Nature Plants, Published online: 5 May 2015; | doi:10.1038/nplants.2015.67 ............ Some researchers already consider Arabidopsis as too complex an organism to help inform us about the fundamentals of plant biology and evolution. Plants whose common ancestor with trees and grasses was much more ancient than that of Arabidopsis are becoming popular subjects of investigation. The moss Physcomitrella patens, whose standard laboratory strain was collected from a wood near Cambridge, UK, in 1962, was the subject of over 500 publications in the past five years, while the liverwort Marchantia polymorpha could be the model plant du jour with 126 publications over the same period.
Physcomitrella patens, a haploid dominant plant, is fast becoming a useful molecular genetics and bioinformatics tool due to its key phylogenetic position as a bryophyte in the post-genomic era. Genome sequences from select reference species were compared bioinformatically to Physcomitrella patens using reciprocal blasts with the InParanoid software package. A reference protein interaction database assembled using MySQL by compiling BioGrid, BIND, DIP, and Intact databases was queried for moss orthologs existing for both interacting partners. This method has been used to successfully predict interactions for a number of angiosperm plants.
Results show that moss cells contain extended peptide pools that are hydrolysis products of cell proteins. The peptide pool composition depends on the type of tissue yet always contains peptides derived from the major chloroplast proteins. We observe no correlation between protein abundance, its transcription level, and the amount of endogenous peptides. Active peptidogenesis in protoplasts is probably due to a range of mechanisms, with stress during isolation and immune reaction to Driselase treatment being the key ones. Eighty-nine peptides of protoplasts possess high antimicrobial potential. Genes involved in JA synthesis, as well as those associated with biotic stress, had increased transcription levels in protoplasts. Changes in the peptidome in protoplasts are accompanied by suppression of photosynthetic activity. In our future research, we aim to study which mechanisms of degradation are responsible for the formation of endogenous peptide pools in cells, evaluate biological activity of the peptides, and study the effects of hormones on peptidome formation.
GMO regulation is built on false premises in the EU and the Cartagena biosafety protocols. •
Molecular processes of transgenesis and natural mutation are similar. •
It is time to change GMO regulation toward a science based product oriented legislation. •
Some legislations like the one from Canada rely on Novel crops, conventional or GMOs.
The regulation of genetically engineered crops, in Europe and within the legislation of the Cartagena biosafety protocol is built on false premises: The claim was (and unfortunately still is) that there is a basic difference between conventional and transgenic crops, this despite the fact that this has been rejected on scientifically solid grounds since many years. This contribution collects some major arguments for a fresh look at regulation of transgenic crops, they are in their molecular processes of creation not basically different from conventional crops, which are based in their breeding methods on natural, sometimes enhanced mutation. But the fascination and euphoria of the discoveries in molecular biology and the new perspectives in plant breeding in the sixties and seventies led to the wrong focus on transgenic plants alone. In a collective framing process the initial biosafety debates focused on the novelty of the process of transgenesis. When early debates on the risk assessment merged into legislative decisions, this wrong focus on transgenesis alone seemed uncontested. The process-focused view was also fostered by a conglomerate of concerned scientists and biotechnology companies, both with a vested interest to at least tolerate the rise of the safety threshold to secure research money and to discourage competitors of all kinds. Policy minded people and opponent activists without deeper insight in the molecular science agreed to those efforts without much resistance. It is interesting to realize, that the focus on processes was uncontested by a majority of regulators, this despite of serious early warnings from important authorities in science, mainly of US origin. It is time to change the regulation of genetically modified (GM) crops toward a more science based process — agnostic legislation. Although this article concentrates on the critique of the process-oriented regulation, including some details about the history behind, there should be no misunderstanding that there are other important factors responsible for the failure of this kind of process-oriented regulation, most importantly: the predominance of politics in the decision making processes combined with the lack of serious scientific debates on regulatory matters within the European Union and also in the Cartagena system, the obscure and much too complex decision making structures within the EU, and the active, professional, negative and intimidating role of fundamental opposition against GM crops on all levels dealing with flawed science, often declared as better parallel science published by ‘independent’ scientists.
We communicate the rather remarkable observation that among 291 tested accessions of cultivated sweet potato, all contain one or more transfer DNA (T-DNA) sequences. These sequences, which are shown to be expressed in a cultivated sweet potato clone (“Huachano”) that was analyzed in detail, suggest that an Agrobacterium infection occurred in evolutionary times. One of the T-DNAs is apparently present in all cultivated sweet potato clones, but not in the crop’s closely related wild relatives, suggesting the T-DNA provided a trait or traits that were selected for during domestication. This finding draws attention to the importance of plant–microbe interactions, and given that this crop has been eaten for millennia, it may change the paradigm governing the “unnatural” status of transgenic crops.
•People tend to rely on intuitive reasoning to make a judgment on GMOs. •This intuitive reasoning includes folk biology, teleological and intentional intentions and disgust. •Anti-GMO activists have exploited intuitions successfully to promote their cause. •Intuitive judgments steer people away from sustainable solutions.
Public opposition to genetically modified organisms (GMOs) remains strong. By contrast, studies demonstrate again and again that GM crops make a valuable contribution to the development of a sustainable type of agriculture. The discrepancy between public opinion and the scientific evidence requires an explanation. We argue that intuitive expectations about the world render the human mind vulnerable to particular misrepresentations of GMOs. We explain how the involvement of particular intuitions accounts for the popularity, persistence, and typical features of GM opposition and tackle possible objections to our approach. To conclude, we discuss the implications for science education, science communication, and the environmental movement.
Shoot branching is a primary contributor to plant architecture, evolving independently in flowering plant sporophytes and moss gametophytes. Mechanistic understanding of branching is largely limited to flowering plants such as Arabidopsis, which have a recent evolutionary origin. We show that in gametophytic shoots of Physcomitrella, lateral branches arise by re-specification of epidermal cells into branch initials. A simple model co-ordinating the activity of leafy shoot tips can account for branching patterns, and three known and ancient hormonal regulators of sporophytic branching interact to generate the branching pattern- auxin, cytokinin and strigolactone. The mode of auxin transport required in branch patterning is a key divergence point from known sporophytic pathways. Although PIN-mediated basipetal auxin transport regulates branching patterns in flowering plants, this is not so in Physcomitrella, where bi-directional transport is required to generate realistic branching patterns. Experiments with callose synthesis inhibitors suggest plasmodesmal connectivity as a potential mechanism for transport.
Author Summary Pinot is one of the most ancient grapevine varieties made up of a large panel of clones, most of them used to produce very different wines with specific oenological characteristics in different vineyards around the world. This great diversity of clones, which is due to spontaneous somatic mutations that have occurred over time, makes Pinot a fascinating subject of study. It is the reason why we have undertaken a study focused on the color locus to identify the mutations respons
Field trails are indispensable for the scientific analysis of risks and potential benefits of genetically modified plants (GMP). The dramatic reduction of field trials in the European Union (EU) coincides with increasing safety demands, decreases in funding, and changes in the European directives. In parallel, opposition from non-governmental organizations (NGOs) has grown, and public acceptance has decreased. The cultivation of events approved by the EU is still allowed in principle, nevertheless, at least in Germany, there is a de facto moratorium on cultivation. In Switzerland, where development was much more hesitant compared to Germany, field trials are now possible, and a protected site has been established by the government. Public acceptance for scientific trials in Switzerland has risen, despite the continued moratorium on the cultivation based on a referendum.
"The natural history of maize began nine thousand years ago when Mexican farmers started to collect the seeds of the wild grass, teosinte. Invaluable as a food source, maize permeated Mexican culture and religion. Its domestication eventually led to its adoption as a model organism, aided in large part by its large chromosomes, ease of pollination and growing agricultural importance. Genome comparisons between varieties of maize, teosinte and other grasses are beginning to identify the genes responsible for the domestication of modern maize and are also providing ideas for the breeding of more hardy varieties."
Improvement in crop water-use efficiency (WUE) is a critical priority for regions facing increased drought or diminished groundwater resources. Despite new tools for the manipulation of stomatal development, the engineering of plants with high WUE remains a challenge. We used Arabidopsis epidermal patterning factor (EPF) mutants exhibiting altered stomatal density to test whether WUE could be improved directly by manipulation of the genes controlling stomatal density. Specifically, we tested whether constitutive overexpression of EPF2 reduced stomatal density and maximum stomatal conductance (gw(max)) sufficiently to increase WUE. We found that a reduction in gw(max) via reduced stomatal density in EPF2-overexpressing plants (EPF2OE) increased both instantaneous and long-term WUE without altering significantly the photosynthetic capacity. Conversely, plants lacking both EPF1 and EPF2 expression (epf1epf2) exhibited higher stomatal density, higher gw(max) and lower instantaneous WUE, as well as lower (but not significantly so) long-term WUE. Targeted genetic modification of stomatal conductance, such as in EPF2OE, is a viable approach for the engineering of higher WUE in crops, particularly in future high-carbon-dioxide (CO2) atmospheres.
Arabidopsis LrgB (synonym PLGG1) is a plastid glycolate/glycerate transporter associated with recycling of 2-phosphoglycolate generated via the oxygenase activity of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). We isolated two homologous genes (PpLrgB1 and B2) from the moss Physcomitrella patens. Phylogenetic tree analysis showed that PpLrgB1 was monophyletic with LrgB proteins of land plants, whereas PpLrgB2 was divergent from the green plant lineage. Experiments with PpLrgB–GFP fusion proteins suggested that both PpLrgB1 and B2 proteins were located in chloroplasts. We generated PpLrgB single (∆B1 and ∆B2) and double (∆B1/∆B2)-knockout lines using gene targeting of P. patens. The ∆B1 plants showed decreases in growth and photosynthetic activity, and their protonema cells were bent and accumulated glycolate. However, because ∆B2 and ∆B1/∆B2 plants showed no obvious phenotypic change relative to the wild-type or ∆B1 plants, respectively, the function of PpLrgB2 remains unclear. Arabidopsis LrgB could complement the ∆B1 phenotype, suggesting that the function of PpLrgB1 is the same as that of AtLrgB. When ∆B1 was grown under high-CO2 conditions, all novel phenotypes were suppressed. Moreover, protonema cells of wild-type plants exhibited a bending phenotype when cultured on media containing glycolate or glycerate, suggesting that accumulation of photorespiratory metabolites caused P. patens cells to bend.
A cluster of three rice lectin receptor kinases confers resistance to planthopper insects.
Insect pests reduce yields of crops worldwide through direct damage and because they spread devastating viral diseases. In Asia, the brown planthopper (BPH) decimates rice (Oryza sativa) crops, causing the loss of billions of dollars annually1. In this issue, Liu et al.2 report the cloning of a rice genetic locus that confers broad-spectrum resistance to BPH and at least one other planthopper species (white back planthopper). Introducing this locus into plant genomes is likely to provide an effective means of combating insect pests of rice and of other cereals such as maize.
In modern rice agriculture, BPH damage is controlled through breeding and the application of vast amounts of chemical pesticides1. Pesticides are not a sustainable approach, however, owing to high costs, harmful environmental effects and rapid development of resistant insects. Breeding programs have identified more than 20 genetic loci in cultivated or wild rice species that confer BPH resistance1. However, these Bph loci are usually only effective against specific BPH biotypes, and newly evolved BPH populations have rapidly overcome several Bph resistance loci deployed in the field..
Of the >20 identified Bph loci, only Bph14 and Bph26 have been cloned. Both of these loci encode coiled-coil, nucleotide-binding and leucine-rich repeat proteins3, 4, the main class of plant intracellular immune receptors5. Bph3 is a resistance locus that was first pinpointed genetically in the Sri Lankan rice indica cultivar Rathu Heenati. Notably, unlike most other Bph loci, including Bph14 and Bph26, Bph3 confers broad-spectrum resistance to many BPH biotypes as well as to the white back planthopper1, 2. The success of Bph3 as a resistance locus might be linked to the fact that it acts against BPH at an early stage of the feeding cycle, before the insect can deploy its arsenal of virulence proteins that circumvent plant defenses.
Despite the huge potential of Bph3 for rice agriculture, its molecular identity has been unknown. Liu et al.2 now identify Bph3 through map-based cloning in a cross between the resistant indica cultivar Rathu Heenati and the susceptible japonica cultivar 02428. Bph3 maps to a 79-kb genomic region that contains a cluster of three lectin receptor kinases, OsLecRK1–3 (ref. 2) (Fig. 1). The authors find that single-nucleotide polymorphisms in these genes are associated with BPH resistance in different cultivated rice accessions. They also show that ectopic expression of the OsLecRK1–3 gene cluster in the susceptible japonica Kitaake cultivar confers BPH resistance.
Mapping agricultural crops is an important application of remote sensing. However, in many cases it is based either on hyperspectral imagery or on multitemporal coverage, both of which are difficult to scale up to large-scale deployment at high spatial resolution. In the present paper, we evaluate the possibility of crop classification based on single images from very high-resolution (VHR) satellite sensors. The main objective of this work is to expose performance difference between state-of-the-art parcel-based smoothing and purely data-driven conditional random field (CRF) smoothing, which is yet unknown. To fulfill this objective, we perform extensive tests with four different classification methods (Support Vector Machines, Random Forest, Gaussian Mixtures, and Maximum Likelihood) to compute the pixel-wise data term; and we also test two different definitions of the pairwise smoothness term. We have performed a detailed evaluation on different multispectral VHR images (Ikonos, QuickBird, Kompsat-2). The main finding of this study is that pairwise CRF smoothing comes close to the state-of-the-art parcel-based method that requires parcel boundaries (average difference ≈ 2.5%). Our results indicate that a single multispectral (R, G, B, NIR) image is enough to reach satisfactory classification accuracy for six crop classes (corn, pasture, rice, sugar beet, wheat, and tomato) in Mediterranean climate. Overall, it appears that crop mapping using only one-shot VHR imagery taken at the right time may be a viable alternative, especially since high-resolution multitemporal or hyperspectral coverage as well as parcel boundaries are in practice often not available.
Shoot phototropism enables plants to position their photosynthetic organs in favorable light conditions and thus benefits growth and metabolism in land plants. To understand the evolution of this response, we established an experimental system to study phototropism in gametophores of the moss Physcomitrella patens. The phototropic response of gametophores occurs slowly; a clear response takes place more than 24 hours after the onset of unilateral light irradiation, likely due to the slow growth rate of gametophores. We also found that red and far-red light can induce phototropism, with blue light being less effective. These results suggest that plants used a broad range of light wavelengths as phototropic signals during the early evolution of land plants.
Music performance by professional musicians involves a wide-spectrum of cognitive and multi-sensory motor skills, whose biological basis is unknown. Several neuroscientific studies have demonstrated that the brains of professional musicians and non-musicians differ structurally and functionally and that musical training enhances cognition. However, the molecules and molecular mechanisms involved in music performance remain largely unexplored. Here, we investigated the effect of music performance on the genome-wide peripheral blood transcriptome of professional musicians by analyzing the transcriptional responses after a 2-hr concert performance and after a /`music-free/' control session. The up-regulated genes were found to affect dopaminergic neurotransmission, motor behavior, neuronal plasticity, and neurocognitive functions including learning and memory. Particularly, candidate genes such as SNCA, FOS and DUSP1 that are involved in song perception and production in songbirds, were identified, suggesting an evolutionary conservation in biological processes related to sound perception/production. Additionally, modulation of genes related to calcium ion homeostasis, iron ion homeostasis, glutathione metabolism, and several neuropsychiatric and neurodegenerative diseases implied that music performance may affect the biological pathways that are otherwise essential for the proper maintenance of neuronal function and survival. For the first time, this study provides evidence for the candidate genes and molecular mechanisms underlying music performance.
Barley (Hordeum vulgare ssp. vulgare) is an excellent model for understanding agricultural responses to climate change. Its initial domestication over 10 millennia ago and subsequent wide migration provide striking evidence of adaptation to different environments, agro-ecologies and uses. A bottleneck in the selection of modern varieties has resulted in a reduction in total genetic diversity and a loss of specific alleles relevant to climate-smart agriculture. However, extensive and well-curated collections of landraces, wild barley accessions (H. vulgare ssp. spontaneum) and other Hordeum species exist and are important new allele sources. A wide range of genomic and analytical tools have entered the public domain for exploring and capturing this variation, and specialized populations, mutant stocks and transgenics facilitate the connection between genetic diversity and heritable phenotypes. These lay the biological, technological and informational foundations for developing climate-resilient crops tailored to specific environments that are supported by extensive environmental and geographical databases, new methods for climate modelling and trait/environment association analyses, and decentralized participatory improvement methods. Case studies of important climate-related traits and their constituent genes – including examples that are indicative of the complexities involved in designing appropriate responses – are presented, and key developments for the future highlighted.
There’s no doubt that the next generation of GM crops will look very little like the oft-maligned varieties available today. The possibilities are nearly limitless, as are the rewards. And with the world’s climate changing rapidly, there’s no doubt that agriculture will need to change with it, to keep pace with an unpredictable environment. The future of agriculture may very well depend on the ingenuity of geneticists and the GMOs they create. The real question is, will these new varieties be able to do what current ones cannot: win over the hearts and minds of the people they’re designed for.
Many phylogenomic studies based on transcriptomes have been limited to “single-copy” genes due to methodological challenges in homology and orthology inferences. Only a relatively small number of studies have explored analyses beyond reconstructing species relationships. We sampled 69 transcriptomes in the hyperdiverse plant clade Caryophyllales and 27 outgroups from annotated genomes across eudicots. Using a combined similarity- and phylogenetic tree-based approach, we recovered 10,960 homolog groups, where each was represented by at least eight ingroup taxa. By decomposing these homolog trees, and taking gene duplications into account, we obtained 17,273 ortholog groups, where each was represented by at least ten ingroup taxa. We reconstructed the species phylogeny using a 1,122-gene data set with a gene occupancy of 92.1%. From the homolog trees we found that both synonymous and nonsynonymous substitution rates in herbaceous lineages are up to three times as fast as in their woody relatives. This is the first time such a pattern has been shown across thousands of nuclear genes with dense taxon sampling. We also pinpointed regions of the Caryophyllales tree that were characterized by relatively high frequencies of gene duplication, including three previously unrecognized whole genome duplications. By further combining information from homolog tree topology and synonymous distance between paralog pairs, phylogenetic locations for 13 putative genome duplication events were identified. Genes that experienced the greatest gene family expansion were concentrated among those involved in signal transduction and oxidoreduction, including a cytochrome P450 gene that encodes a key enzyme in the betalain synthesis pathway. Our approach demonstrates a new approach for functional phylogenomic analysis in non-model species that is based on homolog groups in addition to inferred ortholog groups.
Plenty of molecular markers have been developed by contemporary sequencing technologies, whereas few of them are successfully applied in breeding, thus we present a review on how sequencing can facilitate marker-assisted selection in plant breeding.
The growing global population and shrinking arable land area require efficient plant breeding. Novel strategies assisted by certain markers have proven effective for genetic gains. Fortunately, cutting-edge sequencing technologies bring us a deluge of genomes and genetic variations, enlightening the potential of marker development. However, a large gap still exists between the potential of molecular markers and actual plant breeding practices. In this review, we discuss marker-assisted breeding from a historical perspective, describe the road from crop sequencing to breeding, and highlight how sequencing facilitates the application of markers in breeding practice.
Double-stranded RNAs (dsRNAs) targeted against essential genes can trigger a lethal RNA interference (RNAi) response in insect pests. The application of this concept in plant protection is hampered by the presence of an endogenous plant RNAi pathway that processes dsRNAs into short interfering RNAs. We found that long dsRNAs can be stably produced in chloroplasts, a cellular compartment that appears to lack an RNAi machinery. When expressed from the chloroplast genome, dsRNAs accumulated to as much as 0.4% of the total cellular RNA. Transplastomic potato plants producing dsRNAs targeted against the β-actin gene of the Colorado potato beetle, a notorious agricultural pest, were protected from herbivory and were lethal to its larvae. Thus, chloroplast expression of long dsRNAs can provide crop protection without chemical pesticides.
The aim of this study was to assess whether endosperm-specific carotenoid biosynthesis influenced core metabolic processes in maize embryo and endosperm and how global seed metabolism adapted to this expanded biosynthetic capacity. Although enhancement of carotenoid biosynthesis was targeted to the endosperm of maize kernels, a concurrent up-regulation of sterol and fatty acid biosynthesis in the embryo was measured. Targeted terpenoid analysis, and non-targeted metabolomic, proteomic, and transcriptomic profiling revealed changes especially in carbohydrate metabolism in the transgenic line. In-depth analysis of the data, including changes of metabolite pools and increased enzyme and transcript concentrations, gave a first insight into the metabolic variation precipitated by the higher up-stream metabolite demand by the extended biosynthesis capacities for terpenoids and fatty acids. An integrative model is put forward to explain the metabolic regulation for the increased provision of terpenoid and fatty acid precursors, particularly glyceraldehyde 3-phosphate and pyruvate or acetyl-CoA from imported fructose and glucose. The model was supported by higher activities of fructokinase, glucose 6-phosphate isomerase, and fructose 1,6-bisphosphate aldolase indicating a higher flux through the glycolytic pathway. Although pyruvate and acetyl-CoA utilization was higher in the engineered line, pyruvate kinase activity was lower. A sufficient provision of both metabolites may be supported by a by-pass in a reaction sequence involving phosphoenolpyruvate carboxylase, malate dehydrogenase, and malic enzyme.
We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost 400,000 polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of Western and Far Eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, [sim]8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a [sim]24,000-year-old Siberian. By [sim]6,000-5,000 years ago, farmers throughout much of Europe had more hunter-gatherer ancestry than their predecessors, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but also from a population of Near Eastern ancestry. Western and Eastern Europe came into contact [sim]4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced [sim]75% of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least [sim]3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for a steppe origin of at least some of the Indo-European languages of Europe.
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