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.
During the transition from water to land, plants had to cope with the loss of water through transpiration, the inevitable result of photosynthetic CO2 fixation on land [1 and 2]. Control of transpiration became possible through the development of a new cell type: guard cells, which form stomata. In vascular plants, stomatal regulation is mediated by the stress hormone ABA, which triggers the opening of the SnR kinase OST1-activated anion channel SLAC1 [3 and 4]. To understand the evolution of this regulatory circuit, we cloned both ABA-signaling elements, SLAC1 and OST1, from a charophyte alga, a liverwort, and a moss, and functionally analyzed the channel-kinase interactions. We were able to show that the emergence of stomata in the last common ancestor of mosses and vascular plants coincided with the origin of SLAC1-type channels capable of using the ancient ABA drought signaling kinase OST1 for regulation of stomatal closure.
During the development of a genetically modified (GM) crop product, extensive phenotypic and agronomic data are collected to characterize the plant in comparison to a conventional control with a similar genetic background. The data are evaluated for potential differences resulting from the genetic modification process or the GM trait, and the differences—if any—are subsequently considered in the context of contributing to the pest potential of the GM crop. Ultimately, these study results and those of other studies are used in an ecological risk assessment of the GM crop. In the studies reported here, seed germination, vegetative and reproductive growth, and pollen morphology of Roundup Ready 2 Yield® soybean, MON 89788, were compared to those of A3244, a conventional control soybean variety with the same genetic background. Any statistically significant differences were considered in the context of the genetic variation known to occur in soybean and were evaluated as indicators of an effect of the genetic modification process and assessed for impact on plant pest (weed) characteristics and adverse ecological impact (ecological risk). The results of these studies revealed no effects attributable to the genetic modification process or to the GM trait in the plant that would result in increased pest potential or adverse ecological impact of MON 89788 compared with A3244. These results and the associated risk assessments obtained from diverse geographic and environmental conditions in the United States and Argentina can be used by regulators in other countries to inform various assessments of ecological risk.
In recent years, tetracyclines, such as doxycycline, have become broadly used to control gene expression by virtue of the Tet-on/Tet-off systems. However, the wide range of direct effects of tetracycline use has not been fully appreciated. We show here that these antibiotics induce a mitonuclear protein imbalance through their effects on mitochondrial translation, an effect that likely reflects the evolutionary relationship between mitochondria and proteobacteria. Even at low concentrations, tetracyclines induce mitochondrial proteotoxic stress, leading to changes in nuclear gene expression and altered mitochondrial dynamics and function in commonly used cell types, as well as worms, flies, mice, and plants. Given that tetracyclines are so widely applied in research, scientists should be aware of their potentially confounding effects on experimental results. Furthermore, these results caution against extensive use of tetracyclines in livestock due to potential downstream impacts on the environment and human health.
Jean-Pierre Zryd's insight:
Do leftover tetracyclin affect plants in the real world of agriculture - the question remain open ?
Emerging and re-emerging pathogens imperil public health and global food security. Responding to these threats requires improved surveillance and diagnostic systems. Despite their potential, genomic tools have not been readily applied to emerging or re-emerging plant pathogens such as the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici (PST). This is due largely to the obligate parasitic nature of PST, as culturing PST isolates for DNA extraction remains slow and tedious.
Environmental reservoirs are essential in the maintenance and transmission of anthrax but are poorly characterized. The anthrax agent, Bacillus anthracis was long considered an obligate pathogen that is dormant and passively transmitted in the environment. However, a growing number of laboratory studies indicate that, like some of its close relatives, B. anthracis has some activity outside of its vertebrate hosts. Here we show in the field that B. anthracis has significant interactions with a grass that could promote anthrax spore transmission to grazing hosts. Using a local, virulent strain of B. anthracis, we performed a field experiment in an enclosure within a grassland savanna. We found that B. anthracis increased the rate of establishment of a native grass (Enneapogon desvauxii) by 50% and that grass seeds exposed to blood reached heights that were 45% taller than controls. Further we detected significant effects of E. desvauxii, B. anthracis, and their interaction on soil bacterial taxa richness and community composition. We did not find any evidence for multiplication or increased longevity of B. anthracis in bulk soil associated with grass compared to controls. Instead interactions between B. anthracis and plants may result in increased host grazing and subsequently increased transmission to hosts.
Let us cast our minds back half a billion years and look around us. We do not see a green and pleasant land. Instead, we see a barren wasteland. We see a land without plants, the landscape comprising bare rock and its erosion products – at best a mineral sludge. But it was around this time that the first land plants emerged, evolving from pond slime – an aquatic algal ancestor most likely left on the banks of a receding body of water. Unlike today's climax vegetation, the first land plants were simple. They lacked the complex anatomical adaptations characteristic of the modern flora –ramifying root systems scavenging water from deep below the surface, vascular tissues to deliver this to aerial parts of the plant, whence it evaporates via the stomatal apertures of the leaves. The first land plants were not initially equipped for the vagaries of the terrestrial environment, with its rapid fluctuations of temperature, high incident radiation and uncertain availability of water. Directly equilibrating with the atmosphere and unable to prevent water loss, the first land plants must necessarily have possessed molecular and biochemical mechanisms to protect their cellular machinery from the lethal consequences of dehydration. In this issue of New Phytologist, a report from the laboratories of Daisuke Takezawa and Yoichi Sakata (Takezawa et al., pp. 209–219) highlights how osmotic stress in the model moss Physcomitrella patens induces abscisic acid (ABA) biosynthesis through a long-conserved biochemical pathway, implicating this as a vital early adaptation that enabled plants to conquer the land.
Mitochondrial genomes of lycophytes are surprisingly diverse, including strikingly different transfer RNA (tRNA) gene complements: No mitochondrial tRNA genes are present in the spikemoss Selaginella moellendorffii, whereas 26 tRNAs are encoded in the chondrome of the clubmoss Huperzia squarrosa. Reinvestigating the latter we found that trnL(gag) and trnS(gga) had never before been identified in any other land plant mitochondrial DNA. Sensitive sequence comparisons showed these two tRNAs as well as trnN(guu) and trnS(gcu) to be very similar to their respective counterparts in chlamydial bacteria. We identified homologs of these chlamydial-type tRNAs also in other lycophyte, fern, and gymnosperm DNAs, suggesting horizontal gene transfer (HGT) into mitochondria in the early vascular plant stem lineages. These findings extend plant mitochondrial HGT to affect individual tRNA genes, to include bacterial donors, and suggest that Chlamydiae on top of their recently proposed key role in primary chloroplast establishment may also have participated in early tracheophyte genome evolution.
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.
We tend to think that everyone deserves an equal say in a debate. This seemingly innocuous assumption can be damaging when we make decisions together as part of a group. To make optimal decisions, group members should weight their differing opinions according to how competent they are relative to one another; whenever they differ in competence, an equal weighting is suboptimal. Here, we asked how people deal with individual differences in competence in the context of a collective perceptual decision-making task. We developed a metric for estimating how participants weight their partner’s opinion relative to their own and compared this weighting to an optimal benchmark. Replicated across three countries (Denmark, Iran, and China), we show that participants assigned nearly equal weights to each other’s opinions regardless of true differences in their competence—even when informed by explicit feedback about their competence gap or under monetary incentives to maximize collective accuracy. This equality bias, whereby people behave as if they are as good or as bad as their partner, is particularly costly for a group when a competence gap separates its members.
Plant phenotyping refers to a quantitative description of the plant’s anatomical, ontogenetical, physiological and biochemical properties. Today, rapid developments are taking place in the field of non-destructive, image-analysis -based phenotyping that allow for a characterization of plant traits in high-throughput. During the last decade, ‘the field of image-based phenotyping has broadened its focus from the initial characterization of single-plant traits in controlled conditions towards ‘real-life’ applications of robust field techniques in plant plots and canopies. An important component of successful phenotyping approaches is the holistic characterization of plant performance that can be achieved with several methodologies, ranging from multispectral image analyses via thermographical analyses to growth measurements, also taking root phenotypes into account.
The use of plant (cell) suspension cultures in phototrophic mode on an industrially relevant scale is limited to two systems worldwide. These are the moss-based BryoTechnology™ and the duckweed-based SYNLEX™ production systems being developed by greenovation biotech GmbH and Synthon, respectively. Both production platforms make use of intact plants, rather than isolated cells, which are grown in simple salt media to manufacture recombinant, high value pharmaceutical proteins. They exploit unique features of plants like homogenous N-glycosylation, absolute genetic stability, and pathogen safety to create biopharmaceuticals of outstanding quality. On the equipment side, both processes build on single use, disposable solutions bringing about high flexibility and regulatory safety. Despite sharing all of the above-mentioned aspects, these two systems differ remarkably in several details. Physcomitrella patens, the moss behind BryoTechnology™, is unique in its potential for genetic engineering. Resembling yeast systems in that aspect, it allows for rapid generation of product-tailored production platforms. The SYNLEX™-system on the other hand, with Lemna minor as producing organism has a very basic process setup with few controls and good scale-up potential. This chapter discusses strengths and weaknesses of both systems side-by-side, describes their current technological development status, and gives a short future outlook.
Bougainvilleas, are one of the unique plant families with an unusual class of pigments, known as betalains replaced the more common anthocyanins. However, little is known on the molecular mechanism on the mutual exclusion of anthocyanins and betalains. In order to explore the unique phenomena in Bougainvilleas, we used open inflorescences of B. spectabilis ‘Speciosas’ for transcriptome analysis by pyrosequencing, which is the first attempt to obtain the transcriptome of this specific plant. In this study, we obtained 111.9 M raw data, after assembling, 17,728 unigenes sequence with average length of 607 bp long were available, the annotation including Gene Ontology, COG/KOG and associated Kyoto Encyclopedia of Genes and Genomics (KEGG) pathway maps were conducted. Important genes involved in flavonoid/Betalains/anthocyanins motablisms were identified including FLS/F3H, UGT, DFR, DODA, anthocyanidin reductase and Anthocyanidin 3-O-glucosyltransferase, as well as some transcriptional factors (Myb, YABBY, MADS-box, F-box, WD-40 and bHLH) in this study. The obtained unigenes which will provide a database for discovering genes involved in secondary metabolic synthesis pathway. The discovered genes can be used for future bioengineering of various secondary metabolites for health improvement, pigments, medicine and agricultural production, etc. Specially, these genes such as DFR, anthocyanidin reductase and anthocyanidin 3-O-glucosyltransferase, were detected in betalain-synthesizing plants, which is exciting for researchers. Furthermore, a total of 877 simple sequence repeat motifs (SSRs) were identified, among the perfect SSRs, the most abundant repeat units were mononucleotide repeats (61 %) with (A/T)n and the second one is tri-nucleotide repeats (24 %). The obtained EST-SSRs can be used for marker development which will be beneficial for the studies in the aspects of genetic diversity, evolution and phenotype variation of B. spectabilis ‘Speciosas’ as well as its related species. Euphytica Euphytica Look Inside Other actions
Export citation Register for Journal Updates About This Journal Reprints and Permissions Add to Papers
Share Share this content on Facebook Share this content on Twitter Share this content on LinkedIn
What has long been suspected is true: genetically modified (GM) crops do have real benefits for the environment and for the economic well-being of farmers. A meta-analysis of peer-reviewed journal articles and other literature... reveals that the adoption of GM crops reduces pesticide input and increases crop yields and farmers’ income. The results confirm earlier and smaller studies and therefore are not unexpected. But they are particularly welcome for significantly informing the public debate on GM crops...
Large-scale and chemical-intensive monoculture production is also found for non-GM crops, but this is conveniently ignored by GMO opponents in the debate on GM crops. Changing agriculture to sustainable production does not exclude GM crops because insect- and pathogen-resistant GM crops would also be useful and beneficial in integrated and organic agriculture to reduce pesticide inputs.
The meta-analysis of the impacts of GM crops... confirm and extend earlier and smaller studies that already reported benefits of GM crops based on existing farm-level impact data for GM crops... One can only hope that the collective evidence for the beneficial impacts of GM crops will now enable a more informed and rational debate. Even if opposition and false claims continue to spur public skepticism, farmers must be allowed to choose and grow the crops - GM or non-GM - that improve their economic situation and help them to contribute to global food security.
Production of Dihydroxylated Betalains and Dopamine in Cell Suspension Cultures of Celosia argentea var. ... Betalains are plant pigments of hydrophilic nature with demonstrated chemopreventive potential in cancer cell lines and animal models. ... Among the betalains, those containing an aromatic moiety with two free hydroxyl groups possess the strongest antioxidant and free radical scavenging activities. ...
Lesson from Ebola: Tobacco plant key to developing GMO drugs of the future | David Warmflash | February 25, 2015 | Genetic Literacy Project
With an approach similar to that used for ZMapp, GM tobacco is also being used to develop flu vaccines, while potatoes are being used for vaccines against hepatitis B and noroviruses, another kind of hepatitis B vaccine is being developed from GM corn, and other plants are being considered to host genes for making vaccines against certain rhinoviruses and even immunodeficiency virus (HIV, the virus that causes AIDS). Additionally, chemical compounds taken from spinach are being adapted for immunization against rabies, while enzymes made by carrot cells are being used for treatment of a genetic condition called Gaucher disease. Finally, the gene for human insulin has been transferred into safflower plants to improve diabetes treatment.
We’re at the beginning of a new age, the era of GMO medicine. While it’s moving extremely rapidly and the public may be overwhelmed, the potential benefits are enormous. People will live longer and higher quality lives as a result of the new treatments, and if it’s explained right and the benefits made clear, the public will embrace it. Well, maybe except for a few ideologues at the end of the spectrum.
Sharing your scoops to your social media accounts is a must to distribute your curated content. Not only will it drive traffic and leads through your content, but it will help show your expertise with your followers.
How to integrate my topics' content to my website?
Integrating your curated content to your website or blog will allow you to increase your website visitors’ engagement, boost SEO and acquire new visitors. By redirecting your social media traffic to your website, Scoop.it will also help you generate more qualified traffic and leads from your curation work.
Distributing your curated content through a newsletter is a great way to nurture and engage your email subscribers will developing your traffic and visibility.
Creating engaging newsletters with your curated content is really easy.