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Plants have developed several external and internal aluminium (Al) tolerance mechanisms. The external mechanism best characterised is the exudation of organic acids induced by Al. Rye ( Secale cereale L.), one of the most Al-tolerant cereal crops, secretes both citrate and malate from its roots in response to Al. However, the role of malate dehydrogenase ( MDH) genes in Al-induced stress has not been studied in rye. We have isolated the ScMDH1 and ScMDH2 genes, encoding two different mitochondrial MDH isozymes, in three Al-tolerant rye cultivars (Ailés, Imperial and Petkus) and one sensitive inbred rye line (Riodeva). These genes, which have seven exons and six introns, were located on the 1R ( ScMDH1) and 3RL ( ScMDH2) chromosomes. Exon 1 of ScMDH1 and exon 7 of ScMDH2 were the most variable among the different ryes. The hypothetical proteins encoded by these genes were classified as putative mitochondrial MDH isoforms. The phylogenetic relationships obtained using both c DNA and protein sequences indicated that the ScMDH1 and ScMDH2 proteins are orthologous to mitochondrial MDH1 and MDH2 proteins of different Poaceae species. The expression studies of the ScMDH1 and ScMDH2 genes indicate that it is more intense in roots than in leaves. Moreover, the amount of their corresponding m RNAs in roots from plants treated and not treated with Al was higher in the tolerant cultivar Petkus than in the sensitive inbred line Riodeva. In addition, ScMDH1 and ScMDH2 m RNA levels decreased in response to Al stress (repressive behaviour) in the roots of both the tolerant Petkus and the sensitive line Riodeva. [ABSTRACT FROM AUTHOR]

Soluble aluminum (Al) is a major constraint to plant growth in highly acidic soils, which comprise up to 50% of the world's arable land. The primary mechanism of Al resistance described in plants is the chelation of Al cations by release of organic acids into the rhizosphere. Candidate aluminum tolerance genes encoding organic acid transporter of the ALMT (aluminum-activated malate transporter) and MATE (multi-drug and toxic compound extrusion) families have been characterized in several plant species. In this study, we have isolated in five different cultivars the rye ScAACT1 gene, homolog to barley aluminum activated citrate transporter HvAACT1. This gene mapped to the 7RS chromosome arm, 25 cM away from the ScALMT1 aluminum tolerance gene. The gene consisted of 13 exons and 12 introns and encodes a predicted membrane protein that contains the MatE domain and at least seven putative transmembrane regions. Expression of the ScAACT1 gene is Al-induced, but there were differences in the levels of expression among the cultivars analyzed. A new quantitative trait locus for Al tolerance in rye that co-localizes with the ScAACT1 gene was detected in the 7RS chromosome arm. These results suggest that the ScAACT1 gene is a candidate gene for increased Al tolerance in rye. The phylogenetic relationships between different MATE proteins are discussed. [ABSTRACT FROM AUTHOR]

Wheat, a staple cereal crop, faces challenges due to climate change and increasing global population. Maintaining genetic diversity is vital for developing drought-tolerant cultivars. This study evaluated the genetic diversity and drought response of five wheat cultivars and their corresponding F1 hybrids under well-watered and drought stress conditions. Molecular profiling using ISSR and SCoT-PCR markers revealed 28 polymorphic loci out of 76 amplified. A statistically significant impact of parental genotypes and their crosses was observed on all investigated agro-morphological traits, including root length, root weight, shoot length, shoot weight, proline content, spikelet number/spike, spike length, grain number/spike, and grain weight/spike. The parental genotypes P1 and P3 had desirable positive and significant general combining ability (GCA) effects for shoot fresh weight, shoot dry weight, root fresh weight, root dry weight, shoot length, and root length under well-watered conditions, while P3 and P5 recorded the highest GCA estimates under drought stress. P3 and P4 showed the highest GCA effects for number of spikelets per spike, the number of grains per spike, and grain weight per spike under normal conditions. P5 presented the maximum GCA effects and proved to be the best combiner under drought stress conditions. The cross P1× P3 showed the highest positive specific combining ability (SCA) effects for shoot fresh weight under normal conditions, while P2×P3 excelled under water deficit conditions. P1× P2, P1 × P3, and P4× P5 were most effective for shoot dry weight under normal conditions, whereas P1×P3 and P3×P5 showed significant SCA effects under drought stress. Positive SCA effects for root fresh weight and shoot length were observed for P3×P5 under stressed conditions. Additionally, P4×P5 consistently recorded the highest SCA for root length in both environments, and P3×P5 excelled in the number of spikelets, grains per spike, and grain weight per spike under drought conditions. The evaluated genotypes were categorized based on their agronomic performance under drought stress into distinct groups ranging from drought-tolerant genotypes (group A) to drought-sensitive ones (group C). The genotypes P5, P2×P5, and P3×P5 were identified as promising genotypes to improve agronomic performance under water deficit conditions. The results demonstrated genetic variations for drought tolerance and highlighted the potential of ISSR and SCoT markers in wheat breeding programs for developing drought-tolerant cultivars., Competing Interests: Diaa Abd El-Moneim and Elsayed Mansour are Academic Editors for PeerJ., (©2024 Ezzat et al.)

Meiosis is a critical process in sexual reproduction, and errors during this cell division can significantly impact fertility. Successful meiosis relies on the coordinated action of numerous genes involved in DNA replication, strand breaks, and subsequent rejoining. DNA topoisomerase enzymes play a vital role by regulating DNA topology, alleviating tension during replication and transcription. To elucidate the specific function of DNA topoisomerase 1α ( A t T O P 1 α ) in male reproductive development of Arabidopsis thaliana , we investigated meiotic cell division in Arabidopsis flower buds. Combining cytological and biochemical techniques, we aimed to reveal the novel contribution of A t T O P 1 α to meiosis. Our results demonstrate that the absence of A t T O P 1 α leads to aberrant chromatin behavior during meiotic division. Specifically, the top1α1 mutant displayed altered heterochromatin distribution and clustered centromere signals at early meiotic stages. Additionally, this mutant exhibited disruptions in the distribution of 45s rDNA signals and a reduced frequency of chiasma formation during metaphase I, a crucial stage for genetic exchange. Furthermore, the atm-2×top1α1 double mutant displayed even more severe meiotic defects, including incomplete synapsis, DNA fragmentation, and the presence of polyads. These observations collectively suggest that A t T O P 1 α plays a critical role in ensuring accurate meiotic progression, promoting homologous chromosome crossover formation, and potentially functioning in a shared DNA repair pathway with ATAXIA TELANGIECTASIA MUTATED (ATM) in Arabidopsis microspore mother cells., Competing Interests: Diaa Abd El-Moneim is an Academic Editor for PeerJ., (© 2024 Elesawi et al.)

As rice has no physiological capacity of fixing nitrogen in the soil, its production had always been reliant on the external application of nitrogen (N) to ensure enhanced productivity. In the light of improving nitrogen use efficiency (NUE) in rice, several advanced agronomic strategies have been proposed. However, the soared increase of the prices of N fertilizers and subsequent environmental downfalls caused by the excessive use of N fertilizers, reinforces the prerequisite adaptation of other sustainable, affordable, and globally acceptable strategies. An appropriate alternative approach would be to develop rice cultivars with better NUE. Conventional breeding techniques, however, have had only sporadic success in improving NUE, and hence, this paper proposes a new schema that employs the wholesome benefits of the recent advancements in omics technologies. The suggested approach promotes multidisciplinary research, since such cooperation enables the synthesis of many viewpoints, approaches, and data that result in a comprehensive understanding of NUE in rice. Such collaboration also encourages innovation that leads to developing rice varieties that use nitrogen more effectively, facilitate smart technology transfer, and promotes the adoption of NUE practices by farmers and stakeholders to minimize ecological impact and contribute to a sustainable agricultural future., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Plant breeding, aimed at enhancing desired traits, depends on genetic diversity. Mutation breeding is a powerful method of rapidly expanding genetic diversity, facilitating crop improvement, and ensuring food security. In a recent study, researchers evaluated the genetic variability of Trigonella species using different doses of sodium azide (SA) (0.2%, 0.4%, 0.6%, 0.8%, and 1.0%) through morphological, physiological, and cytogenetic studies. Morphological variations were observed in cotyledonary leaves, vegetative leaves, and overall plant growth and habit. Several quantitative parameters, such as plant height, fertile branches per plant, pods per plant (or clusters), seeds per pod, and seed yield, increased when treated with 0.2% and 0.4% SA compared to the control. Furthermore, the total chlorophyll content and carotenoids increased in the sample treated with 0.2% SA over the control but decreased with higher concentrations. Scanning electron microscopy revealed that stomatal aperture and seed dimensions increased at lower concentrations of sodium azide treatment. The study found a positive correlation between the different parameters studied in the Trigonella species, as indicated by high r-values. Based on their findings, it was concluded that the genotype of fenugreek can be improved by using 0.2% and 0.4% concentrations of sodium azide. However, the evaluation of observed variants in successive generations is a critical and necessary process to validate their potential as keystones for crop genetic improvements., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Naaz, Choudhary, Hasan, Sharma, Alharbi and Abd El Moneim.)

Drought and salinity are the major abiotic stress factors negatively affecting the morphophysiological, biochemical, and anatomical characteristics of numerous plant species worldwide. The detrimental effects of these environmental factors can be seen in leaf and stem anatomical structures including the decrease in thickness of cell walls, palisade and spongy tissue, phloem and xylem tissue. Also, the disintegration of grana staking, and an increase in the size of mitochondria were observed under salinity and drought conditions. Drought and salt stresses can significantly decrease plant height, number of leaves and branches, leaf area, fresh and dry weight, or plant relative water content (RWC%) and concentration of photosynthetic pigments. On the other hand, stress-induced lipid peroxidation and malondialdehyde (MDA) production, electrolyte leakage (EL%), and production of reactive oxygen species (ROS) can increase under salinity and drought conditions. Antioxidant defense systems such as catalase, peroxidase, glutathione reductase, ascorbic acid, and gamma-aminobutyric acid are essential components under drought and salt stresses to protect the plant organelles from oxidative damage caused by ROS. The application of safe and eco-friendly treatments is a very important strategy to overcome the adverse effects of drought and salinity on the growth characteristics and yield of plants. It is shown that treatments with plant growth-promoting bacteria (PGPB) can improve morphoanatomical characteristics under salinity and drought stress. It is also shown that yeast extract, mannitol, proline, melatonin, silicon, chitosan, α -Tocopherols (vitamin E), and biochar alleviate the negative effects of drought and salinity stresses through the ROS scavenging resulting in the improvement of plant attributes and yield of the stressed plants. This review discusses the role of safety and eco-friendly treatments in alleviating the harmful effects of salinity and drought associated with the improvement of the anatomical, morphophysiological, and biochemical features in plants., Competing Interests: Diaa Abd El Moneim is an Academic Editor for PeerJ., (©2024 Alshammari et al.)

Aerobic rice cultivation represents an innovative approach to reduce water consumption and enhance water use efficiency compared to traditional transplanting methods. Simultaneously, cultivating drought-tolerant rice genotypes becomes crucial to ensure their sustainable production under abrupt climate fluctuations. Hence, this study aimed to explore the physiological, agronomic, and grain quality responses of ten diverse rice genotypes to various irrigation levels under aerobic cultivation conditions. A field experiment was performed for two summer seasons of 2019 and 2020 in an arid Mediterranean climate. The irrigation regimes were well watered (13,998 m 3 /ha), mild drought (10,446 m 3 /ha), moderate drought (7125 m 3 /ha), and severe drought (5657 m 3 /ha). The results revealed considerable variations among rice genotypes under tested irrigation regimes in all physiological, agronomic, and quality traits. According to drought response indices, rice genotypes were classified into three groups (A-C), varying from tolerant to sensitive genotypes. The identified drought-tolerant genotypes (Giza-179, Hybrid-1, Giza-178, and Line-9399) recorded higher yields and crop water productivity with reduced water usage compared to drought-sensitive genotypes. Thus, these genotypes are highly recommended for cultivation in water-scarce environments. Furthermore, their characteristics could be valuable in breeding programs to improve drought tolerance in rice, particularly under aerobic cultivation conditions. The PCA biplot, heatmap, and hierarchical clustering highlighted specific physiological parameters such as relative water content, chlorophyll content, proline content, peroxidase content, and catalase content exhibited robust associations with yield traits under water deficit conditions. These parameters offer valuable insights and could serve as rapid indicators for assessing drought tolerance in rice breeding programs in arid environments.

Plants possess various defense mechanisms to cope with genotoxic and environmental challenges, with high temperatures posing a significant threat due to global warming. In this investigation, ten-day-old Trigonella foenum-graecum (fenugreek) seedlings were cultivated in a controlled environment chamber with conditions set at 70-80% relative humidity, a day/night cycle of 25/18 °C, and a photosynthetically active radiation (PAR) of 1000 μmol m -2  s -1 . Other groups of seedlings were subjected to temperatures of 30, 35, or 40 °C. Our research aimed to investigate the relationship between temperature intensity, duration, growth responses, physiological and metabolic activities, and the stress alleviation by salicylic acid. The results demonstrated that high temperatures significantly reduced plant growth, membrane stability, while increasing proline and protein content, as well as electrolyte leakage in the leaves. The most pronounced results were observed when exposed to 40 °C for 24 h. Salicylic acid completely mitigated the negative impacts of high-temperature stress when it was applied at 40 °C for 24 h. We utilized two-dimensional electrophoresis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to examine proteins across three groups: control plants, stressed plants, and plants subjected to salicylic acid treatment. Our results revealed that, among the proteins influenced by high-temperature stress, 12 displayed the most significant differences in regulation. These stress-responsive proteins played roles in signal transduction, stress defense, detoxification, amino acid metabolism, protein metabolism (including translation, processing, and degradation), photosynthesis, carbohydrate metabolism, and energy pathways. These proteins may hold practical implications for diverse biological activities. In conclusion, salicylic acid treatment enhanced thermotolerance in fenugreek plants, although further investigation is required at the genome level to elucidate the mechanism of salicylic acid action under heat stress., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

Wheat is an important cereal crop constrained by several biotic and abiotic stresses including drought stress. Understating the effect of drought stress and the genetic basis of stress tolerance is important to develop drought resilient, high-yielding wheat cultivars. In this study, we investigated the effects of drought stress on seedling characteristics in an association panel consisting of 198 germplasm lines. Our findings revealed that drought stress had a detrimental effect on all the seedling characteristics under investigation with a maximum effect on shoot length (50.94% reduction) and the minimum effect on germination percentage (7.9% reduction). To gain a deeper understanding, we conducted a genome-wide association analysis using 12,511 single nucleotide polymorphisms (SNPs), which led to the identification of 39 marker-trait associations (MTAs). Of these 39 MTAs, 13 were particularly noteworthy as they accounted for >10% of the phenotypic variance with a LOD score >5. These high-confidence MTAs were further utilized to extract 216 candidate gene (CGs) models within 1 Mb regions. Gene annotation and functional characterization identified 83 CGs with functional relevance to drought stress. These genes encoded the WD40 repeat domain, Myb/SANT-like domain, WSD1-like domain, BTB/POZ domain, Protein kinase domain, Cytochrome P450, Leucine-rich repeat domain superfamily, BURP domain, Calmodulin-binding protein60, Ubiquitin-like domain, etc. Findings from this study hold significant promise for wheat breeders as they provide direct assistance in selecting lines harboring favorable alleles for improved drought stress tolerance. Additionally, the identified SNPs and CGs will enable marker-assisted selection of potential genomic regions associated with enhanced drought stress tolerance in wheat., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The reviewer KS declared a past collaboration with the authors SG and AS to the handling editor., (Copyright © 2024 Gudi, Halladakeri, Singh, Kumar, Singh, Alwutayd, Abd El-Moneim and Sharma.)

Background: Okra is a plant farmed for its pods, leaves, and stems all of which are edible. It is famous for its ability to tolerate long desiccation periods. It belongs to the Malvaceae family and is a sister species to hibiscus, cotton, and cacao plants., Methods: In the current study, okra plants were used as a model to sequence, assemble, and analyze the evolutionary and functional characteristics of the Dicer-like protein gene family (DCL) based on DNAseq and qPCR techniques., Results: Four Dicer-like (DCL) single-copy genes of the okra plant Abelmoschus esculentus (L.) Moench (AeDCL) were successfully assembled. The lengths of the AeDCL copies were 8,494, 5,214, 4,731, and 9,329 bp. The detected exons in these samples ranged from a single exon in AeDCL3 to 24 exons in AeDCL4 . AeDCLs had five functional domains of two DEAD-like helicase superfamilies, N and C; one Dicer domain; one ribonuclease III domain (a and b); and one double-stranded RNA-binding domain. The PAZ domain was completely annotated only for AeDCL1 and AeDCL3 . All AeDCLs were up-regulated under drought conditions, with leaves showing more extensive fold changes than roots. The study focused on a comprehensive genome-wide identification and analysis of the DCL gene family in naturally drought-tolerant okra plants, an orphan crop that can be used as a model for further genomic and transcriptomic studies on drought-tolerance mechanisms in plants., Competing Interests: Diaa Abd El-Moneim is an Academic Editor for PeerJ., (©2023 Elhefnawi et al.)

Mutation breeding is one of the effective techniques used for improving desired traits such as yield quality and quantity in economic crops. The present study aims to develop oil and protein contents in addition to high yield attributes in soybean using gamma rays as a mutagen. Seeds of the soybean genotypes Giza 21, Giza 22, Giza 82, Giza 83 and 117 were treated with gamma rays doses 50, 100, 200 and 300 Gy. Plants were then scored based on morphological parameters correlated with yield quantity including plant height, seed weight and valuable protein and oil contents. Mutant lines exhibiting the highest yield attributes were selected and used as parents for M2 generation. The M2 progeny was further assessed based on their ability to maintain their yield attributes. Twenty mutant lines were selected and used as M3 lines. The yield parameters inferred a positive effect of gamma irradiation on the collected M3 mutant lines compared to their parental genotypes. 100 Gy of gamma rays gave the highest effect on the number of pods, branches and seeds per plant in addition to protein content, while 200 Gy was more effective in increasing plant height, number of pods per plant, and oil content. Six mutant lines scored the highest yield parameters. Further assessment inferred an inverse relationship between oil and protein content in most of the tested cultivars with high agronomic features. However, four mutant lines recorded high content of oil and protein besides their high seed yield as well, which elect them as potential candidates for large-scale evaluation. The correlation among examined parameters was further confirmed via principal component analysis (PCA), which inferred a positive correlation between the number of pods, branches, seeds, and seed weight. Conversely, oil and protein content were inversely correlated in most of yielded mutant lines. Together, those findings introduce novel soybean lines with favorable agronomic traits for the market. In addition, our research sheds light on the value of using gamma rays treatment in enhancing genetic variability in soybean and improving oil, protein contents and seed yield., Competing Interests: Elsayed Mansour and Diaa Abd El-Moneim are Academic Editors for PeerJ., (©2023 Mohsen et al.)

Durum and bread wheat are well adapted to the Mediterranean Basin. Twenty-three genotypes of each species were grown to evaluate the intra- and inter-genetic diversity based on omega ( ω ), gamma ( γ ) and alpha ( α )-gliadin profiles. To achieve this purpose, the endosperm storage proteins (both gliadins and glutenins) were extracted from wheat grains and electrophoresed on sodium dodecyl sulfate (SDS)-polyacrylamide gels. The results of SDS-Polyacrylamide Gel Electrophoresis (SDS-PAGE) revealed nine polymorphic loci out of 16 loci with durum wheat genotypes and nine polymorphic loci out of 18 loci with bead wheat genotypes. The polymorphisms revealed by the SDS-PAGE were 56% and 50% in durum and bread wheat genotypes, respectively. Using the cluster analysis, the durum wheat genotypes were clustered into five groups, while the bread wheat genotypes were grouped into six clusters using un-weighed pair group mean analyses based on ω , γ , and α -gliadins profiles. The 46 durum and bread wheat genotypes were grouped into seven clusters based on the combined ω , γ , and α -gliadins profiles revealed by the SDS-PAGE. The in silico analysis determined the intra-genetic diversity between bread and durum wheat based on the sequences of ω , γ , and α -gliadins. The alignment of ω -gliadin revealed the highest polymorphism (52.1%) between bread and durum wheat, meanwhile, the alignment of γ and α -gliadins revealed very low polymorphism 6.6% and 15.4%, respectively. According to computational studies, all gliadins contain a lot of glutamine and proline residues. The analysis revealed that the bread wheat possessed ω and γ -gliadins with a lower content of proline and a higher content of glutamine than durum wheat. In contrast, durum wheat possessed α -gliadin with a lower content of proline and a higher content of glutamine than bread wheat. In conclusion, the SDS-PAGE, in silico and computational analyses are effective tools to determine the intra- and inter-genetic diversity in tetraploid and hexaploid wheat genotypes based on ω , γ , and α -gliadins profiles., Competing Interests: Diaa Abd El-Moneim is an Academic Editor for PeerJ., (©2023 Al-Khayri et al.)

Introduction: The Capsicum annuum nuclear factor Y subunit B (CaNFYB) gene family plays a significant role in diverse biological processes, including plant responses to abiotic stressors such as salinity. Methods: In this study, we provide a comprehensive analysis of the CaNFYB gene family in pepper, encompassing their identification, structural details, evolutionary relationships, regulatory elements in promoter regions, and expression profiles under salinity stress. Results and discussion: A total of 19 CaNFYB genes were identified and subsequently characterized based on their secondary protein structures, revealing conserved domains essential for their functionality. Chromosomal distribution showed a non-random localization of these genes, suggesting potential clusters or hotspots for NFYB genes on specific chromosomes. The evolutionary analysis focused on pepper and comparison with other plant species indicated a complex tapestry of relationships with distinct evolutionary events, including gene duplication. Moreover, promoter cis-element analysis highlighted potential regulatory intricacies, with notable occurrences of light-responsive and stress-responsive binding sites. In response to salinity stress, several CaNFYB genes demonstrated significant temporal expression variations, particularly in the roots, elucidating their role in stress adaptation. Particularly CaNFYB01 , CaNFYB18 , and CaNFYB19 , play a pivotal role in early salinity stress response, potentially through specific regulatory mechanisms elucidated by their cis-elements. Their evolutionary clustering with other Solanaceae family members suggests conserved ancestral functions vital for the family's survival under stress. This study provides foundational knowledge on the CaNFYB gene family in C. annuum , paving the way for further research to understand their functional implications in pepper plants and relative species and their potential utilization in breeding programs to enhance salinity tolerance., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Abd El Moneim, Mansour, Alshegaihi, Safhi, Alwutayd, Alshamrani, Alamri, Felembam, Abuzaid and Magdy.)

Genetic improvement mainly depends on the level of genetic variability present in the population, and the degree of genetic diversity in a population largely determines the rate of genetic advancement. For analyzing genetic diversity and determining cultivar identities, a molecular marker is a useful tool. Using 30 SSR (simple sequence repeat) and 30 RAPD (randomly amplified polymorphic DNA) markers, this study evaluated the genetic divergence of 17 mango cultivars. The effectiveness of the two marker systems was evaluated using their genetic diversity characteristics. Additionally, the effects of SM (simple matching) and Dice similarity coefficients and their effects on mango clustering were evaluated. The findings showed that SSR markers generated 192 alleles, all of which were polymorphic (100%). With RAPD markers, 434 bands were obtained, 361 of which were polymorphic (83%). The average polymorphic information content (PIC) for RAPD and SSR was 0.378 and 0.735, respectively. Using SSR markers resulted in much higher values for other genetic diversity parameters compared to RAPD markers. Furthermore, grouping the genotypes according to the two similarity coefficients without detailed consideration of these coefficients could not influence the study results. The RAPD markers OPA_01, OPM_12 followed by OPO_12 and SSR markers MIAC_4, MIAC_5 followed by mMiCIR_21 were the most informative in terms of describing genetic variability among the cultivars under study; they can be used in further investigations such as genetic mapping or marker-assisted selection. Overall, 'Zebda' cultivar was the most diverse of the studied cultivars., Competing Interests: Diaa Abd El-Moneim is an Academic Editor for PeerJ., (©2023 A. A. Hussein et al.)

Background: Water deficit is one of the most significant abiotic factors affecting rice and agricultural production worldwide. In hybrid rice, cytoplasmic male sterility (CMS) is an important technique for creating high-yielding crop based on heterosis. The phytohormone kinetin (Kin) regulates cell division in plant during the early stages of grain formation, as well as flow assimilation and osmotic regulation under water stress. The present study performed to estimate the effects of irrigation intervals (irrigation each six days (I 6 ), nine days (I 9 ), twelve days (I 12 ) and fifteen days (I 15 ) against continuous flooding (CF, each three days)) and kinetin exogenously application (control, 15 mg L -1 and 30 mg L -1 ) on hybrid rice (L1, IR69625A; L2, G46A and R, Giza 178 R) seed production., Results: Leaves traits (Chlorophyll content (CHC), relative water content (RWC), stomatal conductance (SC), Leaf temperature (LT) and transpiration rate (TR)), floral traits such as style length (SL) and total stigma length (TSL), in addition to root traits (i.e., root length (RL), root volume (RV), root: shoot ratio (RSR), root thickness (RT), root xylem vessels number (RXVN) and root xylem vessel area (RXVA) were evaluated and a significant enhancement in most traits was observed. Applying 30 mg L -1 kinetin significantly and positively enhanced all growth, floral and roots traits (RV and RXVA recorded the most increased values by 14.8% and 23.9%, respectively) under prolonging irrigation intervals, in comparison to non-treated plants., Conclusions: Subsequently, spraying kinetin exogenously on foliar could be an alternative method to reduce the harmful influences of water deficiency during seed production in hybrid rice., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Although trace elements are essential for life, environmental contamination due to metal accumulation and overuse in various sectors, such as healthcare, agriculture, industry, and cosmetics, poses significant health concerns. Exposure of plants to heavy metals leads to the overproduction of reactive oxygen species (ROS) due to their ability to change mitochondrial membrane permeability and restrict the action of ROS clearance enzymes in the cellular antioxidant system. The interaction of ROS with cellular membranes, heavy-metal-induced interactions directly or indirectly with different macromolecules, and signaling pathways leads to the accumulation of environmental pollutants and oxidative stress in exposed organisms. The heavy metal-ROS-cell signaling axis affects various pathological processes such as ATP depletion, excess ROS production, mitochondrial respiratory chain damage, decoupling of oxidative phosphorylation, and mitochondrial death. This review focuses on discussing the toxic effects of different heavy metals on plants, with particular emphasis on oxidative stress, its consequences, and mitigation strategies.

Introduction: Osmotic imbalance is one of the major consequences of drought stress, negatively affecting plant growth and productivity. Acetic acid has modulatory roles in osmotic balance in plants; however, the mechanistic insights into acetic acid-mediated osmotic adjustment under drought stress remains largely unknown., Methods: Here, we investigated how seed priming and seedling root treatment with acetic acid enabled maize plants overcoming polyethylene glycol (PEG)-induced drought effects., Results: Maize seeds primed with acetic acid showed better growth performance when compared with unprimed seeds under PEG application. This growth performance was mainly attributed to improved growth traits, such as fresh weight, dry weight, length of shoots and roots, and several leaf spectral indices, including normalized difference vegetation index (NDVI) and chlorophyll absorption in reflectance index (MCARI). The levels of oxidative stress indicators hydrogen peroxide (H 2 O 2 ) and malondialdehyde (MDA) did not alter significantly among the treatments, but proline content as well as the expression of proline biosynthetic gene, Δ1-PYRROLINE-5-CARBOXYLATE SYNTHETASE 1 ( P5CS1 ) was significantly elevated in plants receiving acetic acid under PEG-treatments. On the other hand, treating the seedlings root with acetic acid led to a significant recovery of maize plants from drought-induced wilting. Although growth traits remained unchanged among the treatments, the enhancement of leaf water content, photosynthetic rate, proline level, expression of P5CS1 , and antioxidant enzyme activities along with reduced level of H 2 O 2 and MDA in acetic acid-supplemented drought plants indicated a positive regulatory role of acetic acid in maize tolerance to drought. Moreover, the high expression of P5CS1 and the subsequent elevation of proline level upon acetic acid application were further validated using wild type and proline biosynthetic mutant p5cs1 of Arabidopsis. Results showed that acetic acid application enabled wild type plants to maintain better phenotypic appearance and recovery from drought stress than p5cs1 plants, suggesting a crosstalk between acetic acid and proline metabolism in plants under drought stress., Discussion: Our results highlight the molecular and intrinsic mechanisms of acetic acid conferring plant tolerance to drought stress., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Mahmud, Kamruzzaman, Bhattacharyya, Alharbi, Abd El Moneim and Mostofa.)

Cordia monoica is a member of the Boraginaceae family. This plant is widely distributed in tropical regions and has a great deal of medical value as well as economic importance. In the current study, the complete chloroplast (cp) genome of C. monoica was sequenced, assembled, annotated, and reported. This circular chloroplast genome had a size of 148,711 bp, with a quadripartite structure alternating between a pair of repeated inverted regions (26,897-26,901 bp) and a single copy region (77,893 bp). Among the 134 genes encoded by the cp genome, there were 89 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. A total of 1387 tandem repeats were detected, with the hexanucleotides class making up 28 percent of the repeats. Cordia monoica has 26,303 codons in its protein-coding regions, and leucine amino acid was the most frequently encoded amino acid in contrast to cysteine. In addition, 12 of the 89 protein-coding genes were found to be under positive selection. The phyloplastomic taxonomical clustering of the Boraginaceae species provides further evidence that chloroplast genome data are reliable not only at family level but also in deciphering the phylogeny at genus level (e.g., Cordia ).

Banana plantation has been introduced recently to a temperate zone in the southeastern parts of Saudi Arabia (Fifa, Dhamadh, and Beesh, located in Jazan province). The introduced banana cultivars were of a clear origin without a recorded genetic background. In the current study, the genetic variability and structure of five common banana cultivars (i.e., Red, America, Indian, French, and Baladi) were analyzed using the fluorescently labeled AFLP technique. Nine different primer pairs combinations yielded 1468 loci with 88.96% polymorphism. Among all locations, high expected heterozygosity under the Hardy-Weinberg assumption was found (0.249 ± 0.003), where Dhamadh was the highest, followed by Fifa and Beesh, respectively. Based on the PCoA and Structure analysis, the samples were not clustered by location but in pairs in accordance with the cultivar's names. However, the Red banana cultivar was found to be a hybrid between the American and Indian cultivars. Based on Φ ST , 162 molecular markers (i.e., loci under selection) were detected among cultivars. Identifying those loci using NGS techniques can reveal the genetic bases and molecular mechanisms involved in the domestication and selection indicators among banana cultivars.

Trigonella foenum graecum L. (Fenugreek) is a valuable medicinal plant cultivated for decades for its therapeutic characteristics. Still no pronounced improvement concerning wild form was accomplished as it is a self-pollinating crop. Induced mutagenesis is encouraged as a remarkable tool on this plant to circumvent the genetic bottleneck of cultivated germplasms. As a result, novel allelomorphic combinations for short-term agronomic attributes were developed. Fenugreek cultivar Pusa Early Bunching, selected for the present experiment, was mutagenized with five doses (0.2%, 0.4%, 0.6%, 0.8%, and 1.0%) of caffeine and sodium azide (SA) to evaluate its impact on the qualitative and quantitative traits of M 1 and M 2 generation conducted in a Complete Randomized Block Design (CRBD), replicated five times during 2019-2020 and 2020-2021, respectively. The frequency of induced phenotypic variations was assessed in M 2 progenies, resulting in the identification and isolation of a broad spectrum of mutants with altered phenotypes. Mutagenic effectiveness and efficiency were found to be maximum at lower concentrations of the mutagen treatments and highest in SA, followed by caffeine. Various morphological mutants with modified characters were observed at different concentrations in M 2 generation. The spectrum of mutations was wider in SA than in caffeine, as caffeine produced 51 while SA produced 54 individual mutants under seven major categories. The maximum frequency of morphological mutants was associated with leaf, followed by plant size, plant growth habit, pod, seed size, seed shape, and seed color. Morphological and structural variations in the guard cells of stomata and seeds were observed through scanning electron microscopy. The variations created in the economically important traits may enrich the genetic diversity of this plant species. Moreover, these morphological mutants may serve as a source of elite genes in further breeding programs of fenugreek., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Naaz, Choudhary, Sharma, Hasan, Al Shaye and Abd El-Moneim.)

To better understand the diversity and evolution of cichlids, we sequenced, assembled, and annotated the complete mitochondrial genomes of three Nile tilapiine species ( Coptodon zillii , Oreochromis niloticus , and Sarotherodon galilaeus ) dominating the Nile River waters. Our results showed that the general mitogenomic features were conserved among the Nile tilapiine species. The genome length ranged from 16,436 to 16,631 bp and a total of 37 genes were identified (two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and 1 control region). The ND6 was the only CDS that presented a negative AT skew and a positive GC skew. The most extended repeat sequences were in the D-loop followed by the pseudogenes (trnS GCU ). The ND5 showed relatively high substitution rates whereas ATP8 had the lowest substitution rate. The codon usage bias displayed a greater quantity of NNA and NNC at the third position and anti-bias against NNG. The phylogenetic relationship based on the complete mitogenomes and CDS was able to differentiate the three species as previously reported. This study provides new insight into the evolutionary connections between various subfamilies within cichlids while providing new molecular data that can be applied to discriminate between Nile tilapiine species and their populations.

The genetic diversity and the relationships among sesame cultivars were investigated using physiological and cyto/molecular analysis. To our information, no studies have yet been conducted on the genetic evaluation of sesame genotypes based on cyto/molecular analysis in Saudi Arabia. This study showed that genotype Bah-312 had the highest values from physiological and biochemical traits (plant height, harvest index, total plant dry matter, seed yield, oil content, and fatty acids content). Using 20 ISSR and 25 SCoT primers, the studied genotypes amplified 233 and 275 alleles, while the average polymorphism percentage (P%) was 65.32% (ISSR) and 77.8% (SCoT) across all the studied genotypes, respectively. To assess the markers efficiency analysis the polymorphism information contents (PIC), Marker Index (MI), Effective Multiplex Ratio (EMR), Resolving Power (Rp) were estimated. In general, primers (ISSR 2 & SCoT 21) and (ISSR 4 & SCoT 3) revealed the highest and lowest values for P %, PIC, MI, and EMR%. Furthermore, 188 positive and negative unique bands were detected, out of which ISSR generated 84, while 104 were amplified by SCoT analysis. In this regard, genotype Bah-312 generated 41 unique amplicons, and Jiz-511 genotype 23 unique amplicons. In the same context, the population genetics parameters, number of different alleles (Na), number of effective alleles (Ne), Shannon's index (I), expected heterozygosity (He), and Unbiased Expected Heterozygosity (uHe), were calculated. ISSR marker showed the highest values for all the estimated parameters. In this regard, genotype Bah-312 exhibited the highest values (1.35, 1.37, 0.31, 0.21, 0.29) & (1.31, 1.35, 0.30, 0.20, 0.27) while, genotype Ahs-670 revealed the least values (1.29, 1.31, 0.26, 0.16, 0.23) &(1.14, 1.26, 0.22, 0.15, 0.20) for ISSR and SCoT markers respectively. For cytological data, according to the highest asymmetry index (AsK%) and lowest total form percentage (TF%) values, genotype Ahs-670 was the most advanced cultivar, and genotype Bah-312 was the most primitive one. According to the degree of asymmetry of karyotype (A) and intrachromosomal asymmetry index (A1), sesame genotype Ahs-670 was the most asymmetrical, and Bah-312 was the most symmetrical genotype. This study gives some helpful information about the genetic diversity of six sesame landraces. The variation harbored by these landraces could be used in sesame breeding programs., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Mesfer ALshamrani, Safhi, Alshaya, Ibrahim, Mansour and Abd El Moneim.)

Developing high-yielding rice genotypes is decisive to ensure global food security with current population growth and the threat of environmental pressures. Cytoplasmic male sterility (CMS) system provides a valuable approach for commercial exploitation of heterosis and producing high-yielding and quality hybrid rice. Three CMS lines and ten diverse restorers were crossed using line × tester mating design. The obtained thirty F 1 hybrids and their thirteen parents were evaluated. Yield traits as well as certain floral traits characters that influence the efficiency of crossing and hybrid seed production as the duration of floret opening (min), stigma exsertion (mm), stigma length (mm), opening floret angle, and anther length (mm) were assessed. Highly significant variations were detected among parents, crosses, and parents vs. crosses for all the studied traits. The CMS line L2 and the restorer T5 were determined as good combiners for stigma exsertion, stigma length, opining floret angle, and duration of floret opening. Besides, the hybrids L1 × T1, L1 × T3, L2 × T2, L2 × T5, L3 × T4, L3 × T5, and L3 × T9 exhibited positive SCA effects for most floral traits. Moreover, the CMS lines L1 and L3 as well as the restorers T1, T2, T3, T6, and T9 were identified as good general combiners for grain yield and certain related traits. The hybrids L1 × T1, L1 × T5, L1 × T7, L2 × T3, L2 × T4, L2 × T5, L2 × T10, L3 × T1, L3 × T2, and L3 × T6 displayed positive SCA effects for grain yield and one or more of its attributes. Both additive and non-additive gene effects were involved in the governing inheritance of all evaluated traits. The biochemical variations among the certain evaluated genotypes were further studied. The esterase and peroxidase isozymes were applied for verifying the genetic diversity at the protein level among the used CMS lines, restorers, and their crosses. All the applied isozymes displayed polymorphism for the parents and their crosses. The banding pattern and intensity differences provided accurate results on the reliable variability among the tested genotypes., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Author(s).)

Aluminum (Al) toxicity in acid soils influences plant development and yield. Almost 50% of arable land is acidic. Plants have evolved a variety of tolerance mechanisms for Al. In response to the presence of Al, various species exudate citrate from their roots. Rye ( Secale cereale L.) secretes both citrate and malate, making it one of the most Al-tolerant cereal crops. However, no research has been done on the role of the mitochondrial citrate synthase ( mCS ) gene in Al-induced stress in the rye. We have isolated an mCS gene, encoding a mitochondrial CS isozyme, in two S. cereale cultivars (Al-tolerant cv. Ailés and Al-sensitive inbred rye line Riodeva; ScCS4 gene) and in two Brachypodium distachyon lines (Al-tolerant ABR8 line and Al-sensitive ABR1 line; BdCS4 gene). Both mCS4 genes have 19 exons and 18 introns. The ScCS4 gene was located on the 6R L rye chromosome arm. Phylogenetic studies using cDNA and protein sequences have shown that the ScCS4 gene and their ScCS protein are orthologous to mCS genes and CS proteins of different Poaceae plants. Expression studies of the ScCS4 and BdSC4 genes show that the amount of their corresponding mRNAs in the roots is higher than that in the leaves and that the amounts of mRNAs in plants treated and not treated with Al were higher in the Al-tolerant lines than that in the Al-sensitive lines of both species. In addition, the levels of ScCS4 and BdCS4 mRNAs were reduced in response to Al (repressive behavior) in the roots of the tolerant and sensitive lines of S. cereale and B. distachyon ., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Abd El-Moneim, Contreras, Silva-Navas, Gallego, Figueiras and Benito.)

Water scarcity is a major environmental stress that adversatively impacts wheat growth, production, and quality. Furthermore, drought is predicted to be more frequent and severe as a result of climate change, particularly in arid regions. Hence, breeding for drought-tolerant and high-yielding wheat genotypes has become more decisive to sustain its production and ensure global food security with continuing population growth. The present study aimed at evaluating different parental bread wheat genotypes (exotic and local) and their hybrids under normal and drought stress conditions. Gene action controlling physiological, agronomic, and quality traits through half-diallel analysis was applied. The results showed that water-deficit stress substantially decreased chlorophyll content, photosynthetic efficiency (FV/Fm), relative water content, grain yield, and yield attributes. On the other hand, proline content, antioxidant enzyme activities (CAT, POD, and SOD), grain protein content, wet gluten content, and dry gluten content were significantly increased compared to well-watered conditions. The 36 evaluated genotypes were classified based on drought tolerance indices into 5 groups varying from highly drought-tolerant (group A) to highly drought-sensitive genotypes (group E). The parental genotypes P 3 and P 8 were identified as good combiners to increase chlorophyll b, total chlorophyll content, relative water content, grain yield, and yield components under water deficit conditions. Additionally, the cross combinations P 2 × P 4 , P 3 × P 5 , P 3 × P 8 , and P 6 × P 7 were the most promising combinations to increase yield traits and multiple physiological parameters under water deficit conditions. Furthermore, P 1 , P 2 , and P 5 were recognized as promising parents to improve grain protein content and wet and dry gluten contents under drought stress. In addition, the crosses P 1 × P 4 , P 2 × P 3 , P 2 × P 5 , P 2 × P 6 , P 4 × P 7 , P 5 × P 7 , P 5 × P 8 , P 6 × P 8 , and P 7 × P 8 were the best combinations to improve grain protein content under water-stressed and non-stressed conditions. Certain physiological traits displayed highly positive associations with grain yield and its contributing traits under drought stress such as chlorophyll a, chlorophyll b, total chlorophyll content, photosynthetic efficiency (Fv/Fm), proline content, and relative water content, which suggest their importance for indirect selection under water deficit conditions. Otherwise, grain protein content was negatively correlated with grain yield, indicating that selection for higher grain yield could reduce grain protein content under drought stress conditions.

Plant growth and crop productivity under unfavorable environmental challenges require a unique strategy to scavenge the severely negative impacts of these challenges such as soil salinity and water stress. Compost and plant growth-promoting rhizobacteria (PGPR) have many beneficial impacts, particularly in plants exposed to different types of stress. Therefore, a field experiment during two successive seasons was conducted to investigate the impact of compost and PGPR either separately or in a combination on exchangeable sodium percentage (ESP), soil enzymes (urease and dehydrogenase), wheat physiology, antioxidant defense system, growth, and productivity under deficient irrigation and soil salinity conditions. Our findings showed that exposure of wheat plants to deficit irrigation in salt-affected soil inhibited wheat growth and development, and eventually reduced crop productivity. However, these injurious impacts were diminished after soil amendment using the combined application of compost and PGPR. This combined application enhanced soil urease and dehydrogenase, ion selectivity, chlorophylls, carotenoids, stomatal conductance, and the relative water content (RWC) whilst reducing ESP, proline content, which eventually increased the yield-related traits of wheat plants under deficient irrigation conditions. Moreover, the coupled application of compost and PGPR reduced the uptake of Na and resulted in an increment in superoxide dismutase (SOD), catalase (CAT), and peroxidase (POX) activities that lessened oxidative damage and improved the nutrient uptake (N, P, and K) of deficiently irrigated wheat plants under soil salinity. It was concluded that to protect wheat plants from environmental stressors, such as water stress and soil salinity, co-application of compost with PGPR was found to be effective.

The aim of the study was to estimate the impact of soil amendments (i.e., phosphogypsum and plant growth-promoting rhizobacteria (PGPR)) separately or their combination on exchangeable sodium percentage (ESP), soil enzymes' activity (urease and dehydrogenase), pigment content, relative water content (RWC), antioxidant enzymatic activity, oxidative stress, productivity, and quality of quinoa under deficient irrigation conditions in two field experiments during the 2019-2020 and 2020-2021 seasons under salt-affected soil. Results revealed that ESP, soil urease activity, soil dehydrogenase activity, leaf chlorophyll a, b, and carotenoids, leaf K content, RWC, SOD (superoxide dismutase), CAT (catalase), and POD (peroxidase) activities were declined, resulting in overproduction of leaf Na content, proline content, and oxidative stress indicators (H 2 O 2 , malondialdehyde (MDA) and electrolyte leakage) under water stress and soil salinity, which negatively influence yield-related traits, productivity, and seed quality of quinoa. However, amendment of salt-affected soil with combined phosphogypsum and seed inoculation with PGPR under deficient irrigation conditions was more effective than singular application and control plots in ameliorating the harmful effects of water stress and soil salinity. Additionally, combined application limited Na uptake in leaves and increased K uptake and leaf chlorophyll a, b, and carotenoids as well as improved SOD, CAT, and POD activities to ameliorate oxidative stress indicators (H 2 O 2 , MDA, and electrolyte leakage), which eventually positively reflected on productivity and quality in quinoa. We conclude that the potential utilization of phosphogypsum and PGPR are very promising as sustainable eco-friendly strategies to improve quinoa tolerance to water stress under soil salinity.

Quinoa ( Chenopodium quinoa Willd.) is a halophytic crop that can withstand a variety of abiotic stresses, including salt. The present research examined the mechanisms of salt tolerance in five different quinoa genotypes at four different salinity levels (control (60), 80, 120, and 160 mM NaCl). ISSR and SCoT analysis revealed high polymorphism percentages of 90.91% and 85.26%, respectively. Furthermore, ISSR 1 and SCoT 7 attained the greatest number of polymorphic amplicons (27 and 26), respectively. Notably, LINE-6 and M-28 genotypes demonstrated the greatest number of unique positive and negative amplicons (50 and 42) generated from ISSR and SCoT, respectively. Protein pattern analysis detected 11 bands with a polymorphism percentage 27.27% among the quinoa genotypes, with three unique bands distinguishable for the M-28 genotype. Similarity correlation indicated that the highest similarity was between S-10 and Regeolone-3 (0.657), while the lowest similarity was between M-28 and LINE-6 (0.44). Significant variations existed among the studied salinity treatments, genotypes, and the interactions between them. The highest and lowest values for all the studied morpho-physiological and biochemical traits were recorded at 60 and 160 mM NaCl concentrations, respectively, except for the Na and proline contents, which exhibited the opposite relationship. The M-28 genotype demonstrated the highest values for all studied characteristics, while the LINE-6 genotype represented the lowest in both seasons. On the other hand, mRNA transcript levels for CqSOS1 did not exhibit differential expression in roots and leaf tissues, while the expression of CqNHX1 was upregulated more in both tissues for the M-28 genotype than for the LINE-6 genotype, and its maximum induction was seen in the leaves. Overall, the genotypes M-28 and LINE-6 were identified as the most and least salinity-tolerant, respectively.

Wheat has remarkable importance among cereals in Egypt. Salt stress affects plant growth, development, and crop productivity. Therefore, salinity tolerance is an essential trait that must be incorporated in crops. This research aimed to investigate molecular and biochemical indicators and defence responses in seedlings of 14 Egyptian wheat genotypes to distinguish the most contrasting salt-responsive genotypes. Analysis of ISSR and SCoT markers revealed high polymorphism and reproducible fingerprinting profiles for evaluating genetic variability within the studied genotypes. The HB-10 and SCoT 1 primers had the highest values for all the studied parameters. All the tested primers generated a set of 66 polymorphic bands among tolerant and sensitive genotypes. The transcript profiles of eight TaWRKY genes showed significant induction under the salinity treatments. Moreover, the expression of TaWRKY6 for genotypes Sids 14 and Sakha 93 sharply increased and recorded the highest expression, while the expression of TaWRKY20 for Misr 1 recorded the lowest expression. Under salt stress, the total sugar, proline, and phenolic contents increased significantly, while the chlorophyll content decreased significantly. Additionally, five peroxidase and polyphenol oxidase isoforms were observed in treated leaves and clustered into five different patterns. Some isoforms increased significantly as salinity levels increased. This increase was clearer in salt-tolerant than in salt-sensitive genotypes. Eighteen protein bands appeared, most of which were not affected by salinity compared with the control, and specific bands were rare. Generally, the Sids 14, Sakha 93, Sohag 4, and Gemmeiza 12 genotypes are considered salt tolerant in comparison to the other genotypes., Competing Interests: The authors have declared that no competing interests exist.