Can we use transgenic plants to limit aphid negative impact on plants? And if yes, which efficient technical means can we develop? Guo et al in the lab of Rongxiang Fang in Beijing, propose to generate in planta, small ...
TALEN-induced mutation of all homologous copies of a gene that represses resistance to an important wheat pathogen confers a trait that has eluded plant breeders for decades.
Sequence-specific nucleases have been applied to engineer targeted modifications in polyploid genomes1, but simultaneous modification of multiple homoeoalleles has not been reported. Here we use transcription activator–like effector nuclease (TALEN)2, 3 and clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 (refs. 4,5) technologies in hexaploid bread wheat to introduce targeted mutations in the three homoeoalleles that encode MILDEW-RESISTANCE LOCUS (MLO) proteins6. Genetic redundancy has prevented evaluation of whether mutation of all three MLO alleles in bread wheat might confer resistance to powdery mildew, a trait not found in natural populations7. We show that TALEN-induced mutation of all three TaMLO homoeologs in the same plant confers heritable broad-spectrum resistance to powdery mildew. We further use CRISPR-Cas9 technology to generate transgenic wheat plants that carry mutations in the TaMLO-A1 allele. We also demonstrate the feasibility of engineering targeted DNA insertion in bread wheat through nonhomologous end joining of the double-strand breaks caused by TALENs. Our findings provide a methodological framework to improve polyploid crops.
Bread wheat (hexaploid Triticum aestivum) provides an extraordinary 10,000-y story of a new species, established by early farmers, selecting for simple agronomical traits to facilitate efficient and plentiful grain harvest. The genetic changes underlying wheat domestication over thousands of years, however, included not just a collection of beneficial single gene mutations, but also introgressions and whole genome duplication. The hexaploidization event occurred spontaneously in nature, but the resulting wild species did not survive; it is known only in its domesticated form. Evolutionary bottleneck(s) reduced genetic variation of the species, and it was introduced broadly outside its native geographical range and habitat. Nevertheless, modern breeding programs delivered high-yield elite cultivars, which are planted in most major wheat-producing areas of the world. In the face of quickly declining arable land expansion and challenges from climate change, the following question arises: where can we find the next wave of increase in yield and global production of wheat? In PNAS, Kempe et al. (1) describe molecular engineering of an elegant male sterility–fertility restoration system for the exploration of heterosis (hybrid plant vigor) in wheat. In the future, this system could facilitate introduction of hybrid seeds on a large scale.
Emmer wheat, one of the eight founder crops domesticated in the Middle East about 10,000 y ago, was instrumental in spawning the Agricultural Revolution. The transition of wild to cultivated emmer initiated the extensive genetic restructuring of domesticated wheat, primarily involving mutations that resulted in the transition of types with natural seed dispersal mechanisms (brittle spikes) to types with a nonbrittle rachis (2). The initial transition from the wild habitat to cultivated fields also involved selection for free-threshing seeds, nondormant seeds, uniform and rapid germination, erect plants, and increased grain size. It was a domesticated derivative of emmer that hybridized with goatgrass about 8,000 y ago (3), probably southeast of the Caspian Sea, that resulted in the first hexaploid bread wheat (4).
In vascular plants, strigolactones (SLs) are known for their hormonal role and for their role as signal molecules in the rhizosphere. SLs are also produced by the moss Physcomitrella patens, in which they act as signaling factors for controlling filament extension and possibly interaction with neighboring individuals. To gain a better understanding of SL action at the cellular level, we investigated the effect of exogenously added molecules (SLs or analogs) in moss growth media. We used the previously characterized Ppccd8 mutant that is deficient in SL synthesis and showed that SLs affect moss protonema extension by reducing caulonema cell elongation and mainly cell division rate, both in light and dark conditions. Based on this effect, we set up bioassays to examine chemical structure requirements for SL activity in moss. The results suggest that compounds GR24, GR5, and 5-deoxystrigol are active in moss (as in pea), while other analogs that are highly active in the control of pea branching show little activity in moss. Interestingly, the karrikinolide KAR1, which shares molecular features with SLs, did not have any effect on filament growth, even though the moss genome contains several genes homologous to KAI2 (encoding the KAR1 receptor) and no canonical homologue to D14 (encoding the SL receptor). Further studies should investigate whether SL signaling pathways have been conserved during land plant evolution.
Once again, there are calls to reopen the debate on genetically modified (GM) crops. I find these calls frustrating and unnecessarily decisive. In my opinion the GM debate, on both sides, continues to hamper the urgent need to address the diverse and pressing challenges of global food security and environmental sustainability. The destructive power of the debate comes from its conflation of unrelated issues, coupled with deeply rooted misconceptions of the nature of agriculture.
An analysis of key genes and enzymes of the betacyanin biosynthetic pathway in Amaranthus hypochondriacus (Ah) was performed. Complete cDNA sequence of Ah genes coding for cyclo-DOPA 5-O glucosyltransferase (AhcDOPA5-GT), two 4, 5-DOPA-extradiol-dioxygenase isoforms (AhDODA-1 and AhDODA-2, respectively), and a betanidin 5-O-glucosyltransferase (AhB5-GT), plus the partial sequence of an orthologue of the cytochrome P-450 R gene (CYP76AD1) were obtained. With the exception AhDODA-2, which had a closer phylogenetic relationship to DODA-like genes in anthocyanin-synthesizing plants, all genes analyzed closely resembled those reported in related Caryophyllales species. The measurement of basal gene expression levels, in addition to the DOPA oxidase tyrosinase (DOT) activity, in different tissues of three Ah genotypes having contrasting pigmentation levels (green to red-purple) was determined. Additional analyses were performed in Ah plants subjected to salt and drought stress and to two different insect herbivory regimes. Basal pigmentation accumulation in leaves, stems and roots of betacyanic plants correlated with higher expression levels of AhDODA-1 and AhB5-GT, whereas DOT activity levels coincided with pigment accumulation in stems and roots and with the acyanic nature of green plants, respectively, but not with pigmentation in leaves. Although the abiotic stress treatments tested produced changes in pigment levels in different tissues, pigment accumulation was the highest in leaves and stems of drought stressed betacyanic plants, respectively. However, tissue pigment accumulation in stressed Ah plants did not always correlate with betacyanin biosynthetic gene expression levels and/or DOT activity. This effect was tissue- and genotype-dependent, and further suggested that other unexamined factors were influencing pigment content in stressed Ah. The results obtained from the insect herbivory assays, particularly in acyanic plants, also support the proposal that these genes could have functions other than betacyanin biosynthesis.
no double blindThis article describes the nutrient and elemental composition, including residues of herbicides and pesticides, of 31 soybean batches from Iowa, USA. The soy samples were grouped into three different categories: (i) genetically modified, glyphosate-tolerant soy (GM-soy); (ii) unmodified soy cultivated using a conventional “chemical” cultivation regime; and (iii) unmodified soy cultivated using an organic cultivation regime. Organic soybeans showed the healthiest nutritional profile with more sugars, such as glucose, fructose, sucrose and maltose, significantly more total protein, zinc and less fibre than both conventional and GM-soy. Organic soybeans also contained less total saturated fat and total omega-6 fatty acids than both conventional and GM-soy. GM-soy contained high residues of glyphosate and AMPA (mean 3.3 and 5.7 mg/kg, respectively). Conventional and organic soybean batches contained none of these agrochemicals. Using 35 different nutritional and elemental variables to characterise each soy sample, we were able to discriminate GM, conventional and organic soybeans without exception, demonstrating “substantial non-equivalence” in compositional characteristics for ‘ready-to-market’ soybeans.
Jean-Pierre Zryd's insight:
To be read "cum grano salis"; it's not a double blind study; statistics are at the limit of significance level and finally some authors have huge conflicts of interest
With the advent of deep sequencing technologies and the ability to analyze whole genome sequences and transcriptomes, there has been a growing interest in exploring putative functions of the very large fraction of the genome that is commonly referred to as “junk DNA.” Whereas this is an issue of considerable importance in genome biology, there is an unfortunate tendency for researchers and science writers to proclaim the demise of junk DNA on a regular basis without properly addressing some of the fundamental issues that first led to the rise of the concept. In this review, we provide an overview of the major arguments that have been presented in support of the notion that a large portion of most eukaryotic genomes lacks an organism-level function. Some of these are based on observations or basic genetic principles that are decades old, whereas others stem from new knowledge regarding molecular processes such as transcription and gene regulation.
Over 70 years ago, increased spontaneous mutation rates were observed in Drosophila spp. hybrids, but the genetic basis of this phenomenon is not well understood. The model plant Arabidopsis (Arabidopsis thaliana) offers unique opportunities to study the types of mutations induced upon hybridization and the frequency of their occurrence. Understanding the mutational effects of hybridization is important, as many crop plants are grown as hybrids. Besides, hybridization is important for speciation and its effects on genome integrity could be critical, as chromosomal rearrangements can lead to reproductive isolation. We examined the rates of hybridization-induced point and frameshift mutations as well as homologous recombination events in intraspecific Arabidopsis hybrids using a set of transgenic mutation detector lines that carry mutated or truncated versions of a reporter gene. We found that hybridization alters the frequency of different kinds of mutations. In general, Columbia (Col) × Cape Verde Islands and Col × C24 hybrid progeny had decreased T→G and T→A transversion rates but an increased C→T transition rate. Significant changes in frameshift mutation rates were also observed in some hybrids. In Col × C24 hybrids, there is a trend for increased homologous recombination rates, except for the hybrids from one line, while in Col × Cape Verde Islands hybrids, this rate is decreased. The overall genetic distance of the parents had no influence on mutation rates in the progeny, as closely related accessions on occasion displayed higher mutation rates than accessions that are separated farther apart. However, reciprocal hybrids had significantly different mutation rates, suggesting parent-of-origin-dependent effects on the mutation frequency.
Ferns represent the most closely related extant lineage to seed plants. The aquatic fern Ceratopteris richardii has been subject to research for a considerable period of time, but analyses of the genetic programs underpinning developmental processes have been hampered by a large genome size, a lack of available mutants, and an inability to create stable transgenic lines. In this paper, we report a protocol for efficient stable genetic transformation of C. richardii and a closely related species Ceratopteris thalictroides using microparticle bombardment. Indeterminate callus was generated and maintained from the sporophytes of both species using cytokinin treatment. In proof-of-principle experiments, a 35S::β-glucuronidase (GUS) expression cassette was introduced into callus cells via tungsten microparticles, and stable transformants were selected via a linked hygromycin B resistance marker. The presence of the transgene in regenerated plants and in subsequent generations was validated using DNA-blot analysis, reverse transcription-polymerase chain reaction, and GUS staining. GUS staining patterns in most vegetative tissues corresponded with constitutive gene expression. The protocol described in this paper yields transformation efficiencies far greater than those previously published and represents a significant step toward the establishment of a tractable fern genetic model.
Imprinted gene expression—the biased expression of alleles dependent on their parent of origin—is an important type of epigenetic gene regulation in flowering plants and mammals. In plants, genes are imprinted primarily in the endosperm, the triploid placenta-like tissue that surrounds and nourishes the embryo during its development. Differential allelic expression is correlated with active DNA demethylation by DNA glycosylases and repressive targeting by the Polycomb group proteins. Imprinted gene expression is one consequence of a large-scale remodeling to the epigenome, primarily directed at transposable elements, that occurs in gametes and seeds. This remodeling could be important for maintaining the epigenome in the embryo as well as for establishing gene imprinting.
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
Jean-Pierre Zryd's insight:
Vertical, transgenerational transmission of genetic material occurs through reproduction of living organisms. In addition to vertical inheritance, horizontal gene transfer between reproductively isolated species has recently been shown to be an important, if not dominant, mechanism in the evolution of prokaryotic genomes. In contrast, only a few horizontal transfer (HT) events have been characterized so far in eukaryotes and mainly concern transposable elements (TEs). Whether these are frequent and have a significant impact on genome evolution remains largely unknown. We performed a computational search for highly conserved LTR retrotransposons among 40 sequenced eukaryotic genomes representing the major plant families. We found that 26 genomes (65%) harbor at least one case of horizontal TE transfer (HTT). These transfers concern species as distantly related as palm and grapevine, tomato and bean, or poplar and peach. In total, we identified 32 cases of HTTs, which could translate into more than 2 million among the 13,551 monocot and dicot genera. Moreover, we show that these TEs have remained functional after their transfer, occasionally causing a transpositional burst. This suggests that plants can frequently exchange genetic material through horizontal transfers and that this mechanism may be important in TE-driven genome evolution.
29 April 2014. Cover of PNAS. The issue with the special feature on the "Modern View of Domestication". Cover image: Pictured are the Gamo-Gofa highlands of southern Ethiopia, a traditional agricultural landscape dotted with domesticated plants and animals such as hybrid cattle. Domesticated plants of diverse geographical origins include maize, sorghum, barley, Ethiopian banana, palm kale, and castor oil plant. The Modern View of Domestication Special Feature, appearing in this issue, presents recent genetic and archaeological evidence regarding the origin and spread of domesticated plants and animals, and addresses questions including those concerning the speed and intentionality of early domestication. See the Introduction to the Special Feature by Greger Larson et al. on pages 6139–6146. Image courtesy of Dorian Fuller.
International Business Times UK Chinese Researchers Create Disease-Resistant Wheat by Deleting Genes Mashable The gene-deletion trick is particularly tough to do in wheat because the plant has three genomes — with largely similar copies of the same...
Allopolyploidization, the combination of the genomes from two different species, has been a major source of evolutionary innovation and a driver of speciation and environmental adaptation. In plants, it has also contributed greatly to crop domestication, as the superior properties of many modern crop plants were conferred by ancient allopolyploidization events. It is generally thought that allopolyploidization occurred through hybridization events between species, accompanied or followed by genome duplication. Although many allopolyploids arose from closely related species (congeners), there are also allopolyploid species that were formed from more distantly related progenitor species belonging to different genera or even different tribes. Here we have examined the possibility that allopolyploidization can also occur by asexual mechanisms. We show that upon grafting[mdash]a mechanism of plant-plant interaction that is widespread in nature[mdash]entire nuclear genomes can be transferred between plant cells. We provide direct evidence for this process resulting in speciation by creating a new allopolyploid plant species from a herbaceous species and a woody species in the nightshade family. The new species is fertile and produces fertile progeny. Our data highlight natural grafting as a potential asexual mechanism of speciation and also provide a method for the generation of novel allopolyploid crop species.
Over the last 300 years, plant science research has provided important knowledge and technologies for advancing the sustainability of agriculture. In this Essay, I describe how basic research advances have been translated into crop improvement, explore some lessons learned, and discuss the potential for current and future contribution of plant genetic improvement technologies to continue to enhance food security and agricultural sustainability.
Multiple geranylgeranyl diphosphate synthases (GGPPS) for biosynthesis of geranylgeranyl diphosphate (GGPP) exist in plants. GGPP is produced in the isoprenoid pathway and is a central precursor for various primary and specialized plant metabolites. Therefore, its biosynthesis is an essential regulatory point in the isoprenoid pathway. We selected 119 GGPPSs from 48 species representing all major plant lineages, based on stringent homology criteria. After the diversification of land plants, the number of GGPPS paralogs per species increases. Already in the moss Physcomitrella patens, GGPPS appears to be encoded by multiple paralogous genes. In gymnosperms, neofunctionalization of GGPPS may have enabled optimized biosynthesis of primary and specialized metabolites. Notably, lineage-specific expansion of GGPPS occurred in land plants. As a representative species we focused here on Arabidopsis thaliana, which retained the highest number of GGPPS paralogs (twelve) among the 48 species we considered in this study. Our results show that the A. thaliana GGPPS gene family is an example of evolution involving neo- and subfunctionalization as well as pseudogenization. We propose subfunctionalization as one of the main mechanisms allowing the maintenance of multiple GGPPS paralogs in A. thaliana genome. Accordingly, the changes in the expression patterns of the GGPPS paralogs occurring after gene duplication led to developmental and/or condition specific functional evolution.
The moss Physcomitrella patens is an important model organism to study plant evolution, development, physiology and biotechnology. Here, we have generated microarray gene expression data covering the principal developmental stages, culture forms and some environmental/stress conditions. Example analyses of developmental stages and growth conditions as well as abiotic stress treatments demonstrate that i) growth stage is dominant over culture conditions, ii) liquid culture is not stressful for the plant, iii) low pH might aid protoplastation by reduced expression of cell wall structure genes, iv) largely the same gene pool mediates response to de- and rehydration, and v) AP2/EREBP and NAC transcription factors play important roles in stress response reactions. With regard to the AP2 gene family, phylogenetic analysis and comparison with Arabidopsis thaliana shows commonalities as well as uniquely expressed family members under drought, light perturbations and protoplastation. Gene expression profiles for P. patens are available for the scientific community via the easy-to-use tool at "http://https://www.genevestigator.com" "https://www.genevestigator.com". By providing large scale expression profiles, the usability of this model organism is further enhanced, e.g. by enabling selection of control genes for quantitative Real Time PCR. Now, gene expression levels across a broad range of conditions can be accessed online for P. patens.
Plant growth and development are constantly influenced by temperature fluctuations. To respond to temperature changes, different levels of gene regulation are modulated in the cell. Alternative splicing (AS) is a widespread mechanism increasing transcriptome complexity and proteome diversity. Although genome-wide studies have revealed complex AS patterns in plants, whether AS impacts the stress defense of plants is not known. We used heat shock (HS) treatments at nondamaging temperature and messenger RNA sequencing to obtain HS transcriptomes in the moss Physcomitrella patens. Data analysis identified a significant number of novel AS events in the moss protonema. Nearly 50% of genes are alternatively spliced. Intron retention (IR) is markedly repressed under elevated temperature but alternative donor/acceptor site and exon skipping are mainly induced, indicating differential regulation of AS in response to heat stress. Transcripts undergoing heat-sensitive IR are mostly involved in specific functions, which suggests that plants regulate AS with transcript specificity under elevated temperature. An exonic GAG-repeat motif in these IR regions may function as a regulatory cis-element in heat-mediated AS regulation. A conserved AS pattern for HS transcription factors in P. patens and Arabidopsis (Arabidopsis thaliana) reveals that heat regulation for AS evolved early during land colonization of green plants. Our results support that AS of specific genes, including key HS regulators, is fine-tuned under elevated temperature to modulate gene regulation and reorganize metabolic processes.
Activists destroyed experimental fields of rapeseed plants in France this week to protest growing of mutated crops, national oilseed researcher Cetiom said. (Anti-GMO activists destroy rapeseed trial crops in France.
Jean-Pierre Zryd's insight:
They probably would like to destroy all agriculture - it's just a step further
Asexual reproduction is the simplest form of reproduction, occurring in many plants and animals. Various members of the Kalanchoë genus reproduce asexually through the ectopic formation of plantlets directly from differentiated tissues in the leaf (Garcês et al., 2007). These ectopic plantlets can be formed constitutively in some species or induced in response to various environmental cues and stresses (Garcês and Sinha, 2009). Previously, we have shown that leaf plantlet formation among the constitutive Kalanchoë plantlet-forming species such as Kalanchoë daigremontiana occurs by coopting both organogenesis and embryogenesis programs into the leaves (Garcês et al., 2007). K. daigremontiana somatic embryos develop symmetrically along the leaf margins in serrations, following a developmental program that resembles zygotic embryogenesis. Mature plantlets detach from the mother leaf and grow into new plants. We previously showed that the embryogenic LEAFY CONTYLEDON1 (LEC1) ortholog KdLEC1 is expressed in both somatic and zygotic embryos of K. daigremontiana (Garcês et al., 2007). LEC1 is known as an embryonic key regulator that is required for normal embryo development during early morphogenesis and to initiate and/or maintain the maturation phase and inhibit precocious embryo germination late in embryogenesis
Jean-Pierre Zryd's insight:
Interesting parallel between somatic and zygotic embryogenesis
Secondary plant metabolites are potentially of great value for providing robust resistance in plants against insect pests. Such metabolites often comprise small lipophilic molecules (SLMs), and can be similar also in terms of activity to currently used insecticides, for example, the pyrethroids, neonicotinoids and butenolides, which provide more effective pest management than the resistance traits exploited by breeding. Crop plants mostly lack the SLMs that provide their wild ancestors with resistance to pests. However, resistance traits based on the biosynthesis of SLMs present promising new opportunities for crop resistance to pests. Advances in genetic engineering of secondary metabolite pathways that produce insecticidal compounds and, more recently, SLMs involved in plant colonisation and development, for example, insect pheromones, offer specific new approaches but which are more demanding than the genetic engineering approaches adopted so far. In addition, nature also offers various opportunities for exploiting induction or priming for resistance metabolite generation. Thus, use of non-constitutively expressed resistance traits delivered via the seed is a more sustainable approach than previously achieved, and could underpin development of perennial arable crops protected by sentinel plant technologies.
Herbicides with new modes of action (MOAs) are badly needed because of rapidly evolving resistance to commercial herbicides, for which a new MOA has not been introduced in more than 20 years. The biggest pest management challenge for organic agriculture is the lack of effective natural product herbicides. The structural diversity and evolved biological activity of natural phytotoxins offer opportunities for the development of both directly-used natural compounds and synthetic herbicides with new target sites based on the structure of natural phytotoxins. Natural phytotoxins are also a source of discovery of new herbicide target sites that can be the focus of traditional herbicide discovery efforts. The many examples of strong natural phytotoxins with MOAs other than those used by commercial herbicides indicate that there are herbicide molecular targets to be added to the current repertoire of commercial herbicide MOAs.