M people and the ‘B’ word…

Image: Wikimedia Commons.

Image: Wikimedia Commons.

No, this is not an item about M People, an ‘English house music band which formed in 1990 and achieved success throughout most of the 1990s’, nor about using profane language… Anyway, how would any of that be relevant to a straitlaced, sober, serious botanical news round-up that is the hallmark of a P. Cuttings item? It is about the phenomenon (I don’t think that’s too strong a word) known as ‘Dr M’. If you’ve not encountered this gentleman, then you should – we can probably all learn a little from him in our eternal quest to big-up botany and help to enthuse the next generation of plant biologists (or, at least, attempt to engender plant appreciation into the citizens of tomorrow). Dr M is the moniker of Dr Jonathan Mitchley, botanist and plant ecologist who goes WILD about teaching plant identification at the University of Reading (UK), and also acts as an ecological consultant with RSK Ltd. Looking like one imagines the Peter Pan of phytology should look like, his grinning visage beams botanical radiance upon all who chance upon his various web-based antics. His enthusiasm for all things verdant seems boundless and is evident in his varied offerings, such as his blogvideo-based plant ID quizzes and his YouTube-tastic Poaceae song. Maybe all of his outputs may not be to everyone’s taste, but they’re worth a look – you are highly likely to find something you can ‘borrow’ to enhance your own teaching of botany. In any event it’s really uplifting to see Dr M and ‘his people’ having so much botanical fun! As Dr M himself is wont to say, ‘Rock on, Botanists!!!’ Indeed (!).

 

[The true diehards amongst you might like to consider the extended-play, blooper-enhanced version of the Poaceae song on YouTube. Right, now what is the collective noun for a group of botanists? Answers, on a postcard-sized sheet of herbarium paper, please to… And in breaking news – well it was when this piece was penned – Dr M is now Associate Professor of Field Botany at the University of Reading – Ed.]

Nitrate uptake modelling in plants: root activity

Nitrate uptake modelling in plants: root activity

Nitrate uptake modelling in plants: root activity qNitrate uptake modelling in plants: root activity

Using a thermodynamic flow–force interpretation of nitrate uptake isotherms, Malagoli and Le Deunff  develop a functional– structural model to predict N uptake in winter oilseed rape, Brassica napus. The structural component of the model, the active root biomass, is derived from a combination of root mapping in the field, the relationship between specific root length and external nitrate concentration, and the assignment of an absorption capacity related to integrated root system age. They find that model simulations are well matched to measured data for N uptake under field conditions at three different levels of fertilizer application. Model ouputs indicate that the topsoil layers contain about 80 % of the total root system and account for 90–95 % of N taken up at harvest.

Nitrate uptake modelling in plants: functional components

Nitrate uptake modelling in plants: functional components

Nitrate uptake modelling in plants: functional components

Difficulties in linking the various regulations of nitrate transport acting at different levels of time and on different spatial scales have hindered the development of models for nitrogen uptake. Le Deunff and Malagoli  substitute the more usual enzyme–substrate interpretation for a flow–force approach of nitrogen uptake isotherms and combine it with experimentally determined regulation in order to model nitrate in winter oilseed rape, Brassica napus. This approach avoids the use of unique nitrate uptake reference kinetics and allows root plasticity in response to environmental and in planta factors to be taken into account. Furthermore, it allows the regulation of nitrate uptake by roots to be scaled up relatively easily in time from hours to months.

Wettability of xylem lumenal walls in maize roots

Wettability of xylem lumenal walls in maize roots

Wettability of xylem lumenal walls in maize roots

Maintenance of tension in the transpiration stream requires coherence of the water molecules, but also their adherence to vessel walls (i.e. the lumen-facing surface must be wettable). As lignin is generally considered hydrophobic this presents a conundrum. McCully et al. observe wall contact with oil perfused into emptied vessels of maize (Zea mays) roots, contact angles of refilling sap, and wall substantivity to histochemical probes. Their observations reveal fine-scale heterogeneity of surface wettability, with lumen-facing bordered pits having hydrophilic aperture rims that repel oil, while oil adheres strongly to pit borders in empty vessels. As sap refills vessels through pits their borders become increasingly wettable by sap, which then spreads along the walls with low contact angles.

Deep sequencing coming for three taxa at key phylogenetic nodes

Following his recent visit to Cambridge, Josh Mylne (UWA) will be collaborating with Jill Harrison (Cambridge) and Kingsley Dixon (Perth Botanic Garden) to sequence the transcriptomes of three rare taxa at key phylogenetic nodes.

Kingsley collected the lycophytes Phylloglossum drummondii and Isoetes drummondii and the basal angiosperm representative Trithuria bibracteata from Alison Baird Reserve, Kenwick in Western Australia this week.

Lycophytes from the Alison Baird Reserve.

Isoetes drummondii (A,D), Phylloglossum drummondii (B,E) and Trithuria bibracteata (C,F) collected from the Alison Baird reserve.

Although lycophytes formed the dominant land plant tree flora in coal swamps that existed over 300 million years ago,[1] they are now small herbs forming three distinct relict lineages.[2] Whilst club mosses such as Phylloglossum comprise c. 400 species, spike mosses such as Selaginella comprise c.700 species and quillworts such as Isoetes comprise c. 150 species.

As the evolutionary divergence of these three lineages was ancient, and the taxa sampled are rare, the new sequence data will be useful in comparative and phylogenetic studies that seek to sample densely at the base of the plant tree of life to minimize long branch artefacts.

Phylloglossum also has corms, organs with a unique ‘fuzzy morphology’ and root/shoot-like identity.[3] The new sequence data will be helpful to future evo-devo projects aiming to determine homologies.

In contrast, Trithuria comprises just 12 species and sits at a key evolutionary divergence point higher up the plant tree of life. It is an aquatic angiosperm placed in the family Hydatellaceae, one of three families in the basal angiosperm order Nymphales.[4]

Trithuria differs from other water lilies in that it is tiny with narrow grass-like leaves, and the flowers may not be homologous to other angiosperm flowers, having an ‘inside out’ floral whorl arrangement.[5]

Again, the new sequence data will be useful in future systematic and evo-devo studies.

To access the raw reads or de novo assembled transcriptomes when they become available please contact Josh Mylne at joshua.mylne@uwa.edu.au.

Further reading

  1. Taylor et al. (2009). Palaeobotany: The biology and evolution of fossil plants. Academic Press, Burlington.
  2. Pryer et al. (2001). Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants. Nature 409: 618-622. doi:10.1038/35054555
  3. Bower FO. 1885 On the development and morphology of Phylloglossum drummondii. Philosophical Transactions of the Royal Society of London 176:665–678. doi:10.1098/rstl.1885.0012
  4. Saarela et al. (2007). Hydatellaceae identified as a new branch near the base of the angiosperm phylogenetic tree. Nature 446, 312-315. doi:10.1038/nature05612
  5. Rudall et al. (2009). Nonflowers near the base of extant angiosperms? Spatiotemporal arrangement of organs in reproductive units of Hydatellaceae and its bearing on the origin of the flower. American Journal of Botany 96:67-82. doi:10.3732/ajb.0800027

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

Selection on a CONSTANS-like gene between two red oaks

Selection on a CONSTANS-like gene between two red oaks

Selection on a CONSTANS-like gene between two red oaks

Oaks can provide a model to study hybridization as they often maintain species integrity and distinct environmental adaptations despite recurrent gene flow. Lind-Riehl et al. identify candidate genes potentially involved in local adaptation in the interfertile species Quercus rubra and Q. ellipsoidalis, which are characterized by contrasting adaptations to drought. They find that a CONSTANS-like (COL) gene is nearly fixed on alternative alleles in both species, as reflected by high FST values (55–80 %) between neighbouring Q. rubra and Q. ellipsoidalis populations. All other markers show low interspecific differentiation (approx. 5 %). They conclude that this COL gene may play a role in adaptive divergence and reproductive isolation (via flowering time), making it a promising candidate speciation gene.

New plant journal

Image: Wikimedia Commons.

Image: Wikimedia Commons.

It just had to happen, but we didn’t know it would take nearly 150 years to come to fruition. And fruition is an apt word because the creation of a new botanical journal has recently been announced by the publishers behind Nature, the world’s premier general science journal. Imaginatively entitled Nature Plants, this new organ is due to be officially published in January 2015 but already has interweb presence with a blog and can be ‘followed’ on such social media as Facebook and Twitter. Its aim is to provide a fully rounded picture of the most accomplished and significant advances in the plant sciences, and will cover ‘all aspects of plants be it their evolution, development or metabolism, their interactions with the environment, or their societal significance’. Furthermore, along with original research, Nature Plants will also deliver ‘Commentaries, Reviews, News and Views’ from across the full range of disciplines concerned with the plant sciences (i.e. a bit like the Annals of Botany…). However, with topics covered in the journal including (deep breath) ‘agronomy, genomics, biochemistry, metabolism, biofuels, metabolomics, biophysics, molecular biology, cell biology, photosynthesis, defence physiology, development, plant–microbe interactions, disease resistance, proteomics ecology, secondary metabolism, economics, sociology, evolution, symbiosis, food security, systems biology, forestry and water use’, I do hope they leave something for other – more established – botanical journals, such as the Annals of Botany!

[Have others heard that the original Nature – in keeping with its soon-to-be somewhat impoverished science coverage – is being retitled Nature Cosmology, Palaentology and Non-botany? Whilst we wish this new venture well, it will be interesting to see if anybody publishes in the new journal because, and despite the undoubted cachet and kudos associated with the word Nature in the article’s citation, it won’t have an Impact Factor (IF) for a few years. Now, who wants to risk having publications on their CV in journals with no IF with potential damage to promotion prospects and career advancement (not that IFs should be used for such purposes – see e.g. EASE statement on inappropriate use of Impact Factors? Just saying. – Ed.]

Ongoing gene flow among Australian alpine Poa

Ongoing gene flow among Australian alpine Poa

Ongoing gene flow among Australian alpine Poa

Recently radiated groups pose a taxonomic challenge even with extensive molecular data, as they may be genetically differentiated only at small and/or patchy regions of the genome. Griffin and Hoffmann investigate species’ structure among the Poa that dominate the Australian alpine zone, which have radiated in the last 0.5–1.2 million years. Using a Bayesian approach to co-estimate nuclear and chloroplast gene trees with an overall dated tree, they find that most species are not genetically distinct, despite distinguishable phenotypes, which suggests recent adaptive divergence with ongoing inter-taxon gene flow.