Genetic and morphological signature of ancient Agave cultivation

Genetic and morphological signature of ancient Agave cultivation

Genetic and morphological signature of ancient Agave cultivation

Several species of Agave were cultivated prehistorically for food and fibre in Arizona, USA, and relict populations that remain in the landscape today can provide an insight into ancient cultivation practices. Parker et al. test whether formerly cultivated Agave parryi populations still bear a predictable genetic and morphological signature by comparing populations of uncertain origin with known wild and cultivated populations. They find less genetic and morphological variation and stronger population differentiation in populations actively cultivated in the past than in wild counterparts, and conclude that where archaeological information is lacking, the genetic signature of Agave populations can thus be used to infer their evolutionary history and to identify fruitful sites for archaeological investigation of pre-Columbian cultivation practices. The same approach can clearly be adopted for other species in similar situations.

Adaptation for rodent pollination in Leucospermum arenarium

Adaptation for rodent pollination in Leucospermum arenarium

Adaptation for rodent pollination in Leucospermum arenarium

Numerous studies have documented flower feeding in angiosperms and adaptions for non-flying mammal pollination, but the underlying interactions and structures that facilitate this pollination mode are less well known. Johnson and Pauw investigate the pincushion Leucospermum arenarium (Proteaceae) and find that the nectar is unusually viscous and, although produced deep inside the perianth, is translocated via capillary ducts to the petal tips where rodents can access it without destroying the flowers. Although flowers are presented at ground level, when raised experimentally to higher positions seed production is not reduced, indicating that selection through female function does not drive the evolution of geoflory. This reliance on rodent pollination has apparently evolved despite the fact that they are very adept at removing pollen through grooming.

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

Temperature and reproductive success in arabidopsis

Temperature and reproductive success in arabidopsis

Temperature and reproductive success in arabidopsis

Seed yield and dormancy status are key components of species fitness that are influenced by the maternal environment. Huang et al. grow the Arabidopsis thaliana ecotype Burren (Bur), which is adapted to a cool, damp climate, under conditions normally experienced by the Cape Verdi Isle (Cvi) ecotype, which is adapted to a hot, dry climate. They find that viability of pollen is unaffected, but limited filament extension relative to that of the pistils results in failure to pollinate. Both seed yield and dormancy are reduced, suggesting that higher temperatures predicted in climate change scenarios will impact on the seed performance of the cool-adapted ecotype.

Something fishy in the veggie patch…

Image: Nada Meeks, www.fineartamerica.com.

Image: Nada Meeks, www.fineartamerica.com.

The ‘alpha’ category is widely regarded as the best of its kind; think of alpha (males) in the context of animal behaviour and Aldous Huxley’s Brave New World, an α+ grade on your exams or the sports cars from Alfa Romeo. But omega – right at the other end of the Greek alphabet – is also merit-worthy, especially when it’s omega fatty acids (FAs), which are polyunsaturated FAs needed for human metabolism. However, since they cannot be made de novo by the human body – and are therefore considered ‘essential’ – it is necessary to acquire them in the diet.

Two of the three essential omega FAs needed for human metabolism – Eicosapentaenoic acid (EPA) and Docosahexaenoic acid (DHA) – are derived from marine sources, such as fish. The third – alpha-Linolenic acid (ALA – which, despite its name, is still an omega fatty acid!) comes from plant products and is used in the body to produce EPA, which in turn is used to generate DHA. One way of getting your essential omegas is to consume milk produced by cows that have grazed on fresh grass/red clover, whose milk has been shown to increase in ALA as a result. But if you are milk-averse or lactose intolerant this won’t work for you. Another dietary strategy is to eat fish. However, with concerns about dwindling fish stocks, and recognising that fish themselves actually get their omegas from the algae that they have ingested, a more imaginative – and plant-based – avenue is being promoted.

Using a GMO (genetically modified organism) Noemi Ruiz-Lopez et al. have successfully demonstrated high-level accumulation of fish-oil omega-3 long-chain polyunsaturated fatty acids in a transgenic (which includes at least one gene from an alga…) oilseed crop plant. Using heterologous genes (i.e. genes from organisms different to the host crop species) the Rothamsted Research (Harpenden, UK) -based team have developed Camelina sativa (like arabidopsis, a member of the Brassicaceae) whose seeds accumulate up to 12 % EPA and 14 % DHA (which levels are equivalent to those in fish oils). On the back of expectations that this could represent a sustainable, terrestrial source of these fatty acids, Rothamsted Research has applied to Defra (the UK government’s Department for Environment, Food and Rural Affairs) ‘to conduct a field trial of Camelina plants that have been genetically modified to produce omega-3 oils that may provide health, environmental and societal benefits’. Interestingly, one of the enzymes in the 5-gene cassette used to genetically manipulate EPA levels in the plant is derived from Phytophthora infestans – the potato blight-causing oomycete (definitely NOT a fungus) which infamously caused so much devastation to the potato crop of Europe in the 19th century.  Maybe this is an opportunity for that notorious plant pest to do some good for a change! And something to ponder as you fry your naturally omega FA-enriched fish in GM-enhanced camelina oil…? Regardless, let us hope that false flax (an alternative common name for the plant) does not give false hope but, rather, provides ‘gold-of-pleasure’ (another of its common names). And that this 21st century fish oil project has more to offer than the 19th century’s over-promising, under-delivering pedlars of ‘snake oil’! Here’s a video showcasing the work at the 2014 UKPSF meeting.

[For more on the proposed GM trials, there is a dedicated Questions and Answers Section on the Rothamsted Research website. But what we really want to know is whether there is a hidden agenda to use the GM-crop to produce jet fuel for the F-22 raptor supersonic fighter aircraft, which apparently can fly very well using biofuel produced from Camelina… In which case, maybe GM stands for Go Mach – Ed.]

[Update - since this piece was originally penned, not only has the GM trial been approved but it has taken place and the crop harvested. It is anticipated that the results will be published in an open access journal later this year - Ed.]

Predicting mixed-species litter decomposition

Predicting mixed-species litter decomposition

Predicting mixed-species litter decomposition

The biomass-ratio hypothesis states that ecosystem properties are driven by the characteristics of dominant species in the community. Tardif et al.  measure decomposition rates of litter from four herb species at three sites along a correlated climatic gradient of temperature and precipitation in order to test the predictive value of the hypothesis. They find that community-weighted means of monoculture values provide good predictions of mixed-species’ litter decomposition, converging to the predicted values with increasing species richness and in climates less favourable to decomposition. The results support the idea that the biomass-ratio hypothesis, operationalized as community-weighted means, could offer the opportunity to predict ecosystems processes at larger spatial scales and in a changing environment.

Limonium, bursts of CO2 release and Na+/K+ homeostasis at the whole-plant level – What’s New in Annals of Botany this week

Type specimen of Limonium maritimum Taxonomic complexity in the halophyte Limonium vulgare and related taxa (Plumbaginaceae): insights from analysis of morphological, reproductive and karyological data
Limonium is a well-known example of a group of plants that is taxonomically complex due to certain biological characteristics that hamper species’ delineation. The closely related polyploid species Limonium vulgare Mill., L. humile Mill. and L. narbonense Mill. are defined species and can be used for studying patterns of morphological and reproductive variation. The first two taxa are usually found in Atlantic Europe and the third in the Mediterranean region, but a number of intermediate morphological forms may be present alongside typical examples of these species. This study attempts to elucidate morphological, floral and karyological diversity representative of these taxa in the Iberian Peninsula.

 

Bursts of CO2 released during freezing offer a new perspective on avoidance of winter embolism in trees
Woody plants can suffer from winter embolism as gas bubbles are formed in the water-conducting conduits when freezing occurs: gases are not soluble in ice, and the bubbles may expand and fill the conduits with air during thawing. A major assumption usually made in studies of winter embolism formation is that all of the gas dissolved in the xylem sap is trapped within the conduits and forms bubbles during freezing. The current study tested whether this assumption is actually valid, or whether efflux of gases from the stem during freezing reduces the occurrence of embolism.

 

ZxNHX controls Na+ and K+ homeostasis at the whole-plant level in Zygophyllum xanthoxylum through feedback regulation of the expression of genes involved in their transport
In order to cope with arid environments, the xerohalophyte Zygophyllum xanthoxylum efficiently compartmentalizes Na+ into vacuoles, mediated by ZxNHX, and maintains stability of K+ in its leaves. However, the function of ZxNHX in controlling Na+ and K+ homeostasis at the whole-plant level remains unclear. In this study, the role of ZxNHX in regulating the expression of genes involved in Na+ and K+ transport and spatial distribution was investigated.

 

Nutrient stoichiometry and resorption in karst vegetation

Nutrient stoichiometry and resorption in karst vegetation

Nutrient stoichiometry and resorption in karst vegetation

Elucidating the stoichiometry and resorption patterns of multiple nutrients is an essential requirement for a holistic understanding of plant nutrition and biogeochemical cycling. Liu et al.  examine the relationships between resorption patterns of 13 nutrients and leaf nutrient status in eight plant functional types in the karst region of south-western China. They find that four nutrients (N, P, K and Mg) show resorption, seven (B, Ca, Cu, Fe, Mn, Mo and Zn) accumulate in senesced leaves, and two (Na and S) show no resorption or accumulation.The resorption efficiencies of N, P and K and accumulation of Ca and Zn increase with decreasing concentrations of these nutrients in green leaves. The results emphasize the fact that nutrient resorption patterns strongly depend on the element and the plant functional type.

Fibre cables and tensegrity in Typha leaves

Fibre cables and tensegrity in Typha leaves

Fibre cables and tensegrity in Typha leaves

Some tall species of Typha (cattails/bulrushes) are able to withstand hurricane-force winds. Witztum and Wayne  dissect leaves of various species and examine the fibre cables – composed of long, non-lignified cells – that traverse the air chambers (lacunae). They find that the cellulose microfibrils that make up the walls of the cable-fibres are oriented parallel to the long axis of the fibres and make the cables strong under tension. Dorsal and ventral leaf surfaces and partitions contain lignified fibre bundles and vascular strands that are strong under compression, and in combination the result is a tensegrity structure that creates wind-resistant ‘multiple load paths’ through which stresses can be redistributed throughout the tall, upright leaves.

Plant molecular cytogenetics in the genomic and postgenomic era

Plant Molecular Cytogenetics in the Genomic and Postgenomic Era

Plant Molecular Cytogenetics in the Genomic and Postgenomic Era

The way that we can address questions in genome evolution and expression has changed enormously in the last five years. We can get huge amounts of DNA sequence for any species for a budget within that of most labs. As importantly perhaps, the web and PC-based analytical tools now enable researcher to do something with all those giga-bases of sequence within your own lab. Linking DNA sequence to the physical chromosomes has been a continuing challenge though, despite the widespread use of in situ hybridization. The huge number of whole genome and whole-chromosome evolution processes are not amenable to whole genome sequencing, but chromosome analysis can use the information to understand real biological problems. So this week, I’m thinking about Plant Molecular Cytogenetics in the Genomic and Postgenomic Era at a meeting in Poland. Although my tweets from the conference gained quite some following (thank you for letting me know, Twitter analytics) under the @ChrConf user and #PMC tag, I didn’t have a partner on social media so impressions are a little one-sided. However, I hope the collation below will give some flavour of the range of topics addressed during the meeting – but as usual the posters and social events provided the source of new inspiration. Skype will never replace personal meetings with old friends nor give the opportunity for making new links!

This conference in Katowice, Poland, is bringing together about 150 people, mostly from Europe with a substantial addition from that hive of cytogenetic activity, Brazil. It is organized by Robert Hasterok, a leader in use of the grass Brachypodium as a model species (http://aob.oxfordjournals.org/content/104/5/873.short) and understanding its evolution (http://aob.oxfordjournals.org/content/109/2/385.short). The meeting honours Jola Maluszynska, one of the earliest people to use molecular cytogenetics and who I have been privileged to work with – not least with that other model species, Arabidopsis (some published in Annals of Botany long ago http://aob.oxfordjournals.org/content/71/6/479.short).

The programme includes good time to look at the impressive array of posters showing the vibrancy of the post-genomic research. These are described in the abstract book, but here I will overview a selection of highlights from the talks. Although speaking near the end of the programme, it is only fair to start with Robert Hasterok – it is always a challenge both to talk and organize a meeting in your home town. In a wide-ranging talk about Brachypodium, he presented a diverse range of cytomolecular work going on in his lab, drawing out broader points from the posters we had studied on the first day. He defined a model species as an organism that possesses certain features that make it more amenable to scientific investigation compared with other less tractable members of the group it represents. It is also helpful when it possesses well-developed research resources and infrastructure (including how to grow the plant) that enable efficient work. The Brachypodium genome project was established in 2006 and the Brachypodium distacyhon genomic sequence completed in 2010. At that time, even the definition of key species in the genus was not clear, and it was only in 2012 that use of in situ hybridization clearly showed that there were three species

http://aob.oxfordjournals.org/content/109/2/385.short , now named Brachypodium distachyon (2n=10), B. stacei (2n=20), and the hybrid B. hybridum (2n=30). Robert then addressed the question of “What is known about grass genome evolution at the level of the chromosome?” “How is the development of compound chromosomes from a grass ancestral karyotype?” Cytomolecular work is showing chromosome remodelling and compound chromosomes in Brachy and its nearer and more distant ancestors in work published earlier this year ( http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0093503 _). The next section of his talk looked at nuclear organization. At interphase, there are clear chromosome territories, but for individual pairs of homologous chromosomes, all four possibilities of organization are seen with association of top arms of chromosomes, association of bottom arms, association of two homologous, or no association at all – the four being in very roughly equal proportions (perhaps the first a bit more frequent). A second group of experiments was looking at arrangements of centromeric and telomeric domains at interphase in various Brachypodium species: remarkably, there was a Rabl configuration with centromeres at one pole and telomeres at the opposite end of diploid interphase nuclei, while no such pattern was seen in the tetraploid 4x. This led to discussion of epigenetic effects, where nucleolar dominance is seen B. hybridum: the B. distachyon-origin rDNA genes are dominant over those of B. stacei. As with all good talks we were given insight into the brick walls of research: Brachypodium is nearly an anti-model for studying meiosis, while the obvious question about behaviour of resynthesized B. hybridum compared to the million-year old species is stymied by the lack of viability of the new hybrid.

So back then to the start of the programme with Dieter Schweizer giving insight into structural maintenance of chromosomes and epigenetics effects. The DMS3 structural protein interacts with DME Demeter, a DNA glycosylase domain protein and transcriptional activator, which has a function in directly excising 5 methyl cytosine from DNA and initiating replacement by unmethylated cytosine. In a lecture of two parts, Dieter’s second theme was cytogenetics and immunocytochemistry of triploid endosperm, where, there is parental genome separation and somatic pairing.

I’ll include a discussion of aspects of my talk (particularly one slide on crop production and the contribution of genetics) in a later post  – meanwhile my talk is posted here although with little supporting text. Hans De Jong followed with discussing plant cytogenetics in the era of modern genomics where I wasn’t sure if he was happy or sad that the Dutch contribution to the tomato genome sequence project, chromosome 6, proved to be one of the most rearranged or variable and hence tricky to analyse. Amazing 6-colour in situ hybridization sorted out many complex problems in ordering contigs of continuous blocks of sequence, and then linked orders between tomato and potato. Hans concluded that assembly algorithms placed about 33% of all assembled contigs were in the wrong position or wrong order in tomato. I was also interested to hear his final discussion about wide comparisons at the sequence level now being made between different species and even genera in Solanaceae, although I look forward to seeing how these cope with the proportion of highly variable repeats between the species.

After our first break, Ingo Schubert and collaborator Giang TH Vu talked about break repair – double-strand breaks (DSBs) at meiosis of in somatic cells, linking the molecular with the microscopic level in the monocot crop barley. DSB are ubiquitous, frequent and hazardous to the genome, and if unrepaired are lethal for dividing cells. Ingo could distinguish by molecular constructs and microscopy between the different DSB repair pathways involving homologous recombination or non-homologous end-joining. The latter NHEJ was seen to be the dominant DSBs repair pathway in barley with the consequent small deletions and/or insertions with or without microhomology. In asking my question about the role of enzymes and differences between species, I felt like the notorious “third referee” of important manuscripts wanting even more work for what is the first demonstration of the relationships of the different DSB repair mechanisms!

Andreas Houben, one of a large delegation from IPK in Gatersleben, then discussed centromeres with his interests in haploid technology and doubled haploids. CENH3 is an essential centromere component in almost all eukaryotes as modified histone H3. Andreas showed another hybrid species, Arabidopsis suecica (were natural and this time artificial hybrids can be made), making specific antibodies specific to the CENH3 in the two ancestors. In stable hybrids, both CENH3 sequences immune-hybridized to both centromeres – not like the species-specific centromeric sequences (http://www.le.ac.uk/bl/phh4/openpubs/openpubs/Kamm_Arenosa.pdf ) – but with high-resolution microscopy, his lab could see CENH3 variants are differentially loaded into distinct centromeric subdomains. Used some barley tilling mutation sets of lines, a mutated betaCENH3 was found which was not loaded onto the centromeres which had a normal phenotype except it was rather sterile: 56% univalents and 24% lagging at meiosis. Moving back to Arabidopsis, a mutant CENH3 that generates a haploid induce line (with a single amino acid change) was demonstrated, with the important consequence that hybrids using this could loose the maternal genome, enabling plant breeders to replace the cytoplasm in one generation.

Paul Fransz moved forward our understanding of a major paracentric inversion from 10000 yrs ago seen in Arabidopsis. His sequencing and cytogenetic work allowed detection of the inversion borders and hence the molecular mechanism of the inversion, work with (epi)genetic and phylogenetic consequences. Remarkable genome wide association analyses (GWAS) showed increased fitness under abiotic drought stress – the trait of fruit length and fecundity – was associated with the genes in the low recombination zone around the inversion.

Hanna Weiss-Schneeweiss showed the way modern cytogenetic approaches reveal “More than meets the eye: contrasting evolutionary trajectories in polyploids of the Prospero complex” and she was able to sort out the complex relationships in these species.

Our second day started with display of the wonderful timelapse films of the Polish botanists Bajer & Mole-Bajer, made in 1956, showing mitosis in Haemanthus endosperm. I knew these from my undergraduate days, and in the 1990s was given a 16mm film version by Professor Rachel Leech from York. I had them converted to VHS video tape, but happily we can now all access them freely on the web – whether downloadable from http://www.cellimagelibrary.org/images/11952 or several posts on YouTube such as https://www.youtube.com/watch?v=s1ylUTbXyWU .

An important practical question for breeding and selection, building from several talks on the first day, relate to Glyn Jenkins’ key question: Can we change sites of recombination to release novel recombination, new genetic variation and useful phenotypes? Then we are well on the way to  ‘optimising’ the germplasm of barley by manipulating recombination. The range of meiotic antibodies –  ASY1, ZYP1 and HvMLH3  – allowed study of recombination processes and give a recombination nodule map. Reconstructions of individual bivalents with meiosis antibodies shows distal bias of chiasmata (http://jxb.oxfordjournals.org/content/64/8/2139.short). Remarkably, a substantial but not extreme (15 C to 25 C) increase in temperature of growth for barley altered the genetic length, becoming much longer (more recombination) at high temperatures in male meiosis, although not on the female side. The map expansion was in pericentromeric regions, and significantly shifted HvMLH3 foci locations but not numbers.

AoB Editor Martin Lysak with Terezie Mandakova discussed very extensive work on Brassicaceae chromosome evolution under the title ‘More than the cabbage: chromosome and genome evolution in crucifers’ (eg http://www.plantcell.org/content/25/5/1541.short). The simplicity of the models of evolution of crucifer genomes that Martin showed belie the huge amount of underpinning data on comparative cytogenetics, sequenced genomes, genetic maps and phylogenetics, as well as the number of ‘envelopes’ that must have been used to sketch out models (although I’m not sure what replaces envelopes in the day of e-mails). Basically, the ancestral crucifer karyotype (ACK) in ‘diploids’ (themselves often of polyploid or hybrid origin) and polyploids can be divided into 24 ancestral genomic blocks. One of the most simple situations, in Capsella rubella (Slotte et al. 2013) the ACK  remained largely conserved, while there can be diversification without large scale rearrangements in Cardamine. Arabis alpina is more complex, with seven of 8 ancestral chromosome reshuffled, probably involving  five reciprocal translocations, four pericentric inversions, three centromere repositionings , one centromere loss and one new centromere. Wow! Martin treated us to consideration of all the major lineages in the group, from the extreme of chromosome number reduction to n=5 in Arabidopsis thaliana, through to the most remarkable 72 genome duplication events in oilseed rape/Brassica napus since origin of angiosperms! Clearly, a whole genome triplication spurred genome and taxonomic diversity in Brassica and the tribe Brassiceae and I will need to follow his next publications, with many colleagues but particularly talk co-author Terezie Mandakova, to understand the consequences of descending dysploidy from the ACK ancestral crucifer karyotype and PCK (Proto-Calepineae karyotype), with range of mechanisms involving translocations, loss of minichromosomes, end to end fusions, inversions, and centromere shifts.

The last talks before posting these notes came from Kesara Anamthawat-Jonsson – my first PhD student – addressing Where did birch in Iceland come from? Betula is another genus with lots of hybrids, even though the history of birch in Iceland only extends for the 10000 years of the holocene since Iceland came out from under the ice. Kesara builds on her Annals of Botany paper http://aob.oxfordjournals.org/content/99/6/1183.short showing that 10% of Icelandic birches are 2n=3x=42 hybrids, but only half of these can be seen from their morphology. Kesara has now looked at chloroplast DNA haplotypes across Iceland as well as evidence for extensive introgression between the species via 3x hybrids involving whole genomes of both Betula nana and B. pubescens.

There are still a few more talks, and then I am off for some lab visits – I’m sorry I can’t cover everything but I hope this flavour of the exciting meeting will be useful to a few. It is clear that we are really in a post-genomic era, and cytogenetic approaches are making major advances in this new landscape.