Memory of seasons past controls germination

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Published on: December 18, 2014

Arabidopsis seedling germinating JIC

In research published this week in PNAS, Steve Penfield (formerly Exeter, now John Innes Centre) and Ian Graham (CNAP, York) and collaborators have shown that ‘mother’ plants remember seasons and use this memory to program germination time into their seeds.

Working on Arabidopsis thaliana, Penfield found that the mother plant plays an important role in sensing temperature and forms a long term temperature memory, which she uses to control the behaviour of her progeny seeds. These temperature memories enable seeds to determine time of year and modify their germination rates to ensure that their growth and development is coordinated with the seasons.

If the mother experiences warmer temperatures, it produces more of a protein called Flowering Locus T (FT) which in the fruit of the plant, represses production of tannins, making seed coats thinner, increasing their permeability, meaning they will germinate more quickly.

Conversely if the mother plant experiences cooler temperatures prior to flowering it will produce less FT protein in its fruit and therefore produce more tannins. Seed coats will be thicker and less permeable and will germinate later. In this way the mother plant can manipulate seed germination to be optimal for the time of year.

If the environment during seed production is not optimal this can result in poor germination. With climate change making suboptimal conditions more frequent, having a better understanding how plants program progeny dormancy and germination will help researchers optimise seed quality for crops and domestic use.

Steve Penfield said: “By understanding how the mother plant uses temperature information to influence the vigour of her seeds we can begin to develop strategies for breeding seeds with more resilience to climate change.”

Highlighted paper: Min Chen, Dana R. MacGregor, Anuja Dave, Hannah Florance, Karen Moore, Konrad Paszkiewicz, Nicholas Smirnoff, Ian A. Graham, and Steven Penfield. 2014. Maternal temperature history activates Flowering Locus T in fruits to control progeny dormancy according to time of year. PNAS published ahead of print December 16, 2014, doi:10.1073/pnas.1412274111.

This article is adapted from a news release from the John Innes Centre. The image is c/o John Innes Centre. 

Natural variation in Arabidopsis, the MAGIC way

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Published on: November 24, 2014

The research: Finding the causes of variation in seed size and number

In the Arabidopsis Research Round-up a few weeks ago, Lisa highlighted a paper from a team at the University of Bath about natural variation in Arabidopsis seeds. Lead author Paula Kover and her team investigated the genetic basis of variation in seed size and number.

All plants negotiate a trade-off between the number and size of their seeds, so it was a surprise to learn that of 9 QTL for seed number and 8 for seed size, there was only 1 overlapping QTL. The strong negative correlation seen in size and number is logically due to resource use efficiency, but these data suggest that this is not determined genetically.

There is enough of a positive correlation between seed number and fruit length that fruit length is sometimes used to estimate seed number – though the correlation is not strong. Here too there was only 1 QTL overlapping between the two traits, suggesting that any correlation is not inherent and may vary according to environmental or internal factors.

Based on QTL analysis, Kover et al. identify five potential genes that underlie quantitative variation in seed size and number: AAP1 (AT1G58360) and KLUH (AT1G13710) on chromosome 1; and JAGGED LATERAL ORGANS (AT4G00220), YABBY 3 (AT4G00180), and BEL1 (AT5G41410) on chromosomes 4 and 5.


The tool: MAGIC Arabidopsis lines

All the above work was carried out using Mulitparent Advanced Generation Inter-Cross (MAGIC) Arabidopsis lines. Kover and others developed these lines to improve methods of identifying natural allelic variation that underlies variable phenotypic traits. The lines are recombinant, inbred over 6 generations, that originate from an intermated hereogenous stock. This pedigree means they represent a large diversity of genes in mostly homozygous lines; ideal for accurate QTL mapping. The original MAGIC paper from 2009 paper states ‘MAGIC lines occupy an intermediate niche between naturally occurring accessions and existing synthetic populations.’

The MAGIC lines are an incredible open resource for studying natural variation in Arabidopsis: they enable a researcher to map a trait to within 300kb. All lines in the 2009 paper are available from NASC. A set of digital tools, hosted at the Wellcome Trust Centre for Human Genetics, contains the (open source) software needed to run the QTL analysis and the data files associated with the lines.


Highlighted paper: Gnan, Priest and Kover. The genetic basis of natural variation in seed size and seed number and their trade-off using Arabidopsis thaliana MAGIC lines. Genetics, 2014. 10.1534/genetics.114.170746

Also cited: Kover et al. A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLOS Genetics, 2009. DOI: 10.1371/journal.pgen.1000551

For a comparison of resources for studying natural variation, see Weigel, Plant Phys, 2012 158:2-22

Effector-triggered defence: A new concept in plant pathogen defence

In June, a team of Brassica researchers from the University of Hertfordshire proposed a new classification for a type of plant defence mechanism: effector-triggered defence (ETD).

Henrik Stotz is first author of the paper describing ETD, currently In Press in Trends in Plant Science. He explains, “In the same way that humans have developed immune responses against human disease pathogens, crops can be bred for resistance against disease pathogens, but we need to improve our understanding of effective resistance mechanisms within plants. Our research enhances the traditional understanding of the plant defence system and describes a new concept, which is how plants protect themselves against the pathogens that grow in the space outside plant cells (the apoplast) – a new concept called effector-triggered defence or ETD.”

Traditionally, plant pathogen defence is broken into two broad forms: pathogen-triggered immunity (PTI) and effector-triggered immunity (ETI). PTI is the first action the plant takes against a pathogen and is triggered when the pathogen lands on the plant. The pathogen releases molecules called effectors into the plant cells, which the plant recognises and reacts against. If the effectors are not recognised, the pathogen can spread with little resistance.

The team from Hertfordshire, led by Bruce Fitt, argue that one line of defence, R gene-mediated host resistance against fungal pathogens that grow in the space between cells, is not adequately explained by either mechanism.

Effector-triggered defence (ETD) is mediated by R genes encoding cell surface-bound receptor-like proteins that engage the receptor-like kinase SOBIR1 – an extracellular recognition. The response is host cell death after an extended period of endophytic pathogen growth. This is in contrast to ETI, in which detection of the pathogen occurs within cells and usually triggers fast host cell death.

ETD is described in Stotz et al. (In Press) Trends in Plant Science DOI:

The quotes used in this article are from this BBSRC Press Release. This story was originally posted on the UK Brassica Research Community website.


A sweet surprise: Revealing new roles for sugars in plants

The fifth post of our Celebrating Basic Plant Science series comes from Mike Haydon, a lecturer at the University of York. He and his research group work on understanding signalling in plants. Here he explains some of his work on integrating sugar metabolism with light signals. You can see more about Mike and his group on his website. The work he discusses below was published in the journal Nature last year (Haydon et al. Nature 502:689-692).



A life based on sugar

Most of us think about sugar every day, be it consciously as we consider our calorie intake, or unconsciously when our brain tells us it’s mealtime. Sugars are among the simplest of carbohydrates and they are the raw material for cellular respiration, which produces energy for almost all living cells. Glucose, a monosaccharide, is the preferred sugar for cellular respiration. Sucrose, most familiar to us as the granulated sugar in our kitchens, is a disaccharide made of glucose and fructose. These, and other simple carbohydrates, are used to build complex carbohydrates such as starch and cellulose in plants, and glycogen and chitin in animals. Sugars are the foundation of cellular metabolism, and produce the wide array of molecules that sustain our carbon-based existence.


The most important process on the planet

Plants, along with algae and some species of bacteria, use photosynthesis to convert carbon dioxide in the air into glucose using energy from sunlight, while producing oxygen as a by-product. Photosynthetic bacteria were responsible for the Great Oxidation Event, which occurred from about 2.5 billion years ago and led to the life-sustaining atmosphere we now live in. Photosynthetic organisms are called autotrophs, because they produce their own sugars to use in cellular metabolism. All other organisms, called heterotrophs, must somehow get their sugars from their environment. For animals, this is ultimately through the plant-based component of their diet. So essentially all the carbon in DSC_0010 smallour bodies was, at some point, converted from carbon dioxide into glucose by photosynthesis. Thus, photosynthesis is probably the most important metabolic process on the planet.

You might think that something so fundamental in biology would be completely understood, and we certainly do know a lot about carbohydrate metabolism. We also know that sugars have functions outside of this basic metabolism. For example in plants they can act as hormones, regulating processes such as cell growth, cell division, flowering time and disease resistance. But there is still a lot we don’t know about how plants regulate carbohydrate metabolism, and sometimes we still find entirely new functions for sugars in biological processes.


How time matters in sugar metabolism (more…)

Plant science, by JoVE!

JoVE 2

Researchers from the University of Warwick published a methodology paper with a twist this week. The paper, published online by the Journal of Visualized Experiments (JoVE), gives step-by-step instructions and video demonstration of a method for purifying a protein and identifying proteins that perform its post-translational modifications.

Authors Sophie Piquerez, Alexi Balmuth, Jan Skenář, Alex JonesJohn Rathjen and Vardis Ntoukakis developed the method in order to characterize the interactions between nucleotide-binding leucine-rich-repeat proteins and the Prf/Pto complex in effector-triggered immunity. In principle the method could be applied to any protein – the protein of interest is epitope-tagged, immunoprecipitated and analysed by MS.

A video journal lends itself to new or improved methodology rather than high impact conclusions. As with a lot of JoVE articles, the scientifically significant results obtained using the protocol have already been published; in this case in Ntoukakis et al. 2013 (PLOS Pathogens, 10.1371/journal.ppat.1003123).

The authors conclude the abstract by saying the paper demonstrates:

  1. Dynamic changes in PTMs such as phosphorylation can be detected by mass spectrometry;
  2. It is important to have sufficient quantities of the protein of interest, and this can compensate for the lack of purity of the immunoprecipitate;
  3. The immunoprecipitation step is essential to get enough protein to do the MS. (more…)

A tale of two models

James Lloyd (University of Leeds) was the lead author on last month’s Plant Journal paper on nonsense-mediated mRNA decay, which demonstrated that working on a model plant can sometimes be a hinderance rather than a help. In this guest post he explains how he and his supervisor Brendan Davies overturned widely held assumptions about NMD in plants – by working on moss.

Physcomitrella patens, the model moss, growing on agar.

Plant biology has been greatly advanced by the use of Arabidopsis thaliana as a model. Fantastic community resources, such as mutant collections and numerous genome sequences from natural accessions have aided researchers in all areas of plant sciences. However, A. thaliana is far from perfect. Nonsense-mediated mRNA decay (NMD) is a little heard of pathway to regulate transcript stability and it has recently been shown to be involved in pathogen response in A. thaliana (Rayson et al., 2012).

The mechanism of mRNA decay has largely been worked out in animals and revolves around the phosphorylation of an RNA helicase called UPF1 by a kinase SMG1. However, fungi and A. thaliana both lack the SMG1 kinase, so it has been a mystery how the fungal and plant proteins are phosphorylated. We have recently shown that SMG1 is not animal specific but is an ancient component of the NMD machinery, appearing in the genomes of all plants examined, with the exception of A. thalianaSMG1 is even found in the genome of A. lyrata, a close relative of A. thaliana.

Arabidopsis thaliana, the model plant.

The lack of SMG1 in the genome of A. thaliana meant that we had to use another plant as our model to understand the role of SMG1 in the plant kingdom. Enter moss! Physcomitrella patens is the model moss, with a sequenced genome and a high rate of homologous recombination it is a relatively simple task to identify and delete any gene in the genome. The rate of homologous recombination is much lower in flowering plants than it is in moss, meaning that short (around 1 Kb) of moss genomic DNA from upstream and downstream of a gene of interest can be cloned around an antibiotic selection gene and then transformed into moss cells and a large proportion of antibiotic resistant plants have the gene of interest deleted.

We deleted SMG1 from moss and found that NMD was compromised thus placing plant SMG1 in the NMD pathway (Lloyd and Davies, 2013). Therefore, many plants including crops like rice and maize are likely to rely on SMG1 to control gene expression through NMD. Future research will hopefully reveal why A. thaliana has lost SMG1 and if another kinase has replaced SMG1 in this plant.

A. thaliana has been useful in characterising other components of the NMD pathway in plants, such as UPF1 and understanding the biological role in plants (such as controlling the pathogen response). However, it was limited in helping us understand the NMD pathway of commercially important crops and it was moss to the rescue!

Animal researchers have long used multiple, evolutionarily diverse models, including but not limited to fruit flies, C. elegans, zebrafish, frogs and mice. Despite big differences between invertebrates like fruit flies and vertebrates like humans, a great deal about human biology has been learnt by using these organisms in the lab.

Many important questions cannot be answered by simply studying A. thaliana, big differences in fundamental processes exist between accessions. Therefore, multiple models are needed in plant sciences. Moss is just one plant that can help compliment research in other plant species, using the powerful genetic tool of homologous recombination.


Lloyd JPB and Davies B (2013) SMG1 is an ancient nonsense-mediated mRNA decay effector. The Plant Journal 1365-313X

Rayson S, Arciga-Reyes L, Wootton L, De Torres Zabala M, Truman W, et al. (2012) A Role for Nonsense-Mediated mRNA Decay in Plants: Pathogen Responses Are Induced in Arabidopsis thaliana NMD Mutants. PLoS ONE 7(2): e31917. doi:10.1371/journal.pone.0031917

Images courtesy of James Lloyd. 

A model tree?

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Published on: April 30, 2013

Just how many things can we really use Arabidopsis thaliana as a ‘model’ for? Certainly our favourite weed has an historic advantage for genomic research. As the first plant genome to be fully sequenced, it has had a long head start for all sorts of ‘omics databases and projects. The A. thaliana databases have proved useful for researchers working on other plant species too; even today Arabidopsis genomic sequences are used to fish un-annotated genomes for genes and motifs. A recent paper questions how appropriate it is to transfer in vivo Arabidopsis research on xylem and water flow to woody plant species. Yes, how useful is weedy (in all senses of the word), tiny A. thaliana to understand massive woody trees? The answer? It’s not perfect, but it’s OK.

Tixier et al. (JXB, doi:10.1093/jxb/ert087, Open Access) carried out a series of experiments to test A. thaliana’s value as a model for wood development. It turns out wildtype Arabidopsis is a good xylem hydraulic model, with tissue structure and vessel dimensions that are reliably representative of larger woody plants. To quote Tixier et al., “A. thaliana can be used to measure specific conductivity and cavitation resistance in an accurate and reliable approach,” and far more conveniently than trying to use an 8 metre tall tree to do it. However, the model plant is not appropriate for some xylem parameters, such as end-wall sensitivity. A. thaliana xylem also responded differently to abnormal environmental conditions and cell wall structure manipulation.

As an aside, Wendrich and Weijers present another system for which A. thaliana is an appropriate model in this month’s Tansley review in New Phytologist (doi: 10.1111/nph.12267). They describe current understanding of morphogenesis in the early A. thaliana embryo, and identify five key questions that still remain to be answered.

Image credit: Climbing plant by Heriberto Herrera, via stock.xchng.

Potato Potato

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Published on: March 27, 2013

The potato, brought across the Atlantic by explorers like Christopher Columbus and Francis Drake during the 15th and 16th Centuries, changed Europe forever. During the 18th Century the large, low-maintenance potato harvests eventually provided European working classes with a more reliable food source than they had ever enjoyed. Decades later, arsenic blends to protect potato crops were the first artificial pesticides. Today’s highlighted paper, published in Nature in March, tells us that potato would still be the local speciality of Andean villagers, in spite of those early European explorers, if it weren’t for natural and cultivated variation of a CYCLING DOF FACTOR. 

Wild potato is found largely in Bolivia and Peru.  There are roughly 180 wild potato species, all of which originated in the Andes and now spread along the west coast of South and Central America, with a few in the southern most states of the USA – all within 40° of latitude from the equator, but with a clear focus between 10° and 20° south (Hijmans and Spooner 2000). These equatorial origins meant the original potatoes brought to Europe had an inherent dependence on short day lengths, and only formed tubers in short autumn and winter days.

Kloosterman et al. compared a wild potato population with a potato population domesticated in Europe. They started out by defining more clearly the ‘potato plant maturity’ QTL on chromosome 5 (Visker et al. 2003), which is associated with onset of tuberization and plant life cycle. They identified a homologue of the A. thaliana CYCLING DOF FACTOR 1 protein which they named StCDF1, which when complete causes potato plants to be late maturing and unable to tuberize in long days. Potatoes with a truncated StCDF1 allele mature early, growing tubers four weeks after planting in long day conditions. (more…)

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