Correction: Ramakrishnan et al. The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation. Int. J. Mol. Sci. 2021, 22, 11387

The authors would like to make the following corrections to the original publication [...

Wastewater monitoring of SARS-CoV-2 in on-grid, partially and fully off-grid Bedouin communities in Southern Israel

BackgroundWastewater based epidemiology (WBE) has become an important tool in SARS-CoV-2 surveillance and epidemiology. While WBE measurements generally correlate with observed case numbers in large municipal areas on sewer grids, there are few studies on its utility in communities that are off-grid (non-sewered).Methods and materialsTo explore the applicability of wastewater surveillance in our region, five Bedouin communities along the Hebron Stream in Southern Israel (Negev desert) were sampled. One point (El-Sayed) represents a community with partial connection to the sewer grid system and another point (Um Batin) represents a community with no access to the sewer grid system. The towns of Hura, Lakia, and Tel Al-Sabi/Tel Sheva were on-grid. A total of 87 samples were collected between August 2020 to January 2021 using both grab and composite sampling. RNA was extracted from the raw sewage and concentrated sewage. RT-qPCR was carried out with N1, N2, and N3 gene targets, and findings were compared to human case data from the Israeli Ministry of Health.ResultsSARS-CoV-2 was detected consistently over time in on-grid Bedouin towns (Lakia, Tel Sheva/Tel as-Sabi, and Hura) and inconsistently in smaller, off-grid communities (El-Sayed and Um Batin). The trend in maximum copy number/L appears to be driven by population size. When comparing case numbers normalized to population size, the amount of gene copies/L was inconsistently related to reported case numbers. SARS-CoV-2 was also detected from sewage-impacted environmental waters representing communities with no access to the wastewater grid. When grab sampling and composite sampling data were compared, results were generally comparable however composite sampling produced superior results.ConclusionsThe mismatch observed between detected virus and reported cases could indicate asymptomatic or “silent” community transmission, under-testing within these communities (due to factors like mistrust in government, stigma, misinformation) or a combination therein. While the exact reason for the mismatch between environmental SARS-CoV-2 signals and case numbers remains unresolved, these findings suggest that sewage surveillance, including grab sampling methodologies, can be a critical aspect of outbreak surveillance and control in areas with insufficient human testing and off-grid communities

Improved Agrobacterium-mediated transformation and direct plant regeneration in four cultivars of finger millet (Eleusine coracana (L.) Gaertn.)

peer reviewedWe have developed an improved Agrobacterium-mediated transformation and rapid regeneration system for four cultivars (‘CO(Ra)-14’, ‘PR-202’, ‘Try-1’ and ‘Paiyur-2’) of finger millet using optimized transformation and direct plant regeneration conditions. The shoot apical meristems (SAMs) were used as explants in this study. Agrobacterium strain EHA105 carrying binary vector pCAMBIA1301 was used to optimize the transformation conditions. Concentration of hygromycin, the optical density of the culture, infection time, age of the explants, co-cultivation period, the concentrations of acetosyringone and antibiotics were optimized to improve the transformation frequency. The highest frequency of mean transient gus expression (85.1%) was achieved in cultivar ‘CO(Ra)-14’. The entire transformation procedure, from initiating SAMs to planting putative transgenic plantlets in the greenhouse, was completed within 45 days with the highest stable transformation frequency of 11.8% for ‘CO(Ra)-14’. PCR, gus staining and Southern blot analyses were performed in T0 and T1 generations to confirm the gene integration. Six events from T0 had a single copy of the transgene and showed a normal Mendelian pattern of segregation. To our knowledge, this is the first report on the high frequency transformation of finger millet by Agrobacterium and subsequent recovery of transgenic plants via direct plant regeneration without a callus phase, in short duration (45 days). The proposed protocol could be supportive in breaking through the bottleneck in transformation and regeneration of finger millet cultivars

Finger Millet [Eleusine coracana (L.) Gaertn.] Improvement: Current Status and Future Interventions of Whole Genome Sequence

The whole genome sequence (WGS) of the much awaited, nutrient rich and climate resilient crop, finger millet (Eleusine coracana (L.) Gaertn.) has been released recently. While possessing superior mineral nutrients and excellent shelf life as compared to other major cereals, multiploidy nature of the genome and relatively small plantation acreage in less developed countries hampered the genome sequencing of finger millet, disposing it as one of the lastly sequenced genomes in cereals. The genomic information available for this crop is very little when compared to other major cereals like rice, maize and barley. As a result, only a limited number of genetic and genomic studies has been undertaken for the improvement of this crop. Finger millet is known especially for its superior calcium content, but the high-throughput studies are yet to be performed to understand the mechanisms behind calcium transport and grain filling. The WGS of finger millet is expected to help to understand this and other important molecular mechanisms in finger millet, which may be harnessed for the nutrient fortification of other cereals. In this review, we discuss various efforts made so far on the improvement of finger millet including genetic improvement, transcriptome analysis, mapping of quantitative trait loci (QTLs) for traits, etc. We also discuss the pitfalls of modern genetic studies and provide insights for accelerating the finger millet improvement with the interventions of WGS in near future. Advanced genetic and genomic studies aided by WGS may help to improve the finger millet, which will be helpful to strengthen the nutritional security in addition to food security in the developing countries of Asia and Africa

The dynamism of transposon methylation for plant development and stress adaptation

Correction: Ramakrishnan et al. The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation. Int. J. Mol. Sci. 2021, 22, 11387 https://doi.org/10.3390/ijms232214107Plant development processes are regulated by epigenetic alterations that shape nuclear structure, gene expression, and phenotypic plasticity; these alterations can provide the plant with protection from environmental stresses. During plant growth and development, these processes play a significant role in regulating gene expression to remodel chromatin structure. These epigenetic alterations are mainly regulated by transposable elements (TEs) whose abundance in plant genomes results in their interaction with genomes. Thus, TEs are the main source of epigenetic changes and form a substantial part of the plant genome. Furthermore, TEs can be activated under stress conditions, and activated elements cause mutagenic effects and substantial genetic variability. This introduces novel gene functions and structural variation in the insertion sites and primarily contributes to epigenetic modifications. Altogether, these modifications indirectly or directly provide the ability to withstand environmental stresses. In recent years, many studies have shown that TE methylation plays a major role in the evolution of the plant genome through epigenetic process that regulate gene imprinting, thereby upholding genome stability. The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, leading to genomic stress. These TE-mediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. Thus, TE methylation is essential for plant evolution and stress adaptation, and TEs hold a relevant military position in the plant genome. High-throughput techniques have greatly advanced the understanding of TE-mediated gene expression and its associations with genome methylation and suggest that controlled mobilization of TEs could be used for crop breeding. However, development application in this area has been limited, and an integrated view of TE function and subsequent processes is lacking. In this review, we explore the enormous diversity and likely functions of the TE repertoire in adaptive evolution and discuss some recent examples of how TEs impact gene expression in plant development and stress adaptation.Peer reviewe

Overexpression of Erianthus arundinaceus DREB2 Transcription Factor Ameliorates the Salinity and Drought Tolerance in Eleusine coracana Cultivars

Drought and salinity are the major constraints on agricultural production worldwide and a remarkable attempt is being made to improve the plant yields in the direction of increasing water deficit. We have developed transgenic finger millet cultivars ‘CO(Ra)-14’ and ‘Paiyur-2’ overexpressing Erianthus arundinaceous DREB2 (EaDREB2) transcription factor confirmed by PCR and Southern stably expressed in T0 and T1. These transgenic lines were tolerant to high salinity and severe drought stress conditions without affecting the morphological or agronomic characters. Analysis of morpho-physiological characters revealed that overexpression of EaDREB2 gene was associated with maintenance of chlorophyll content, increased relative water content, improved accumulation of the osmotic substance such as proline and decreased electrolyte leakage, under both saline and drought stresses. After treating the plants to progressive drought and salinity stress, transgenic lines showed less chlorophyll reduction and moderate growth inhibition than the controls. The majority of the transformed lines showed prominent tolerance to salinity and drought with significant spikelet fertility and higher grain yield compared to the controls at stressed and unstressed conditions. This is the first holistic report on development of drought and saline tolerance in finger millet through transgenic modification and it is essential to benefit the farmers from seasonal stress

Effect of salinity stress on finger millet (Eleusine coracana (L.) Gaertn): Histochemical and morphological analysis of coleoptile and coleorhizae

The current study deals with the impact of salinity stress on growth and development of finger millet genotype ‘CO(Ra)-14’. The seeds were germinated on Murashige and Skoog solid medium supplemented with various concentrations of sodium chloride (NaCl) (0, 50, 100, 150 or 200 mM) for 15 days. Several physiological indices, including relative growth rate, electrolyte leakage, proline and chlorophyll (a, b and a + b) content, cell viability, hydrogen peroxide and caspase-like activity were measured to analyze the physiological and biochemical characteristics of saline stress. In addition, we also analyzed saline stress induced histochemical changes and level of lignin in the coleoptile and coleorhizae tissues. Relative growth of leaves and shoots of finger millet genotype ‘CO(Ra)-14’ exposed to 150 mM NaCl concentration was decreased while root length was increased. In addition, there was a significant increase in the levels of electrolyte leakage, contents of proline and hydrogen peroxide, and caspase-like activity from 0 to 200 mM NaCl. Chlorophyll and relative water contents were significantly reduced with decreased leaf succulence under increasing salinity. The microscopic observations of coleoptile and coleorhizae cross sections revealed considerable variations viz., length of epidermal cells, surface area and width of the cells with increasing salinity. Saline treated tissues were severely damaged and were intensely stained with phloroglucinol (suggesting the accumulation of cell bound phenolic compounds). Overall finger millet genotype ‘CO(Ra)-14’ showed a diverse response to salinity stress starting from seed germination to growth, and above 100 mM NaCl salinity is toxic to finger millet genotype ‘CO(Ra)-14’

Correction: Ramakrishnan et al. The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation. Int. J. Mol. Sci. 2021, 22, 11387

The authors would like to make the following corrections to the original publication [...

<i>Cajanus platycarpus</i> Flavonoid 3′5′ Hydroxylase_2 (<i>CpF3′5′H_2</i>) Confers Resistance to <i>Helicoverpa armigera</i> by Modulating Total Polyphenols and Flavonoids in Transgenic Tobacco

Pod borer Helicoverpa armigera, a polyphagus herbivorous pest, tremendously incurs crop damage in economically important crops. This necessitates the identification and utility of novel genes for the control of the herbivore. The present study deals with the characterization of a flavonoid 3′5′ hydroxylase_2 (F3′5′H_2) from a pigeonpea wild relative Cajanus platycarpus, possessing a robust chemical resistance response to H. armigera. Though F3′5′H_2 displayed a dynamic expression pattern in both C. platycarpus (Cp) and the cultivated pigeonpea, Cajanus cajan (Cc) during continued herbivory, CpF3′5′H_2 showed a 4.6-fold increase vis a vis 3-fold in CcF3′5′H_2. Despite similar gene copy numbers in the two Cajanus spp., interesting genic and promoter sequence changes highlighted the stress responsiveness of CpF3′5′H_2. The relevance of CpF3′5′H_2 in H. armigera resistance was further validated in CpF3′5′H_2-overexpressed transgenic tobacco based on reduced leaf damage and increased larval mortality through an in vitro bioassay. As exciting maiden clues, CpF3′5′H_2 deterred herbivory in transgenic tobacco by increasing total flavonoids, polyphenols and reactive oxygen species (ROS) scavenging capacity. To the best of our knowledge, this is a maiden attempt ascertaining the role of F3′5′H_2 gene in the management of H. armigera. These interesting leads suggest the potential of this pivotal branch-point gene in biotic stress management programs

The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

Plant development processes are regulated by epigenetic alterations that shape nuclear structure, gene expression, and phenotypic plasticity; these alterations can provide the plant with protection from environmental stresses. During plant growth and development, these processes play a significant role in regulating gene expression to remodel chromatin structure. These epigenetic alterations are mainly regulated by transposable elements (TEs) whose abundance in plant genomes results in their interaction with genomes. Thus, TEs are the main source of epigenetic changes and form a substantial part of the plant genome. Furthermore, TEs can be activated under stress conditions, and activated elements cause mutagenic effects and substantial genetic variability. This introduces novel gene functions and structural variation in the insertion sites and primarily contributes to epigenetic modifications. Altogether, these modifications indirectly or directly provide the ability to withstand environmental stresses. In recent years, many studies have shown that TE methylation plays a major role in the evolution of the plant genome through epigenetic process that regulate gene imprinting, thereby upholding genome stability. The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, leading to genomic stress. These TE-mediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. Thus, TE methylation is essential for plant evolution and stress adaptation, and TEs hold a relevant military position in the plant genome. High-throughput techniques have greatly advanced the understanding of TE-mediated gene expression and its associations with genome methylation and suggest that controlled mobilization of TEs could be used for crop breeding. However, development application in this area has been limited, and an integrated view of TE function and subsequent processes is lacking. In this review, we explore the enormous diversity and likely functions of the TE repertoire in adaptive evolution and discuss some recent examples of how TEs impact gene expression in plant development and stress adaptation