Plants — Open Access Journal

Mitochondria and chloroplasts perform essential functions in respiration, ATP production, and photosynthesis, and both organelles contain genomes that encode only some of the proteins that are required for these functions. The proteins and mechanisms for organelle DNA replication are very similar to bacterial or phage systems. The minimal replisome may consist of DNA polymerase, a primase/helicase, and a single-stranded DNA binding protein (SSB), similar to that found in bacteriophage T7. In Arabidopsis, there are two genes for organellar DNA polymerases and multiple potential genes for SSB, but there is only one known primase/helicase protein to date. Genome copy number varies widely between type and age of plant tissues. Replication mechanisms are only poorly understood at present, and may involve multiple processes, including recombination-dependent replication (RDR) in plant mitochondria and perhaps also in chloroplasts. There are still important questions remaining as to how the genomes are maintained in new organelles, and how genome copy number is determined. This review summarizes our current understanding of these processes. Full article

Galactolipids, monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG), are the predominant lipid classes in the thylakoid membrane of chloroplasts. These lipids are also major constituents of internal membrane structures called prolamellar bodies (PLBs) and prothylakoids (PTs) in etioplasts, which develop in the cotyledon cells of dark-grown angiosperms. Analysis of Arabidopsis mutants defective in the major galactolipid biosynthesis pathway revealed that MGDG and DGDG are similarly and, in part, differently required for membrane-associated processes such as the organization of PLBs and PTs and the formation of pigment–protein complexes in etioplasts. After light exposure, PLBs and PTs in etioplasts are transformed into the thylakoid membrane, resulting in chloroplast biogenesis. During the etioplast-to-chloroplast differentiation, galactolipids facilitate thylakoid membrane biogenesis from PLBs and PTs and play crucial roles in chlorophyll biosynthesis and accumulation of light-harvesting proteins. These recent findings shed light on the roles of galactolipids as key facilitators of several membrane-associated processes during the development of the internal membrane systems in plant plastids. Full article

The effect of the exogenous hormone and light quality on breaking hypocotyl and epicotyl dormancy was studied. The results showed that the greatest percentage of hypocotyl dormancy breaking was observed with the Murashige and Skoog (MS) medium supplemented with or without 1.0 mg·L⁻¹ gibberellin 3 (GA₃), while ABA and endosperm greatly inhibited hypocotyl dormancy breaking. This suggests that hypocotyl dormancy of the Paeonia ostii ‘Fengdan’ embryo could be easily overcome by removing constraints of the surrounding endosperm, and ABA may be one of the constraint factors contained in the endosperm. The percentage of epicotyl dormancy breaking was also greatly affected by the concentration of 6-benzylaminopurine (BA) and GA₃. Compared to BA by itself, adding GA₃ to the medium containing BA highly enhanced epicotyl dormancy breaking, with the greatest percentage of epicotyl dormancy breaking in MS medium supplemented with both 0.5 mg·L⁻¹ BA and 0.5–1.0 mg·L⁻¹ GA₃. The percentage of hypocotyl and epicotyl dormancy breaking was also affected by light and its quality. Red light-emitting diodes (LEDs) had the same effect as a dark condition on the hypocotyl dormancy breaking, while blue LEDs and a combination of red and blue LEDs had a negative effect on the hypocotyl dormancy breaking. Unexpectedly, blue LEDs greatly enhanced, whereas red LEDs inhibited, epicotyl dormancy breaking. Conclusively, a two-stage culture method was recommended for breaking the hypocotyl and epicotyl dormancy: hypocotyl dormancy was broken first using the MS medium without any plant growth regulators in the dark (25 °C), and epicotyl dormancy was subsequently broken with the MS medium supplemented with both 1.0 mg·L⁻¹ GA₃ and 0.5 mg·L⁻¹ BA under blue light. Full article

The effects of nanoparticles (NPs) on plants are contrasting; these depend on the model plant, the synthesis of the nanoparticles (concentration, size, shape), and the forms of application (foliar, substrate, seeds). For this reason, the objective of this study was to report the impact of different concentrations of selenium (Se) and copper (Cu) NPs on yield, antioxidant capacity, and quality of tomato fruit. The different concentrations of Se and Cu NPs were applied to the substrate every 15 days (five applications). The yield was determined until day 102 after the transplant. Non-enzymatic and enzymatic antioxidant compounds were determined in the leaves and fruits as well as the fruit quality at harvest. The results indicate that tomato yield was increased by up to 21% with 10 mg L⁻¹ of Se NPs. In leaves, Se and Cu NPs increased the content of chlorophyll, vitamin C, glutathione, 2,2′-azino-bis(3-ethylbenzthiazolin-6-sulfonic acid (ABTS), superoxide dismutase (SOD), glutathione peroxidase (GPX) and phenylalanine ammonia liasa (PAL). In fruits, they increased vitamin C, glutathione, flavonoids, firmness, total soluble solids, and titratable acidity. The combination of Se and Cu NPs at optimal concentrations could be a good alternative to improve tomato yield and quality, but more studies are needed to elucidate their effects more clearly. Full article

Genomic approaches are opening avenues for understanding all aspects of biological life, especially as they begin to be applied to multiple individuals and populations. However, these approaches typically depend on the availability of a sequenced genome for the species of interest. While the number of genomes being sequenced is exploding, one group that has lagged behind are weeds. Although the power of genomic approaches for weed science has been recognized, what is needed to implement these approaches is unfamiliar to many weed scientists. In this review we attempt to address this problem by providing a primer on genome sequencing and provide examples of how genomics can help answer key questions in weed science such as: (1) Where do agricultural weeds come from; (2) what genes underlie herbicide resistance; and, more speculatively, (3) can we alter weed populations to make them easier to control? This review is intended as an introduction to orient weed scientists who are thinking about initiating genome sequencing projects to better understand weed populations, to highlight recent publications that illustrate the potential for these methods, and to provide direction to key tools and literature that will facilitate the development and execution of weed genomic projects. Full article

Zanthoxylum zanthoxyloides is a West African forest tree that is used for example against malaria and sickle cell anemia in Burkina Faso. The goal of this study was to analyze the genetic and morphological diversity of the species within wild populations in Burkina Faso, where it is potentially under threat due to the uncontrolled harvesting of its roots. Seventy-two trees from three different sites in Southwestern Burkina Faso were analyzed. Each tree was characterized by 12 traits specifying the period of flowering and maturity as well as morphological characteristics of the stem, leaves, and seeds. The molecular analysis was performed using two plastid DNA regions (psbA-trnH and trnL-trnF) and two nuclear regions (GBSSI and ITS) to identify the genetic diversity of the species for further development of a management plan for ex situ reproduction and in situ conservation. We found variability in morphological traits correlating with the geographic distance of the study sites. The molecular analysis, in contrast, revealed hardly any genetic variability among the tested trees and no population structure. Whether the differences in morphological traits are caused by different environmental conditions or by genetic variability in genes linked to morphological traits needs further testing. The apparent lack of genetic differentiation suggests that germplasm throughout the study region is suitable for planting in conservation actions. Efficient conservation management should involve local communities, especially those interested in traditional medicine. Full article

Strigolactone (SL) is a recently discovered class of phytohormone that inhibits shoot branching. The molecular mechanism underlying SL biosynthesis, perception, and signal transduction is vital to the plant branching phenotype. Some aspects of their biosynthesis, perception, and signaling include the role of four MORE AXILLARY GROWTH genes, MAX3, MAX4, MAX1, and MAX2. It is important to identify downstream genes that are involved in SL signaling. To achieve this, we studied the genomic aspects of the strigolactone biosynthesis pathway using microarray analysis of four max mutants. We identified SL signaling candidate genes that showed differential expression patterns in max mutants. More specifically, 1-AMINOCYCLOPROPANE-1-CARBOXYLATE SYNTHASE 4 (ACC4) and PROTEIN KINASE 3 (PKS3) displayed contrasting expression patterns, indicating a regulatory mechanism in SL signaling pathway to control different phenotypes apart from branching phenotype. Full article

Oryza meyeriana is a wild species of rice with high resistance to Xanthomonas oryzae pv. oryzae (Xoo), but the detailed resistance mechanism is unclear. Ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco) activase (RCA) is an important enzyme that regulates photosynthesis by activating Rubisco. We have previously reported that Xoo infection induced the relocation of RCA from the chloroplast stroma to the thylakoid membrane in O. meyeriana, but the underlying regulating mechanism and physiological significance of this association remains unknown. In this study, “H₂O₂ burst” with rapid and large increase in the amount of H₂O₂ was found to be induced by Xoo invasion in the leaves of O. meyeriana. 3, 3-diaminobenzidine (DAB) and oxidative 2, 7-Dichlorodi-hydrofluorescein diacetate (H₂DCFDA) staining experiments both showed that H₂O₂ was generated in the chloroplast of O. meyeriana, and that this H₂O₂ generation as well as Xoo resistance of the wild rice were dramatically dependent on light. H₂O₂, methyl viologen with light, and the xanthine-xanthine oxidase system all induced RCA to associate with the thylakoid membrane in vitro, which showed that H₂O₂ could induce the relocation of RCA. In vitro experiments also showed that H₂O₂ induced changes in both the RCA and thylakoid membrane that were required for them to associate and that this association only occurred in O. meyeriana and not in the susceptible cultivated rice. These results suggest that the association of RCA with the thylakoid membrane helps to protect the thylakoid membrane against oxidative damage from H₂O₂. Therefore, in addition to its universal function of activating Rubisco, RCA appears to play a novel role in the resistance of O. meyeriana to Xoo. Full article

Although orthodox medications are available for skin diseases, expensive dermatological services have necessitated the use of medicinal plants as a cheaper alternative. This study evaluated the pharmacological and phytochemical profiles of four medicinal plants (Drimia sanguinea, Elephantorrhiza elephantina, Helichrysum paronychioides, and Senecio longiflorus) used for treating skin diseases. Petroleum ether and 50% methanol extracts of the plants were screened for antimicrobial activity against six microbes: Bacillus cereus, Shigella flexneri, Candida glabrata, Candida krusei, Trichophyton rubrum and Trichophyton tonsurans using the micro-dilution technique. Antioxidant activity was conducted using 2,2-diphenyl-1-picryhydrazyl (DPPH) free radical scavenging and β-carotene linoleic acid models. Cytotoxicity was determined against African green monkey Vero kidney cells based on the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) colorimetric assay. Spectrophotometric and Gas Chromatography-Mass Spectrometry (GC-MS) methods were used to evaluate the phytochemical constituents. All the extracts demonstrated varying degrees of antimicrobial potencies. Shigella flexneri, Candida glabrata, Trichophyton rubrum and Trichophyton tonsurans were most susceptible at 0.10 mg/mL. In the DPPH test, EC₅₀ values ranged from approximately 6–93 µg/mL and 65%–85% antioxidant activity in the β-carotene linoleic acid antioxidant activity model. The phenolic and flavonoid contents ranged from 3.5–64 mg GAE/g and 1.25–28 mg CE/g DW, respectively. The LC₅₀ values of the cytotoxicity assay ranged from 0.015–5622 µg/mL. GC-MS analysis revealed a rich pool (94–198) of bioactive compounds including dotriacontane, benzothiazole, heptacosane, bumetrizole, phthalic acid, stigmasterol, hexanoic acid and eicosanoic acid, which were common to the four plants. The current findings provide some degree of scientific evidence supporting the use of these four plants in folk medicine. However, the plants with high cytotoxicity need to be used with caution. Full article

The chief aim of plant breeding is to improve varieties so as to increase their yield and breeding traits. One of the first stages of breeding is the selection of parental forms from the available gene pool of existing varieties. To date, costly and laborious methods based on multiple crossbreeding and phenotypic selection have been necessary to properly assess genetic resources in terms of productivity, quality parameters, and susceptibility to biotic and abiotic stressors. The often long and complicated breeding cycle can be significantly shortened through selection using DNA markers. To this end, use is made of close couplings between the marker and the locus responsible for the inheritance of the functional trait. The aim of this study was to identify single nucleotide polymorphism (SNP) and SilicoDArT markers associated with yield traits and to predict the heterosis effect for yield traits in maize (Zea mays L.). The plant material used in the research consisted of 19 inbred maize lines derived from different starting materials, and 13 hybrids resulting from crossing them. A two-year field experiment with inbred lines and hybrids was established at two Polish breeding stations on 10 m² plots in a randomized block design with three replicates. The biometric measurements included cob length, cob diameter, core length, core diameter, number of rows of grain, number of grains in a row, mass of grain from the cob, weight of one thousand grains, and yield. The isolated DNA was subjected to DArTseq genotyping. Association mapping was performed in this study using a method based on the mixed linear model with the population structure estimated by eigenanalysis (principal component analysis of all markers) and modeled by random effects. Narew, Popis, Kozak, M Glejt, and Grom were the hybrids used in the study that showed the highest significant heterosis effect in 2013 and 2014. The similarity between parental components determined on the basis of SNP and SilicoDArT marker analysis did not exceed 33%. It was found that the genetic similarity between parental components, determined on the basis of SNP and SilicoDArT markers, reflected their degree of relationship, and correlated significantly with the effect of heterosis. As the results indicate, the parental components for heterosis crosses can be selected based on genetic similarity between parental components evaluated using SNP and SilicoDArT markers, supported with information on the origin of parental forms. Of the markers we analyzed, 76 were selected as being significantly associated with at least six traits observed in 2013 and 2014 at both the Łagiewniki and Smolice stations. Full article

Iron deficiency chlorosis (IDC) is an abiotic stress often experienced by soybean, owing to the low solubility of iron in alkaline soils. Here, soybean lines with contrasting Fe efficiencies were analyzed to test the hypothesis that the Fe efficiency trait is linked to antioxidative stress signaling via proper management of tissue Fe accumulation and transport, which in turn influences the regulation of heme and non heme containing enzymes involved in Fe uptake and ROS scavenging. Inefficient plants displayed higher oxidative stress and lower ferric reductase activity, whereas root and leaf catalase activity were nine-fold and three-fold higher, respectively. Efficient plants do not activate their antioxidant system because there is no formation of ROS under iron deficiency; while inefficient plants are not able to deal with ROS produced under iron deficiency because ascorbate peroxidase and superoxide dismutase are not activated because of the lack of iron as a cofactor, and of heme as a constituent of those enzymes. Superoxide dismutase and peroxidase isoenzymatic regulation may play a determinant role: 10 superoxide dismutase isoenzymes were observed in both cultivars, but iron superoxide dismutase activity was only detected in efficient plants; 15 peroxidase isoenzymes were observed in the roots and trifoliate leaves of efficient and inefficient cultivars and peroxidase activity levels were only increased in roots of efficient plants. Full article

Excess salinity is a major environmental stress that limits growth and development of plants. Improving salt stress tolerance of plants is important in order to enhance land utilization and crop yield. Cold priming has been reported to trigger the protective processes in plants that increase their stress tolerance. Bermudagrass (Cynodon dactylon) is one of the most widely used turfgrass species around the world. However, the effect of cold priming on salt tolerance of bermudagrass is largely unknown. In the present study, wild bermudagrass was pre-treated with 4 °C for 6 h before 150 mM NaCl treatment for one week. The results showed that the cell membrane stability, ion homeostasis and photosynthesis process which are usually negatively affected by salt stress in bermudagrass were alleviated by short-term pre-cold treatment. Additionally, the gene expression profile also corresponded to the change of physiological indexes in bermudagrass. The results suggest that cold priming plays a positive role in improving salt stress tolerance of bermudagrass. Full article

Advancements in techniques to rapidly and non-destructively detect the impact of tropospheric ozone (O₃) on crops are required. This study demonstrates the capability of full-range (350–2500 nm) reflectance spectroscopy to characterize responses of asymptomatic sage leaves under an acute O₃ exposure (200 ppb for 5 h). Using partial least squares regression, spectral models were developed for the estimation of several traits related to photosynthesis, the oxidative pressure induced by O₃, and the antioxidant mechanisms adopted by plants to cope with the pollutant. Physiological traits were well predicted by spectroscopic models (average model goodness-of-fit for validation (R²): 0.65–0.90), whereas lower prediction performances were found for biochemical traits (R²: 0.42–0.71). Furthermore, even in the absence of visible symptoms, comparing the full-range spectral profiles, it was possible to distinguish with accuracy plants exposed to charcoal-filtered air from those exposed to O₃. An O₃ effect on sage spectra was detectable from 1 to 5 h from the beginning of the exposure, but ozonated plants quickly recovered after the fumigation. This O₃-tolerance was confirmed by trends of vegetation indices and leaf traits derived from spectra, further highlighting the capability of reflectance spectroscopy to early detect the responses of crops to O₃. Full article

In addition to its role in animals, nowadays nitric oxide (NO) is considered as an emerging signaling molecule in plant systems. It is now believed that NO exerts its pivotal role in various plant physiological processes, such as in seed germination, plant developmental stages, and plant defense mechanisms. In this study, we have taken an initiative to show the biochemical basis of defense response activation in bean leaves during the progression of Colletotrichum gloeosporioides (Penz.) Penz. and Sacc. in detached bean leaves. Stages of pathogen penetration and colonization were successfully established in the detached bean leaves. Results showed up-regulation of different defense-related enzymes and other defense molecules, such as phenols, flavonoids, callose, and lignin molecules, along with NO at early stages of pathogen invasion. Although in the later stages of the disease, development of NO and other defense components (excluding lignin) were down-regulated, the production of reactive oxygen species in the form of H₂O₂ became elevated. Consequently, other stress markers, such as lipid peroxidation, proline content, and chlorophyll content, were changed accordingly. Correlation between the disease index and other defense molecules, along with NO, indicate that production of NO and reactive oxygen species (ROS) might influence the development of anthracnose in common bean. Full article

Sugarcane is an important crop from Poaceae family, contributing about 80% of the total world’s sucrose with an annual value of around US$150 billion. In addition, sugarcane is utilized as a raw material for the production of bioethanol, which is an alternate source of renewable energy. Moving towards sugarcane omics, a remarkable success has been achieved in gene transfer from a wide variety of plant and non-plant sources to sugarcane, with the accessibility of efficient transformation systems, selectable marker genes, and genetic engineering gears. Genetic engineering techniques make possible to clone and characterize useful genes and also to improve commercially important traits in elite sugarcane clones that subsequently lead to the development of an ideal cultivar. Sugarcane is a complex polyploidy crop, and hence no single technique has been found to be the best for the confirmation of polygenic and phenotypic characteristics. To better understand the application of basic omics in sugarcane regarding agronomic characters and industrial quality traits as well as responses to diverse biotic and abiotic stresses, it is important to explore the physiology, genome structure, functional integrity, and collinearity of sugarcane with other more or less similar crops/plants. Genetic improvements in this crop are hampered by its complex genome, low fertility ratio, longer production cycle, and susceptibility to several biotic and abiotic stresses. Biotechnology interventions are expected to pave the way for addressing these obstacles and improving sugarcane crop. Thus, this review article highlights up to date information with respect to how advanced data of omics (genomics, transcriptomic, proteomics and metabolomics) can be employed to improve sugarcane crops. Full article

Hybrid proline-rich proteins (HyPRPs) belong to the family of 8-cysteine motif (8CM) containing proteins that play important roles in plant development processes, and tolerance to biotic and abiotic stresses. To gain insight into the rice HyPRPs, we performed a systematic genome-wide analysis and identified 45 OsHyPRP genes encoding 46 OsHyPRP proteins. The phylogenetic relationships of OsHyPRP proteins with monocots (maize, sorghum, and Brachypodium) and a dicot (Arabidopsis) showed clustering of the majority of OsHyPRPs along with those from other monocots, which suggests lineage-specific evolution of monocots HyPRPs. Based on our previous RNA-Seq study, we selected differentially expressed OsHyPRPs genes and used quantitative real-time-PCR (qRT-PCR) to measure their transcriptional responses to biotic (Magnaporthe oryzae) and abiotic (heat, cold, and salt) stresses and hormone treatment (Abscisic acid; ABA, Methyl-Jasmonate; MeJA, and Salicylic acid; SA) in rice blast susceptible Pusa Basmati-1 (PB1) and blast-resistant near-isogenic line PB1+Pi9. The induction of OsHyPRP16 expression in response to the majority of stresses and hormonal treatments was highly correlated with the number of cis-regulatory elements present in its promoter region. In silico docking analysis of OsHyPRP16 showed its interaction with sterols of fungal/protozoan origin. The characterization of the OsHyPRP gene family enables us to recognize the plausible role of OsHyPRP16 in stress tolerance. Full article

SQUAMOSA-promoter binding protein-like (SPL) proteins are plant-specific transcript factors that play essential roles in plant growth and development. Although many SPL genes have been well characterized in model plants like Arabidopsis, rice and tomato, the functions of SPLs in strawberry are still largely elusive. In the present study, we cloned and characterized FvSPL10, the ortholog of AtSPL9, from woodland strawberry. Subcellular localization shows FvSPL10 localizes in the cell nucleus. The luciferase system assay indicates FvSPL10 is a transcriptional activator, and both in vitro and in vivo assays indicate FvSPL10 could bind to the promoter of FvAP1 and activate its expression. Ectopic expression of FvSPL10 in Arabidopsis promotes early flowering and increases organs size. These results demonstrate the multiple regulatory roles of FvSPL10 in plant growth and development and lay a foundation for investigating the biological functions of FvSPL10 in strawberry. Full article

Herbicides represent about 60% of the pesticides (by volume) used worldwide. The success of herbicides can be attributed in part to a relatively steady discovery of one unique mechanisms of action (MOA) every two years from the early 1950s to the mid-1980s. While this situation changed dramatically after the introduction of glyphosate-resistant crops, evolution of resistance to glyphosate has renewed the agrichemical industry interest in new chemistry interacting with novel target sites. This review analyses recent characterization of new herbicide target sites, the chemical classes developed to inhibit these target sites, and where appropriate the innovative technologies used in these discovery programs. Full article

Heavy metal redistribution is relevant for the quality of edible crops and the suitability of hyperaccumulators for bioremediation. Root-to-shoot transfer via the xylem and redistribution in the aerial parts via the phloem differ between various heavy metals. In general, cadmium is more slowly released to the shoot than zinc (e.g., in wheat, bean, and lupin). However, rapid cadmium transport to the shoot was detected in the hyperaccumulator Solanum nigrum L. This is a key aspect in this article and might be important for bioremediation. The radionuclides ¹⁰⁹Cd and ⁶⁵Zn were used to investigate the respective influence of elevated cadmium or zinc in the root medium on the dynamics of the two heavy metals in S. nigrum. Although transport via the xylem to the leaves was similar for ¹⁰⁹Cd and ⁶⁵Zn, the further redistribution from older leaves to younger leaves, flowers, and fruits via the phloem was far less efficient for ¹⁰⁹Cd than for ⁶⁵Zn. Furthermore, the redistribution of ¹⁰⁹Cd within the shoot was negatively influenced by increased cadmium (but not by increased zinc) concentrations in the nutrient medium. The redistribution of ⁶⁵Zn in the shoot was selectively decreased by increased zinc concentrations (but generally not by cadmium). Full article