Its scientists have much to offer the world, but are being held back by scattered administration and changing policies, argues Pablo Astudillo Besnier.
Andres Zurita's insight:
Yet, despite the glossy images of the telescopes promising a high-tech future, in 2012, Chile spent just 0.35% of its gross domestic product on research and development (R&D) — the least of all countries in the Organisation for Economic Co-operation and Development. Two-thirds of the academic publications come from just five universities. And, perhaps most importantly, a heavy focus on applied science threatens to stifle basic research and its potential to innovate.
This year celebrates the 100th anniversary of the birth of Norman Borlaug, the Nobel Prize-winning plant geneticist who, through his contribution to the “green revolution,” reminds us of the importance of applying scientific knowledge to develop crop varieties. This is even more important today as we face a rapidly expanding global population, climate change, and the need to keep agricultural efforts sustainable while minimizing environmental impacts. Accessing the fundamental information of crop genomes aids in accelerating breeding pipelines and improves our understanding of the molecular basis of agronomically important traits, such as yield and tolerance to abiotic and biotic stresses.
Cellular signals evoke rapid and broad changes in gene regulatory networks. To uncover these network dynamics, we developed an approach able to monitor primary targets of a transcription factor (TF) based solely on gene regulation, in the absence of detectable binding. This enabled us to follow the transient propagation of a nitrogen (N) nutrient signal as a direct impact of the master TF Basic Leucine Zipper 1 (bZIP1). Unexpectedly, the largest class of primary targets that exhibit transient associations with bZIP1 is uniquely relevant to the rapid and dynamic propagation of the N signal. Our ability to uncover this transient network architecture has revealed the “dark matter” of dynamic N nutrient signaling in plants that has previously eluded detection.
Genome sequences of nine species of citrus, including oranges, pummelos and mandarins, reveal pathways of domestication and provide resources for breeding.
Andres Zurita's insight:
Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes—a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes—and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin speciesCitrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement.
Horticulture Research, Published online: 11 June 2014; | doi:10.1038/hortres.2014.27
Andres Zurita's insight:
Plant regeneration from grapevine (Vitis spp.) via somatic embryogenesis typically is poor. Recovery of plants from Vitis rotundifolia Michx. (muscadine grape) is particularly problematic due to extremely low efficiency, including extended culture durations required for embryo–plant conversion. Poor plant recovery is an obstacle to the selection of improved genetically modified lines. Somatic embryos (SEs) of V. rotundifolia cultivar Delicious (Del-HS) and Vitis vinifera L cultivar Thompson Seedless (TS) were used to identify culture media and conditions that promoted embryo differentiation and plant conversion; this resulted in a two-step culture system. In comparative culture experiments, C2D medium containing 6% sucrose was the most effective, among four distinct formulae tested, for inducing precocious SE germination and cell differentiation. This medium, further supplemented with 4 µM 6-benzylaminopurine (C2D4B), was subsequently determined to enhance post-germinative growth of SE. MS medium supplemented with 0.5 µM 1-naphthaleneacetic acid (MSN) was then utilized to stimulate root and shoot growth of germinated SE. An average of 35% and 80% ‘Del-HS’ and ‘TS’ SE, respectively, developed into plants. All plants developed robust root and shoot systems and exhibited excellent survival following transfer to soil. Over 150 plants of ‘Del-HS’ were regenerated and established within 2.5 months, which is a dramatic reduction from the 6- to 12-month time period previously required. Similarly, 88 ‘TS’ plant lines were obtained within the same time period. Subsequently, seven out of eight Vitis cultivars exhibited significantly increased plant conversion percentages, demonstrating broad application of the two-step culture system to produce the large numbers of independent plant lines needed for selection of desired traits.
Plants master the art of coping with environmental challenges in two ways: on the one hand, through their extensive defense systems, and on the other, by their developmental plasticity. The plant hormone auxin plays an important role in a plant's adaptations to its surroundings, as it specifies organ orientation and positioning by regulating cell growth and division in response to internal and external signals. Important in auxin action is the family of PIN-FORMED (PIN) auxin transport proteins that generate auxin maxima and minima by driving polar cell-to-cell transport of auxin through their asymmetric subcellular distribution. Here, we review how regulatory proteins, the cytoskeleton, and membrane trafficking affect PIN expression and localization. Transcriptional regulation of PIN genes alters protein abundance, provides tissue-specific expression, and enables feedback based on auxin concentrations and crosstalk with other hormones. Post-transcriptional modification, for example by PIN phosphorylation or ubiquitination, provides regulation through protein trafficking and degradation, changing the direction and quantity of the auxin flow. Several plant hormones affect PIN abundance, resulting in another means of crosstalk between auxin and these hormones. In conclusion, PIN proteins are instrumental in directing plant developmental responses to environmental and endogenous signals.
The term stress can be broadly construed, with some forms constituting an essential part of developmental processes and others representing potentially harmful changes in the environment. How an organism deals with stress is also varied and can develop on various times scales, from milliseconds, as in rapid homeostatic responses, to evolutionary time, as in the adaptation of an organism to a new environment.
Roots and shoots communicate with each other to synchronize and optimize plant growth and respond to environmental changes. Shoots and roots exchange signals to sense the status and respond to the needs of the other organ. Cytokinins, which are phytohormones that regulate various aspects of growth and development, are recognized as the most important signal transmitted from roots to shoots. Whereas the enzymes underlying cytokinin biosynthesis and the corresponding receptors have been identified, our knowledge of cytokinin transport is limited. In this study, we identified the Arabidopsis ATP-binding cassette transporter subfamily G14 as a major component in the transfer of cytokinins from roots to shoots and hence as a regulator of shoot development. This finding represents a major breakthrough in the field.
Polyamine (PA) transport as well as PA biosynthesis, degradation and conjugation plays a vital role in the regulation of intracellular PA levels, which are essential for cell growth. Generally, PA uptake activity is elevated in rapidly proliferating cells. Previous studies showed that PA uptake in plant cells occurred via energy-dependent, protein-mediated transport systems. Numerous lines of evidence suggest that paraquat (PQ), one of the most widely used herbicides, is transported by the PA transport system in diverse organisms including plants. The PA/PQ transport interactions are proposed to be due to specific structural similarities between PA and PQ. The understanding of PA transport mechanisms has progressed in parallel with that of PQ transport, but the molecular identity of the plant PA/PQ transporter has remained an enigma. Recently, independent studies identified the L-type amino acid transporter (LAT) family transmembrane proteins as transporters of both PA and PQ. Arabidopsis LAT family proteins showed different subcellular localization properties, which suggested that these transporters were involved in intracellular PA trafficking and PA uptake across the plasma membrane. The identification of plant PA transporters is an important step in understanding the mechanism of PA homeostasis in plant cells. In this review, we highlight recent advances in the study of PA transport systems that are linked to the understanding of PQ translocation.
Stomata are an attractive experimental system in plant biology, because the responses of guard cells to environmental signals can be directly linked to changes in the aperture of stomatal pores. In this review, the mechanics of stomatal movement are discussed in relation to ion transport in guard cells. Emphasis is placed on the ion pumps, transporters, and channels in the plasma membrane, as well as in the vacuolar membrane. The biophysical properties of transport proteins for H+, K+, Ca2+, and anions are discussed and related to their function in guard cells during stomatal movements. Guard cell signaling pathways for ABA, CO2, ozone, microbe-associated molecular patterns (MAMPs) and blue light are presented. Special attention is given to the regulation of the slow anion channel (SLAC) and SLAC homolog (SLAH)-type anion channels by the ABA signalosome. Over the last decade, several knowledge gaps in the regulation of ion transport in guard cells have been closed. The current state of knowledge is an excellent starting point for tackling important open questions concerning stress tolerance in plants.
The stress phytohormone, abscisic acid (ABA), plays important roles in facilitating plants to survive and grow well under a wide range of stress conditions. Previous gene expression studies mainly focused on plant responses to short-term ABA treatment, but the effect of sustained ABA treatment and their difference are poorly studied. Here, we treated plants with ABA for 1 h or 9 d, and our genome-wide analysis indicated the differentially regulated genes under the two conditions were tremendously different. We analyzed other hormones’ signaling changes by using their whole sets of known responsive genes as reporters and integrating feedback regulation of their biosynthesis. We found that, under short-term ABA treatment, signaling outputs of growth-promoting hormones, brassinosteroids and gibberellins, and a biotic stress-responsive hormone, jasmonic acid, were significantly inhibited, while auxin and ethylene signaling outputs were promoted. However, sustained ABA treatment repressed cytokinin and gibberellin signaling, but stimulated auxin signaling. Using several sets of hormone-related mutants, we found candidates in corresponding hormonal signaling pathways, including receptors or transcription regulators, are essential in responding to ABA. Our findings indicate interactions of ABA-dependent stress signals with hormones at different levels are involved in plants to survive under transient stress and to adapt to continuing stressful environments.
Plant growth and productivity are adversely affected by various abiotic stressors and plants develop a wide range of adaptive mechanisms to cope with these adverse conditions, including adjustment of growth and development brought about by changes in stomatal activity. Membrane ion transport systems are involved in the maintenance of cellular homeostasis during exposure to stress and ion transport activity is regulated by phosphorylation/dephosphorylation networks that respond to stress conditions. The phytohormone abscisic acid (ABA), which is produced rapidly in response to drought and salinity stress, plays a critical role in the regulation of stress responses and induces a series of signaling cascades. ABA signaling involves an ABA receptor complex, consisting of an ABA receptor family, phosphatases and kinases: these proteins play a central role in regulating a variety of diverse responses to drought stress, including the activities of membrane-localized factors, such as ion transporters. In this review, recent research on signal transduction networks that regulate the function ofmembrane transport systems in response to stress, especially water deficit and high salinity, is summarized and discussed. The signal transduction networks covered in this review have central roles in mitigating the effect of stress by maintaining plant homeostasis through the control of membrane transport systems.
Global threats of ssDNA geminivirus and ss(-)RNA tospovirus on crops necessitate the development of transgenic resistance. Here, we constructed a two-T DNA vector carrying a hairpin of the intergenic region (IGR) of Ageratum yellow vein virus (AYVV), residing in an intron inserted in an untranslatable nucleocapsid protein (NP) fragment of Melon yellow spot virus (MYSV). Transgenic tobacco lines highly resistant to AYVV and MYSV were generated. Accumulation of 24-nt siRNA, higher methylation levels on the IGR promoters of the transgene, and suppression of IGR promoter activity of invading AYVV indicate that AYVV resistance is mediated by transcriptional gene silencing. Lack of NP transcript and accumulation of corresponding siRNAs indicate that MYSV resistance is mediated through post-transcriptional gene silencing. Marker-free progenies with concurrent resistance to both AYVV and MYSV, stably inherited as dominant nuclear traits, were obtained. Hence, we provide a novel way for concurrent control of noxious DNA and RNA viruses with less biosafety concerns.
Using a whole-genome-sequencing approach to explore germplasm resources can serve as an important strategy for crop improvement, especially in investigating wild accessions that may contain useful genetic resources that have been lost during the domestication process. Here we sequence and assemble a draft genome of wild soybean and construct a recombinant inbred population for genotyping-by-sequencing and phenotypic analyses to identify multiple QTLs relevant to traits of interest in agriculture. We use a combination of de novo sequencing data from this work and our previous germplasm re-sequencing data to identify a novel ion transporter gene, GmCHX1, and relate its sequence alterations to salt tolerance. Rapid gain-of-function tests show the protective effects of GmCHX1 towards salt stress. This combination of whole-genome de novo sequencing, high-density-marker QTL mapping by re-sequencing and functional analyses can serve as an effective strategy to unveil novel genomic information in wild soybean to facilitate crop improvement.
This study utilized Solanum lycopersicum (tomato) mutants with altered flavonoid biosynthesis to understand the impact of these metabolites on root development. The mutant anthocyanin reduced (are) has a mutation in the gene encoding flavonoid 3-hydroxylase (F3H), the first step in flavonol synthesis, and accumulates higher concentrations of the F3H substrate, naringenin, and lower levels of the downstream products, kaempferol, quercetin, myricetin, and anthocyanins, than wild-type. Complementation of are with the p35S:F3H transgene reduced naringenin and increased flavonols to wild-type levels. The initiation of lateral roots is reduced in are and p35S:F3H complementation restores wild-type root formation. The flavonoid mutant anthocyanin without (aw) has a defect in the gene encoding dihydroflavonol reductase, resulting in elevated flavonols and the absence of anthocyanins and displays increased lateral root formation. These results are consistent with a positive role of flavonols in lateral root formation. The are mutant has increased IAA transport and greater sensitivity to the inhibitory effect of the auxin transport inhibitor naphthylphthalamic acid on lateral root formation. Expression of the auxin-induced reporter (DR5-GUS) is reduced in initiating lateral roots and increased in primary root tips of are. Levels of reactive oxygen species are elevated in are root epidermal tissues and root hairs, and are forms more root hairs, consistent with a role of flavonols as antioxidants that modulate root hair formation. Together these experiments identify positive roles of flavonols in formation of lateral roots and negative roles in formation of root hairs through modulation of auxin transport and ROS, respectively.
Allocation of limiting resources, such as nutrients, is an important adaptation strategy for plants. Plants may allocate different nutrients within a specific organ or the same nutrient among different organs. In this study, we investigated the allocation strategies of nitrogen (N) and phosphorus (P) in leaves, stems and roots of 126 shrub species from 172 shrubland communities in Northern China using scaling analyses. Results showed that N and P have different scaling relationships among plant organs. The scaling relationships of N concentration across different plant organs tended to be allometric between leaves and non-leaf organs, and isometric between non-leaf organs. Whilst the scaling relationships of P concentration tended to be allometric between roots and non-root organs, and isometric between non-root organs. In arid environments, plant tend to have higher nutrient concentration in leaves at given root or stem nutrient concentration. Evolutionary history affected the scaling relationships of N concentration slightly, but not affected those of P concentration. Despite fairly consistent nutrients allocation strategies existed in independently evolving lineages, evolutionary history and environments still led to variations on these strategies.
PLOS Biology is an open-access, peer-reviewed journal that features works of exceptional significance in all areas of biological science, from molecules to ecosystems, including works at the interface with other disciplines.
Andres Zurita's insight:
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.
The Journal Environmental and Experimental Botany (EEB)
Andres Zurita's insight:
The Journal Environmental and Experimental Botany (EEB) aims to develop knowledge about the mechanisms of the adaptation of plants to environmental factors.
In addition to research papers, EEB invites the best authors to write reviews on the main priorities of the Journal.
We have compiled here some of the best reviews published in EEB these recent years.
In this Virtual Special Issue, are presented eighteen papers related to several main scientific areas such as temperature (high or low) (six reviews), salinity and water deficit (four reviews) and heavy metal stresses (five reviews). The three other reviews are devoted to the mechanisms involved in the responses of plants to environment including hormonal pathways.
We hope that this virtual special issue will encourage discussion among experts in these fields and will attract novel and exciting papers in the future issues of The Journal Environmental and Experimental Botany.
The debate over genetically modified (GM) crops has raged in Europe since 1996, but had barely risen above a whisper in the USA until recent labeling debates raised public attention. This article will explain GM crops and traits discuss safety assessment provide a view on safety from authoritative organizations discuss selected issues of current debate, and provide the author’s perspective as to why the public debate has drifted so far from scientific reality.
The economic and environmental benefits of GM crops are beyond scope, but references are provided. GM food and feed undergo comprehensive assessments using recognized approaches to assure they are as safe as the conventional congener. Issues of food safety and nutrition, unrelated to the GM process, may arise when GM foods display novel components or composition. Unanticipated genetic effects in GM crops appear to be limited in contrast to existing variations among conventional varieties resulting from breeding, mutation, and natural mobile genetic elements.
Allergenic potential is assessed when selecting genes for introduction into GM crops and remains a theoretical risk to date. Emerging weed and insect resistance is not unique to GM technology and will require the use of integrated pest management/best practices for pest control. Gene flow from GM crops to wild relatives is limited by existing biological barriers but can at time be a relevant consideration in gene selection and planting practices.Insect-resistant GM crops have significantly reduced use of chemical insecticides and appear to have reduced the incidence of pesticide poisoning in areas where small scale farming and hand application are common. Changes in herbicide patterns are more complex and are evolving over time in response to weed resistance management needs.
Recent public debate is driven by a combination of unfounded allegations about the technology and purveyors, pseudoscience, and attempts to apply a strict precautionary principle... Authoritative organizations such as the FDA, World Health Organization, AAAS, the Royal Society of Medicine, and the National Academy of Science have affirmed the safety of GM crops. So, how did the public conversation on GM crops become so negative? Opponents of GM have used three approaches to drive negative public opinion. The first approach has been to create negative impressions about the developers and purveyors of this technology... A second approach is to question the science underlying GM safety, often via misinterpretation of data obtained in inappropriate test systems...
A third approach is to invoke the “precautionary principle.” As originally proposed, the principle stated that risk assessors and policy makers should take account of uncertainties... to provide adequate margins of safety. The absolute version employed by some suggests that in the presence of any uncertainty, we should not move forward. This is of course a “black hole”—one can never prove a negative and hence one can never move forward when employing the absolute precautionary principle. The latter ignores both the risks of existing technology and the benefits of innovation and leaves decision making in the hands of anyone who chooses to raise doubts. GM crops have a more than 20-year track record of being grown and used commercially without a single human illness known to be caused by GM food or feed. Moreover, billions of animals have been fed predominantly GM diets for consecutive generations with no evidence that animal health and productivity were affected. The safety assessment paradigm for GM crops is robust and well established, and the approach has been confirmed by authoritative regulatory agencies and scientific organizations around the globe. These are, by far, the most thoroughly assessed foods and feeds in human history, and the National Academies of Science concluded that risk or unintended effects of GM technologies falls within the range of risks for conventional breeding technologies—which include forced inter-species crosses and radiation-induced mutagenesis. We can move forward with high confidence that GM food and feed are as safe and nutritious as their conventional congeners and perhaps look forward to rationalizing food safety assessment across conventional, GM, and other new breeding technologies to achieve a more focused and resource-efficient safety assessment process.
The gain-of-function mutant edt1 shows significantly enhanced drought tolerance and a well-developed root system including deeper primary roots and more lateral roots. To explore the molecular mechanisms underlying the improved root system of edt1, we performed transcriptome comparison between the wild-type and edt1 roots. One of the interesting findings from the analysis was that several gene families of cell-wall-loosening proteins were upregulated in the mutant roots, including expansins, extensins, xyloglucan endotransglucosylase/hydrolases (XTHs), pectin-related enzymes, and cellulases. Most of these genes contain HD-binding cis-elements in their promoters predominantly with the TTTAATTT sequence, which can be bound by HDG11 in vitro and in vivo. The coordinated expression of these gene families overlaps fast root elongation. Furthermore, overexpression of AtEXPA5, which was dramatically upregulated in edt1, resulted in longer primary roots because cells were more extended longitudinally. When combined by crossing theAtEXPA5-overexpression lines with one pectin methylesterase inhibitor family protein (PMEI) gene (At5g62360)- or one cellulase (CEL) gene (At2g32990)-overexpression lines, the primary roots of the progeny even exceeded both parents in length. Our results demonstrate that HDG11 directly upregulates cell-wall-loosening protein genes, which is correlated with altered root system architecture, and confirm that cell-wall-loosening proteins play important roles in coordinating cell-wall extensibility with root development. The results of transgene experiments showed that expansin works together with PMEI and CEL to generate synergistic effects on primary root elongation, suggesting that different cell-wall-loosening protein families may function in combination to generate optimal effects on root extensibility.
Here, we describe a method for the combined metabolomic, proteomic, transcriptomic and genomic analysis from one single sample as a major step for multilevel data integration strategies in systems biology. While extracting proteins and DNA, this protocol allows also separation of metabolites into polar and lipid fractions, as well as RNA fractionation into long and small RNAs allowing a broad range of transcriptional studies. The isolated biomolecules are suitable for analysis with different methods ranging from electrophoresis and blotting to state-of-the-art procedures based on mass spectrometry (accurate metabolite profiling, shotgun proteomics) or massive sequencing technologies (transcript analysis). The low amount of starting tissue, its cost-efficiency compared to the utilization of commercial kits, and its performance over a wide set of plant, microbial, and algal species such as Chlamydomonas, Arabidopsis, Populus, or Pinus, makes this method to a universal alternative for multiple molecular isolation from plant tissues.
While the greatest strength of systems biology may be to measure tens of thousands of variables across different genotypes, this simultaneously presents an enormous challenge to statistical analysis that cannot be completely solved with conventional approaches that identify and rank differences. Here we examine a diverse panel of conventional and transgenic, field-grown tomato fruits (Solanum lycopersicum L.) by liquid chromatography–mass spectrometry (LC-MS) metabolic fingerprinting. We used a progression of statistics to examine phenotypic variation observed. While clear trends were found by principal component analysis (PCA) related to genetic background and ripeness, it could not detect differences between transgenic genotypes and their nontransgenic parent variety. Partial least squares discriminant analysis (PLS-DA), a supervised method, identified 15 metabolic features of potential interest, but only five were significantly different between the transgenic lines and their nontransgenic parent. Weighted correlation network analysis (WGCNA) recognized relationships among these features and others, suggesting that a small suite of highly correlated compounds accumulated to significantly lower levels in the transgenic genotypes. We assert that metabolic fingerprinting with a series of statistical methods is an efficient and powerful approach to examine both large and small genetic effects on phenotypes of high value or interest.