Next generation sequencing (NGS) technologies are being used to generate whole genome sequences for a wide range of crop species. When combined with precise phenotyping methods, these technologies ...provide a powerful and rapid tool for identifying the genetic basis of agriculturally important traits and for predicting the breeding value of individuals in a plant breeding population. Here we summarize current trends and future prospects for utilizing NGS-based technologies to develop crops with improved trait performance and increase the efficiency of modern plant breeding. It is our hope that the application of NGS technologies to plant breeding will help us to meet the challenge of feeding a growing world population.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
•Summarized the current status of genomic-assisted breeding in three legumes.•Highlighted the progress in development of genomics resources in three legumes.•Presented future prospects of ...translational genomics for crop improvement.
Legume crops such as chickpea, pigeonpea and groundnut, mostly grown in marginal environments, are the major source of nutrition and protein to the human population in Asia and Sub-Saharan Africa. These crops, however, have a low productivity, mainly due to their exposure to several biotic and abiotic stresses in the marginal environments. Until 2005, these crops had limited genomics resources and molecular breeding was very challenging. During the last decade (2005–2015), ICRISAT led demand-driven innovations in genome science and translated the massive genome information in breeding. For instance, large-scale genomic resources including draft genome assemblies, comprehensive genetic and physical maps, thousands of SSR markers, millions of SNPs, several high-throughput as well as low cost marker genotyping platforms have been developed in these crops. After mapping several breeding related traits, several success stories of translational genomics have become available in these legumes. These include development of superior lines with enhanced drought tolerance in chickpea, enhanced and pyramided resistance to Fusarium wilt and Ascochyta blight in chickpea, enhanced resistance to leaf rust in groundnut, improved oil quality in groundnut and utilization of markers for assessing purity of hybrids/parental lines in pigeonpea. Some of these stories together with future prospects have been discussed.
A ureido-pyrimidinone (UPy)-functionalized poly(acrylic acid) grafted with poly(ethylene glycol)(PEG), designated PAU-g-PEG, was developed as a high performance polymer binder for Si anodes in ...lithium-ion batteries. By introducing both a ureido-pyrimidinone (UPy) unit, which is capable of self-healing through dynamic hydrogen bonding within molecules as well as with Si, and an ion-conducting PEG onto the side chain of the poly(acrylic acid), this water-based self-healable and conductive polymer binder can effectively accommodate the volume changes of Si, while maintaining electronic integrity, in an electrode during repeated charge/discharge cycles. The Si@PAU-g-PEG electrode retained a high capacity of 1,450.2 mAh g
and a Coulombic efficiency of 99.4% even after 350 cycles under a C-rate of 0.5 C. Under a high C-rate of 3 C, an outstanding capacity of 2,500 mAh g
was also achieved, thus demonstrating its potential for improving the electrochemical performance of Si anodes.
Abstract
Precision medicine is rapidly emerging as a strategy to tailor medical treatment to a small group or even individual patients based on their genetics, environment and lifestyle. Precision ...medicine relies heavily on developments in systems biology and omics disciplines, including metabolomics. Combination of metabolomics with sophisticated bioinformatics analysis and mathematical modeling has an extreme power to provide a metabolic snapshot of the patient over the course of disease and treatment or classifying patients into subpopulations and subgroups requiring individual medical treatment. Although a powerful approach, metabolomics have certain limitations in technology and bioinformatics. We will review various aspects of metabolomics technology and bioinformatics, from data generation, bioinformatics analysis, data fusion and mathematical modeling to data management, in the context of precision medicine.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
•P. nitroreducens AR-3 isolated from contaminated soil degrades 97% of chlorpyrifos.•Chlorpyrifos degradation achieved in 8 h, fastest reported among Pseudomonads.•An inducible organophosphate ...hydrolase is implicated for chlorpyrifos degradation.•The organophosphate hydrolase could also effectively remove methyl parathion.
The indiscriminate use of pesticides leads to serious food safety and toxicity issues and threatens the environment and biodiversity. Pseudomonas nitroreducens AR-3 isolated from pesticide contaminated agricultural soil removed 97% of chlorpyrifos (CP) in just 8 h, in a mineral salt medium (MSM) containing glucose (1.0 g/L) and yeast extract (0.5 g/L) at 30 °C and 2% (v/v) inoculum when challenged with 100 mg/L CP. 3, 5, 6-trichloro 2-pyridinol (TCP), the degradation product of CP was detected only in low levels, indicating its further degradation. Organophosphate hydrolase (OPH), the enzyme considered responsible for CP degradation, had an intracellular localization. Crude OPH (1 mg/ml) removed 42% of 100 mg/L chlorpyrifos in just 2 h, indicating a rapid rate of degradation. Ultra-fast degradation of chlorpyrifos with an inducible OPH marks the potential of P. nitroreducens AR-3 for bioremediation of organophosphates. The strain AR-3 has the fastest rate of organophosphate degradation reported till date among Pseudomonads.
•Simple and inexpensive wavelength/intensity modulation based SPR setup was developed.•SPR sensor chip using mixed alkanethiol SAM and monoclonal antibodies were developed.•Cardiac marker proteins ...CTnI and CTnT were detected in PBS buffer.
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A wavelength modulation based surface plasmon resonance (SPR) sensor setup was developed with inexpensive components. The developed setup is utilized for the detection of cardiac marker proteins, cardiac troponin I (CTnI), and cardiac troponin T (CTnT). A simple approach was used for the fabrication of CTnI/CTnT antibody sensor chip. A self-assembled monolayer (SAM) of 1-octanethiol and 11-mercaptoundecanoic acid (11-MUA) was formed on annealed Au thin film. The −COOH group of 11-MUA was modified with EDC-NHS for amine coupling to monoclonal antibodies of CTnI and CTnT. The developed SPR setup and the sensor chip with monoclonal antibodies showed good performance for the detection of CTnI and CTnT in direct assay. For CTnI, the lowest concentration detected was 0.03125 ng/mL whereas for CTnT, it was 0.0625 μg/mL. The detected concentrations are well below the onset concentration of these two proteins in blood following the acute myocardial infarction (AMI). The performance of this direct assay based on the developed setup and sensor chip therefore can be used easily for detection of CTnI and CTnT during their onset period.
Extreme environmental conditions, such as heat, salinity, and decreased water availability, can have a devastating impact on plant growth and productivity, potentially resulting in the collapse of ...entire ecosystems. Stress-induced systemic signaling and systemic acquired acclimation play canonical roles in plant survival during episodes of environmental stress. Recent studies revealed that in response to a single abiotic stress, applied to a single leaf, plants mount a comprehensive stress-specific systemic response that includes the accumulation of many different stress-specific transcripts and metabolites, as well as a coordinated stress-specific whole-plant stomatal response. However, in nature plants are routinely subjected to a combination of two or more different abiotic stresses, each potentially triggering its own stress-specific systemic response, highlighting a new fundamental question in plant biology: are plants capable of integrating two different systemic signals simultaneously generated during conditions of stress combination? Here we show that plants can integrate two different systemic signals simultaneously generated during stress combination, and that the manner in which plants sense the different stresses that trigger these signals (i.e., at the same or different parts of the plant) makes a significant difference in how fast and efficient they induce systemic reactive oxygen species (ROS) signals; transcriptomic, hormonal, and stomatal responses; as well as plant acclimation. Our results shed light on how plants acclimate to their environment and survive a combination of different abiotic stresses. In addition, they highlight a key role for systemic ROS signals in coordinating the response of different leaves to stress.
Summary
Climate change‐driven extreme weather events, combined with increasing temperatures, harsh soil conditions, low water availability and quality, and the introduction of many man‐made ...pollutants, pose a unique challenge to plants. Although our knowledge of the response of plants to each of these individual conditions is vast, we know very little about how a combination of many of these factors, occurring simultaneously, that is multifactorial stress combination, impacts plants.
Seedlings of wild‐type and different mutants of Arabidopsis thaliana plants were subjected to a multifactorial stress combination of six different stresses, each applied at a low level, and their survival, physiological and molecular responses determined.
Our findings reveal that, while each of the different stresses, applied individually, had a negligible effect on plant growth and survival, the accumulated impact of multifactorial stress combination on plants was detrimental. We further show that the response of plants to multifactorial stress combination is unique and that specific pathways and processes play a critical role in the acclimation of plants to multifactorial stress combination.
Taken together our findings reveal that further polluting our environment could result in higher complexities of multifactorial stress combinations that in turn could drive a critical decline in plant growth and survival.
Over the past decade, genomics-assisted breeding (GAB) has been instrumental in harnessing the potential of modern genome resources and characterizing and exploiting allelic variation for germplasm ...enhancement and cultivar development. Sustaining GAB in the future (GAB 2.0) will rely upon a suite of new approaches that fast-track targeted manipulation of allelic variation for creating novel diversity and facilitate their rapid and efficient incorporation in crop improvement programs. Genomic breeding strategies that optimize crop genomes with accumulation of beneficial alleles and purging of deleterious alleles will be indispensable for designing future crops. In coming decades, GAB 2.0 is expected to play a crucial role in breeding more climate-smart crop cultivars with higher nutritional value in a cost-effective and timely manner.
Availability of reference genomes and genome-wide surveys on comprehensive diversity panels pave the way to associate the allelic variation with phenotypes.Methods are now available to evaluate the genetic worth of the vast genetic resources archived in gene banks and streamline application of these resources in crop improvement programs.Precise genome editing technologies in concert with enhanced trait architectures enable innovative solutions to engineer complex trait variation.High-throughput phenotyping methods are beginning to alleviate the challenge of accurate, precise, and large-scale measurements of plant performance.Optimized speed breeding protocols remain crucial to accelerating breeding advance when applied with genomic breeding approaches.Sustaining gains from genomic breeding seeks fast-tracking exploitation of the minor effect alleles, accumulation of favorable alleles, and purging of deleterious alleles.
Abiotic stresses such as drought, heat or salinity are a major cause of yield loss worldwide. Recent studies revealed that the acclimation of plants to a combination of different environmental ...stresses is unique and cannot be directly deduced from studying the response of plants to each of the different stresses applied individually. Here we report on the response of Arabidopsis thaliana to a combination of salt and heat stress using transcriptome analysis, physiological measurements and mutants deficient in abscisic acid, salicylic acid, jasmonic acid or ethylene signaling. Arabidopsis plants were found to be more susceptible to a combination of salt and heat stress compared to each of the different stresses applied individually. The stress combination resulted in a higher ratio of Na+/K+ in leaves and caused the enhanced expression of 699 transcripts unique to the stress combination. Interestingly, many of the transcripts that specifically accumulated in plants in response to the salt and heat stress combination were associated with the plant hormone abscisic acid. In accordance with this finding, mutants deficient in abscisic acid metabolism and signaling were found to be more susceptible to a combination of salt and heat stress than wild type plants. Our study highlights the important role abscisic acid plays in the acclimation of plants to a combination of two different abiotic stresses.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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