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The evolution of multicellular organisms was made possible by the evolution of underlying gene regulatory networks. In animals, the core of gene regulatory networks consists of kernels, stable subnetworks of transcription factors that are highly conserved in distantly related species. However, in plants it is not clear when and how kernels evolved. We show here that RSL (ROOT HAIR DEFECTIVE SIX-LIKE) transcription factors form an ancient land plant kernel controlling caulonema differentiation in the moss Physcomitrella patens and root hair development in the flowering plant Arabidopsis thaliana. Phylogenetic analyses suggest that RSL proteins evolved in aquatic charophyte algae or in early land plants, and have been conserved throughout land plant radiation. Genetic and transcriptional analyses in loss of function A. thaliana and P. patens mutants suggest that the transcriptional interactions in the RSL kernel were remodeled and became more hierarchical during the evolution of vascular plants. We predict that other gene regulatory networks that control development in derived groups of plants may have originated in the earliest land plants or in their ancestors, the Charophycean algae.
Heat stress is a common and, therefore, an important environmental impact on cells and organisms. While much attention has been paid to severe heat stress, moderate temperature elevations are also important. Here we discuss temperature sensing and how responses to heat stress are not necessarily dependent on denatured proteins. Indeed, it is clear that membrane lipids have a pivotal function. Details of membrane lipid changes and the associated production of signalling metabolites are described and suggestions made as to how the interconnected signalling network could be modified for helpful intervention in disease.
Land plants need precise thermosensors to timely establish molecular defenses in anticipation of upcoming noxious heat waves. The plasma membrane-embedded cyclic nucleotide-gated Ca2+ channels (CNGCs) can translate mild variations of membrane fluidity into an effective heat shock response, leading to the accumulation of heat shock proteins (HSP) that prevent heat damages in labile proteins and membranes. Here, we deleted by targeted mutagenesis the CNGCd gene in two Physcomitrella patens transgenic moss lines containing either the heat-inducible HSP-GUS reporter cassette or the constitutive UBI-Aequorin cassette. The stable CNGCd knockout mutation caused a hyper-thermosensitive moss phenotype, in which the heat-induced entry of apoplastic Ca2+ and the cytosolic accumulation of GUS were triggered at lower temperatures than in wild type. The combined effects of an artificial membrane fluidizer and elevated temperatures suggested that the gene products of CNGCd and CNGCb are paralogous subunits of Ca2+channels acting as a sensitive proteolipid thermocouple. Depending on the rate of temperature increase, the duration and intensity of the heat priming preconditions, terrestrial plants may thus acquire an array of HSP-based thermotolerance mechanisms against upcoming, otherwise lethal, extreme heat waves.
Predators and parasitoids often benefit from feeding on nectar and/or pollen, such that the addition of flowering plants should bolster natural enemies and improve biological control. Nonetheless, this conceptually-simple approach often fails to reduce pest numbers. We examined whether flowering annual plants drew more natural enemies to apples (Malus domestica) in Washington State, USA, and in turn whether this improved suppression of woolly apple aphids (Eriosoma lanigerum) on nearby trees. Initial screening of candidate flowers indicated that syrphid flies (Diptera: Syrphidae), thought to be important aphid predators, were particularly attracted to sweet alyssum flowers (Lobularia maritima). Therefore, in two subsequent field experiments we compared aphid densities on trees placed adjacent to, or relatively far from, flowering sweet alyssum. The results were striking: after one week aphid densities were significantly lower on trees adjacent to flowers than on those on control plots, and these differences were maintained for several weeks. It was unlikely that aphid decline was primarily due to syrphid predation, because lower aphid densities were observed despite few syrphid larvae being present. Rather, a diverse group of generalist-predator spiders and bugs increased significantly near sweet alyssum plantings, and may have been responsible for much of the aphid suppression that we observed. Immunomarking revealed that natural enemies regularly moved from sweet alyssum to the surrounding orchard. In summary, the floral resources that sweet alyssum plants provided attracted natural enemies and indirectly suppressed densities of woolly apple aphids, suggesting an effective means for apple growers to enhance biological control.
The rapid adoption of genetically engineered (GE) plants that express insecticidal Cry proteins derived from Bacillus thuringiensis (Bt) has raised concerns about their potential impact on non-target organisms. This includes the possibility that non-target herbivores develop into pests. Although studies have now reported increased populations of non-target herbivores in Bt cotton, the underlying mechanisms are not fully understood. We propose that lack of herbivore-induced secondary metabolites in Bt cotton represents a mechanism that benefits non-target herbivores. We show that, because of effective suppression of Bt-sensitive lepidopteran herbivores, Bt cotton contains reduced levels of induced terpenoids. We also show that changes in the overall level of these defensive secondary metabolites are associated with improved performance of a Bt-insensitive herbivore, the cotton aphid, under glasshouse conditions. These effects, however, were not as clearly evident under field conditions as aphid populations were not correlated with the amount of terpenoids measured in the plants. Nevertheless, increased aphid numbers were visible in Bt cotton compared with non-Bt cotton on some sampling dates. Identification of this mechanism increases our understanding of how insect-resistant crops impact herbivore communities and helps underpin the sustainable use of GE varieties.
In order to establish a reference for analysis of the function of auxin and the auxin biosynthesis regulators SHI/STY during Physcomitrella patens reproductive development, we have described the male (antheridial) and female (archegonial) development in detail, including temporal and positional information of organ initiation. This has allowed us to define discrete stages of organ morphogenesis and to show that reproductive organ development in P. patens is highly organized and that organ phyllotaxis differs between vegetative and reproductive development. Using the PpSHI1 and PpSHI2 reporter- and knock-out lines, the auxin reporters GmGH3pro:GUS and PpPINApro:GFP-GUS, and the auxin conjugating transgene PpSHI2pro:IAAL we could show that the PpSHI genes, and by inference also auxin, play important roles for reproductive organ development in moss. The PpSHI genes are required for the apical opening of the reproductive organs, the final differentiation of the egg cell, and for the progression of canal cells into a cell-death program. The apical cells of the archegonia, the canal cells and the egg cell are also sites of auxin responsiveness, and are affected by reduced levels of active auxin, suggesting that auxin mediates the PpSHI function in the reproductive organs.
Unlike animals, land plants undergo an alternation of generations, producing multicellular bodies in both haploid (1n: gametophyte) and diploid (2n: sporophyte) generations. Plant body plans in each generation are regulated by distinct developmental programs initiated at either meiosis or fertilization, respectively. In mosses, the haploid gametophyte generation is dominant, whereas in vascular plants—including ferns, gymnosperms, and angiosperms—the diploid sporophyte generation is dominant. Deletion of the class 2 KNOTTED1-LIKE HOMEOBOX (KNOX2) transcription factors in the moss Physcomitrella patens results in the development of gametophyte bodies from diploid embryos without meiosis. Thus, KNOX2 acts to prevent the haploid-specific body plan from developing in the diploid plant body, indicating a critical role for the evolution of KNOX2 in establishing an alternation of generations in land plants.
Artificial microRNA (amiRNA) approaches offer a powerful strategy for targeted gene manipulation in any plant species. However, the current unpredictability of amiRNA efficacy has limited broad application of this promising technology. To address this, we developed epitope-tagged protein-based amiRNA (ETPamir) screens, in which target mRNAs encoding epitope-tagged proteins were constitutively or inducibly coexpressed in protoplasts with amiRNA candidates targeting single or multiple genes. This design allowed parallel quantification of target proteins and mRNAs to define amiRNA efficacy and mechanism of action, circumventing unpredictable amiRNA expression/processing and antibody unavailability. Systematic evaluation of 63 amiRNAs in 79 ETPamir screens for 16 target genes revealed a simple, effective solution for selecting optimal amiRNAs from hundreds of computational predictions, reaching ∼100% gene silencing in plant cells and null phenotypes in transgenic plants. Optimal amiRNAs predominantly mediated highly specific translational repression at 5′ coding regions with limited mRNA decay or cleavage. Our screens were easily applied to diverse plant species, including Arabidopsis thaliana, tobacco (Nicotiana benthamiana), tomato (Solanum lycopersicum), sunflower (Helianthus annuus), Catharanthus roseus, maize (Zea mays) and rice (Oryza sativa), and effectively validated predicted natural miRNA targets. These screens could improve plant research and crop engineering by making amiRNA a more predictable and manageable genetic and functional genomic technology.
Root lesion nematodes (RLNs, Pratylenchus species) are a group of economically important migratory endoparasitic plant pathogens that attack host roots of major crops such as wheat and sugarcane, and can reduce crop yields by 7–15%. Pratylenchus thornei and Pratylenchus zeae were treated with double stranded RNA (dsRNA) to study gene silencing, (RNA interference, RNAi), as a potential strategy for their control. Mixed stages of nematodes of both species ingested dsRNA when incubated in a basic soaking solution in the presence of the neurostimulant octopamine. Incubation for up to 16 h in soaking solutions containing 10–50 mM octopamine, 0.1–1.0 mg/mL FITC, and 0.5–6 mM spermidine did not affect vitality. Spermidine phosphate salt hexahydrate rather than spermidine or spermidine trihydrochloride increased uptake of FITC by nematodes, and this resulted in more effective gene silencing. Silencing pat-10 and unc-87 genes of P. thornei and P. zeae resulted in paralysis and uncoordinated movements in both species, although to a higher degree in P. thornei. There was also a greater reduction in transcript of both genes in P. thornei indicating that it may be more susceptible to RNAi. For P. thornei treated with dsRNA of pat-10 and unc-87 there was a significant reduction (77–81%) in nematode reproduction on carrot mini discs over a 5 week period. The results show that RLNs are clearly amenable to gene silencing, and that in planta delivery of dsRNA to target genes in these nematodes should confer host resistance. Moreover, for the two genes, dsRNA derived from either nematode species silenced the corresponding gene in both species. This implies cross-species control of nematodes via RNAi is possible.
Past global climate changes had strong regional expression. To elucidate their spatio-temporal pattern, we reconstructed past temperatures for seven continental-scale regions during the past one to two millennia. The most coherent feature in nearly all of the regional temperature reconstructions is a long-term cooling trend, which ended late in the nineteenth century. At multi-decadal to centennial scales, temperature variability shows distinctly different regional patterns, with more similarity within each hemisphere than between them. There were no globally synchronous multi-decadal warm or cold intervals that define a worldwide Medieval Warm Period or Little Ice Age, but all reconstructions show generally cold conditions between ad 1580 and 1880, punctuated in some regions by warm decades during the eighteenth century. The transition to these colder conditions occurred earlier in the Arctic, Europe and Asia than in North America or the Southern Hemisphere regions. Recent warming reversed the long-term cooling; during the period ad 1971–2000, the area-weighted average reconstructed temperature was higher than any other time in nearly 1,400 years.
In the plant kingdom, events of whole genome duplication or polyploidization are generally believed to occur via alterations of the sexual reproduction process. Thereby, diploid pollen and eggs are formed that contain the somatic number of chromosomes rather than the gametophytic number. By participating in fertilization, these so-called 2n gametes generate polyploid offspring and therefore constitute the basis for the establishment of polyploidy in plants. In addition, diplogamete formation, through meiotic restitution, is an essential component of apomixis and also serves as an important mechanism for the restoration of F1 hybrid fertility. Characterization of the cytological mechanisms and molecular factors underlying 2n gamete formation is therefore not only relevant for basic plant biology and evolution, but may also provide valuable cues for agricultural and biotechnological applications (e.g. reverse breeding, clonal seeds). Recent data have provided novel insights into the process of 2n pollen and egg formation and have revealed multiple means to the same end. Here, we summarize the cytological mechanisms and molecular regulatory networks underlying 2n gamete formation, and outline important mitotic and meiotic processes involved in the ectopic induction of sexual polyploidization
Targeting induced local lesions in genomes (TILLING), initially a functional genomics tool in model plants, has been extended to many plant species and become of paramount importance to reverse genetics in crops species. Because it is readily applicable to most plants, it remains a dominant non-transgenic method for obtaining mutations in known genes. The process has seen many technological changes over the last 10 years; a major recent change has been the application of next-generation sequencing (NGS) to the process, which permits multiplexing of gene targets and genomes. NGS will ultimately lead to TILLING becoming an in silico procedure. We review here the history and technology in brief, but focus more importantly on recent developments in polyploids, vegetatively propagated crops and the future of TILLING for plant breeding.
Le CNRS vient d’annoncer la création d’une mission « sciences citoyennes » en son sein, et en a confié la responsabilité à Marc Lipinski. Celui-ci est biologiste, mais c’est son expérience militante qui lui a valu sa nomination, comme il l’indique lui-même dans un entretien publié sur le site de l’organisme de recherche1. Marc Lipinski est en effet conseiller régional Europe-Ecologie-Les-Verts, et ancien vice-président de la région Ile-de-France. Dans le même entretien, le responsable de la nouvelle mission du CNRS explicite l’objectif de celle-ci : « favoriser le dialogue et le rapprochement entre la recherche et les citoyens, essentiellement représentés et organisés dans des associations ».
Via ArianeBeldi
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eLife: The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine (2013)
Phytophthora infestans, the cause of potato late blight, is infamous for having triggered the Irish Great Famine in the 1840s. Until the late 1970s, P. infestans diversity outside of its Mexican center of origin was low, and one scenario held that a single strain, US-1, had dominated the global population for 150 years; this was later challenged based on DNA analysis of historical herbarium specimens. We have compared the genomes of 11 herbarium and 15 modern strains. We conclude that the nineteenth century epidemic was caused by a unique genotype, HERB-1, that persisted for over 50 years. HERB-1 is distinct from all examined modern strains, but it is a close relative of US-1, which replaced it outside of Mexico in the twentieth century. We propose that HERB-1 and US-1 emerged from a metapopulation that was established in the early 1800s outside of the species' center of diversity. Preprint @ http://arxiv.org/abs/1305.4206
Via Kamoun Lab @ TSL
Recently, bryophytes, which diverged from the ancestor of seed plants more than 400 million years ago, came into focus in photosynthesis research as they can provide valuable insights into the evolution of photosynthetic complexes during the adaptation to terrestrial life. This study isolated intact photosystem I (PSI) with its associated light-harvesting complex (LHCI) from the moss Physcomitrella patens and characterized its structure, polypeptide composition, and light-harvesting function using electron microscopy, mass spectrometry, biochemical, and physiological methods. It became evident thatPhyscomitrella possesses a strikingly high number of isoforms for the different PSI core subunits as well as LHCI proteins. It was demonstrated that all these different subunit isoforms are expressed at the protein level and are incorporated into functional PSI–LHCI complexes. Furthermore, in contrast to previous reports, it was demonstrated thatPhyscomitrella assembles a light-harvesting complex consisting of four light-harvesting proteins forming a higher-plant-like PSI superstructure.
Unlike the other major crops, no genetically modified (GM) varieties of rice have been commercialized at a large scale. Within the next 2–3 years new transgenic rice varieties could be ready for regulatory approval and subsequent commercialization, though. Given the importance of rice as staple crop for many of the world's poorest people, this will have implications for the alleviation of poverty, hunger and malnutrition. Thus, policy-makers need to be aware of the potential benefits of GM rice. We provide an overview of the literature and discuss the evidence on expected agronomic and consumer benefits of genetically engineered rice. We find that while GM rice with improved agronomic traits could deliver benefits similar to already commercialized biotechnology crops, expected benefits of consumer traits could be higher by an order of magnitude. By aggregating the expected annual benefits, we estimate the global value of GM rice to be US$64 billion per year. This is only an indicative value, as more GM varieties will become available in future. Nevertheless, such a figure can help guide policy-makers when deciding on the approval or funding of biotechnology crops and it may also raise awareness among consumers about what is at stake for their societies.
A substantial proportion of the global land surface is used for agricultural production. Agricultural land serves multiple societal purposes; it provides food, fuel and fibre and also acts as habitat for organisms and supports the services they provide. Biodiversity conservation and food production need to be balanced: production needs to be sustainable, while conservation cannot be totally at the expense of crop yield.
To identify the benefits (in terms of biodiversity conservation) and costs (in terms of reduction in yields) of agricultural management, we examined the relationship between crop yield and abundance and species density of important taxa in winter cereal fields on both organic and conventional farms in lowland England.
Of eight species groups examined, five (farmland plants, bumblebees, butterflies, solitary bees and epigeal arthropods) were negatively associated with crop yield, but the shape of this relationship varied between taxa. It was linear for the abundance of bumblebees and species density of butterflies, concave up for the abundance of epigeal arthropods and butterflies and concave down for species density of plants and bumblebees.
Grain production per unit area was 54% lower in organic compared with conventional fields. When controlling for yield, diversity of bumblebees, butterflies, hoverflies and epigeal arthropods did not differ between farming systems, indicating that observed differences in biodiversity between organic and conventional fields are explained by lower yields in organic fields and not by different management practices per se. Only percentage cover and species density of plants were increased by organic field management after controlling for yield. The abundance of solitary wild bees and hoverflies was increased in landscapes with high amount of organic land.
Our results indicate that considerable gains in biodiversity require roughly proportionate reductions in yield in highly productive agricultural systems. They suggest that conservation efforts may be more cost effective in low-productivity agricultural systems or on non-agricultural land. In less productive agricultural landscapes, biodiversity benefit can be gained by concentrating organic farms into hotspots without a commensurate reduction in yield.
Via Alexander J. Stein
Spatial patterns of the hormone auxin are important drivers of plant development. The observed feedback between the active, directed transport that generates auxin patterns and the auxin distribution that influences transport orientation has rendered this a popular subject for modelling studies. Here we propose a new mathematical framework for the analysis of polar auxin transport and present a detailed mathematical analysis of published models. We show that most models allow for self-organised patterning for similar biological assumptions, and find that the pattern generated is typically unidirectional, unless additional assumptions or mechanisms are incorporated. Our analysis thus suggests that current models cannot explain the bidirectional fountain-type patterns found in plant meristems in a fully self-organised manner, and we discuss future research directions to address the gaps in our understanding of auxin transport mechanisms.
Sakakibara et al. now provide critical insight into the evolutionary developmental underpinnings of the diploid sporophyte generation in the first land plants. Working with the model moss species Physcomitrella patens, they show that the creation of the sporophyte and its ontogeny in the life cycle of early land plants may have been facilitated by a mechanism that suppresses the expression of the ancestral gametophyte ontogeny brought onto land by green algal pioneers
Despite receiving the seal of approval from scientists, genetically modified food continues to be unpalatable in many parts of the world. As Cyrus Martin reports, a combination of factors, including economics and culture, may help to explain the differences.
Homozygous state-associated co-suppression is not a very common phenomenon. In our experiments, two transgenic plants 3A29 and 1195A were constructed by being transformed with the constructs pBIN-353A and pBIN119A containing nptII gene as a marker respectively. The homozygous progeny from these two independent transgenic lines 3A29 and 1195A, displayed kanamycin-sensitivity and produced a short main root without any lateral roots as untransformed control (wild-type) seedlings when germinated on kanamycin media. For the seedlings derived from putative hemizygous plants, the percentage of the seedlings showing normal growth on kanamycin media was about 50% and lower than the expected percentage (75%). Southern analysis of the genomic DNA confirmed that the homozygous and hemizygous plants derived from the same lines contained the same multiple nptII transgenes, which were located on the same site of chromosome. Northern analysis suggested that the marker nptII gene was expressed in the primary and the hemizygous transformants, but it was silenced in the homozygous transgenic plants. Further Northern analysis indicated that antisense and sense small nptII-derived RNAs were present in the transgenic plants and the blotting signal of nptII-derived small RNA was much higher in the homozygous transgenic plants than that of hemizygous transgenic plants. Additionally, read-through transcripts from the TRAMP gene to the nptII gene were detected. These results suggest that the read-through transcripts may be involved in homozygous state-associated silencing of the nptII transgene in transgenic tomato plants and a certain threshold level of the nptII-derived small RNAs is required for the homozygous state-associated co-suppression of the nptII transgene.
Maize (Zea mays L.), as one of the most important crops in the world, is deficient in lysine and tryptophan. Environmental conditions greatly impact plant growth, development and productivity.
Malnutrition could be greatly reduced and food security improved by ensuring improved access to nutrient-rich forest-derived foods like berries, bushmeat, roots, insects and nuts for the world’s poorest populations, experts say.
Via Luigi Guarino
Although advances in agronomy, breeding, and biotechnology have dramatically increased corn grain yields, soil test values indicate that producers may not be supplying optimal nutrient levels. Moreover, many current nutrient recommendations, developed decades ago using outdated agronomic management practices and lower-yielding, non-transgenic hybrids, may need adjusting. Researchers with the University of Illinois Crop Physiology Laboratory have been re-evaluating nutrient uptake and partitioning in modern corn hybrids. "Current fertilization practices may not match the uptake capabilities of hybrids that contain transgenic insect protection and that are grown at planting densities that increase by about 400 plants per acre per year," said U of I Ph.D. student Ross Bender. "Nutrient recommendations may not be calibrated to modern, higher-yielding genetics and management." ... "Although macro- and micronutrients are both essential for plant growth and development, two major aspects of plant nutrition are important to better determine which nutrients require the greatest attention: the amount of a nutrient needed for production, or total uptake, and the amount of that nutrient that accumulates in the grain." Study results indicated that high amounts of nitrogen (N), potassium (K), P, and S are needed, with applications made during key growth stages to maximize crop growth. Moreover, adequately accounting for nutrients with high harvest index values the proportion of total nutrient uptake present in corn grain), such as N, P, S, and Zn, which are removed from production fields via the grain, is vital to maintaining long-term soil productivity... "Although nutrient management is a complex process, a greater understanding of the physiology of nutrient accumulation and utilization is critical to maximize the inherent yield potential of corn," concluded Bender. Original study: http://dx.doi.org/10.2134/agronj2012.0352
Via Alexander J. Stein
Rothamsted Research has submitted an application to Defra to extend its current GM wheat field trial to include additional autumn-sown cadenza wheat. Rothamsted scientists believe it would be advantageous to gain further data from their experiment, in wheat planted at a different time of year and under different weather conditions with different aphid populations. This will give us additional data under a more diverse range of environmental conditions... Because the UK’s temperate climate permits wheat plant growth during the winter, Cadenza wheat can be sown in either the autumn or the spring and both sowings are harvested in August/September. As such, the extension of the experiment will further increase the relevance to UK farmers and those in other temperate climates by covering a greater range environmental variability. This weather variability has been particularly evident in the UK in the past 12 months... The controlled experiment being conducted by scientists from Rothamsted Research combines modern genetic engineering with natural plant defences to test whether aphid-repelling wheat works in the field. Wheat is the most important UK crop with an annual value of about £1.2 billion. Currently a large proportion of UK wheat is treated with a broad spectrum of chemical insecticides to control cereal aphids, which reduce yields by sucking sap from plants and by transmitting barley yellow dwarf virus. Unfortunately, repeated use of insecticides can kill other non-target insect species including the natural enemies of aphids, which itself could have further impacts on biodiversity. Rothamsted Research scientists, who receive strategic funding from the UK Government... have been seeking novel ecological solutions to overcome this problem in wheat. One approach has been to use an odour, or alarm pheromone, which aphids produce to alert one another to danger. This odour, (E)-β-farnesene, is also produced by some plants as a natural defence mechanism and not only repels aphids but also attracts the natural enemies of aphids, ladybirds for example. This work has been effective in the laboratory and Rothamsted scientists have already conducted the first field trial to investigate whether the GM plants work outside in the field, as well as in the laboratory... Professor Melanie Welham, BBSRC Director of Science, said: “We face the challenge of producing food in a sustainable way, while minimising effects on the environment. This research is exploring one approach to solving this problem. It is important to carry out these investigations as these data gathered will help to provide answers about the potential of this type of GM technology and what benefits it could offer. Importantly, the findings generated through this extension will add to the picture of how this technology compares to others and is it vital that future decisions are based on scientific evidence.”
Via Alexander J. Stein
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