos genuinely helpful in explaining some of the genetic engineering process.

It’s hard to say why some sites work and some don’t. If it was easy to spot why something was rubbish, then it’d be easy to fix. In this case, I think building it around one specific problem, Soybean Sudden Death Syndrome, means that you have an idea of what the context is. It’s not just random information; there’s actually a point to it. That kind of narrative structure means that the sections follow on from each other in a sensible way.

If you’re a new student and want a little extra help getting your head around what a gene is, and how DNA inheritance works when you start crossing and backcrossing plants, then you should definitely give the site a go. I can’t guarantee you’ll be genetic engineering your own plants by the end of the course, but you might at least have a better understanding of how it happens.

A tip o’ the hat to Agriview for pointing me at this.