Effect of Surface Treatment of Zirconia on the Shear Bond Strength of Resin Cement: A Systematic Review and Meta-Analysis.

This systematic review and meta-analysis aimed to evaluate the effect of different surface treatments on the shear bond strength (SBS) values between zirconia and resin cement compared to untreated specimens. The effects of various surface treatments on the bond strength between zirconia and resin cement were investigated by searching relevant articles on PubMed, ScienceDirect, and Google Scholar databases. A total of 13 studies that met the inclusion and exclusion criteria and addressed the research question were selected for statistical analysis. The studies were evaluated for heterogeneity, and a meta-analysis was performed. In total, 13 in vitro studies were included in accordance with the eligibility criteria. All 13 studies consistently demonstrated that silica coating yielded the highest SBS, followed by sandblasting and laser treatments. The meta-analysis using a random-effect model indicated a significant intergroup comparison, except for a few studies. Among the three treatments examined, the silica coating of zirconia was identified as the most effective in enhancing the bond strength between zirconia and resin cement. Further controlled laboratory and clinical studies are necessary to validate these findings and explore additional factors that may influence the effects of these surface treatments.

Elucidating the molecular responses to waterlogging stress in onion (Allium cepa L.) leaf by comparative transcriptome profiling.

Introduction: Waterlogging is a major stress that severely affects onion cultivation worldwide, and developing stress-tolerant varieties could be a valuable measure for overcoming its adverse effects. Gathering information regarding the molecular mechanisms and gene expression patterns of waterlogging-tolerant and sensitive genotypes is an effective method for improving stress tolerance in onions. To date, the waterlogging tolerance-governing molecular mechanism in onions is unknown. Methods: This study identified the differentially expressed genes (DEGs) through transcriptome analysis in leaf tissue of two onion genotypes (Acc. 1666; tolerant and W-344; sensitive) presenting contrasting responses to waterlogging stress. Results: Differential gene expression analysis revealed that in Acc. 1666, 1629 and 3271 genes were upregulated and downregulated, respectively. In W-344, 2134 and 1909 genes were upregulated and downregulated, respectively, under waterlogging stress. The proteins coded by these DEGs regulate several key biological processes to overcome waterlogging stress such as phytohormone production, antioxidant enzymes, programmed cell death, and energy production. The clusters of orthologous group pathway analysis revealed that DEGs contributed to the post-translational modification, energy production, and carbohydrate metabolism-related pathways under waterlogging stress. The enzyme assay demonstrated higher activity of antioxidant enzymes in Acc. 1666 than in W-344. The differential expression of waterlogging tolerance related genes, such as those related to antioxidant enzymes, phytohormone biosynthesis, carbohydrate metabolism, and transcriptional factors, suggested that significant fine reprogramming of gene expression occurs in response to waterlogging stress in onion. A few genes such as ADH, PDC, PEP carboxylase, WRKY22, and Respiratory burst oxidase D were exclusively upregulated in Acc. 1666. Discussion: The molecular information about DEGs identified in the present study would be valuable for improving stress tolerance and for developing waterlogging tolerant onion varieties.

Predicting the potential geographical distribution of onion thrips, Thrips tabaci in India based on climate change projections using MaxEnt.

Onion thrips, Thrips tabaci Lindeman, an economically important onion pest in India, poses a severe threat to the domestic and export supply of onions. Therefore, it is important to study the distribution of this pest in order to assess the possible crop loss, which it may inflict if not managed in time. In this study, MaxEnt was used to analyze the potential distribution of T. tabaci in India and predict the changes in the suitable areas for onion thrips under two scenarios, SSP126 and SSP585. The area under the receiver operating characteristic curve values of 0.993 and 0.989 for training and testing demonstrated excellent model accuracy. The true skill statistic value of 0.944 and 0.921, and the continuous Boyce index of 0.964 and 0.889 for training and testing, also showed higher model accuracy. Annual Mean Temperature (bio1), Annual Precipitation (bio12) and Precipitation Seasonality (bio15) are the main variables that determined the potential distribution of T. tabaci, with the suitable range of 22-28 °C; 300-1000 mm and 70-160, respectively. T. tabaci is distributed mainly in India's central and southern states, with 1.17 × 106 km2, covering 36.4% of land area under the current scenario. Multimodal ensembles show that under a low emission scenario (SSP126), low, moderate and optimum suitable areas of T. tabaci is likely to increase, while highly suitable areas would decrease by 17.4% in 2050 20.9% in 2070. Whereas, under the high emission scenario (SSP585), the high suitability is likely to contract by 24.2% and 51.7% for 2050 and 2070, respectively. According to the prediction of the BCC-CSM2-MR, CanESM5, CNRM-CM6-1 and MIROC6 model, the highly suitable area for T. tabaci would likely contract under both SSP126 and SSP585. This study detailed the potential future habitable area for T. tabaci in India, which could help monitor and devise efficient management strategies for this destructive pest.

Efficient Elimination of Viruses from Garlic Using a Combination of Shoot Meristem Culture, Thermotherapy, and Chemical Treatment.

Garlic (Allium sativum L.) is a clonally propagated bulbous crop and can be infected by several viruses under field conditions. A virus complex reduces garlic yield and deteriorates the quality of the produce. In the present study, we aimed to eliminate Onion yellow dwarf virus (OYDV), Garlic common latent virus (GCLV), Shallot latent virus (SLV), and Allexiviruses from the infected crop using combination of meristem culture, thermotherapy, and chemotherapy. In this study, seven different treatments, namely shoot meristem culture, thermotherapy direct culture, chemotherapy direct culture, chemotherapy + meristem culture, thermotherapy + meristem culture, thermotherapy + chemotherapy direct culture, and thermotherapy + chemotherapy + meristem culture (TCMC), were used. Multiplex polymerase chain reaction (PCR) was employed to detect virus elimination, which revealed the percentage of virus-free plants was between 65 and 100%, 55 and 100%, and 13 and 100% in the case of GCLV, SLV, and OYDV, respectively. The in vitro regeneration efficiency was between 66.06 and 98.98%. However, the elimination of Allexiviruses could not be achieved. TCMC was the most effective treatment for eliminating GCLV, SLV, and OYDV from garlic, with 66.06% plant regeneration efficiency. The viral titre of the Allexivirus under all the treatments was monitored using real-time PCR, and the lowest viral load was observed in the TCMC treatment. The present study is the first to report the complete removal of GCLV, SLV, and OYDV from Indian red garlic with the application of thermotherapy coupled with chemotherapy and shoot meristem culture.

Biotechnological Interventions in Tomato (Solanum lycopersicum) for Drought Stress Tolerance: Achievements and Future Prospects.

Tomato production is severely affected by abiotic stresses (drought, flood, heat, and salt) and causes approximately 70% loss in yield depending on severity and duration of the stress. Drought is the most destructive abiotic stress and tomato is very sensitive to the drought stress, as cultivated tomato lack novel gene(s) for drought stress tolerance. Only 20% of agricultural land worldwide is irrigated, and only 14.51% of that is well-irrigated, while the rest is rain fed. This scenario makes drought very frequent, which restricts the genetically predetermined yield. Primarily, drought disturbs tomato plant physiology by altering plant-water relation and reactive oxygen species (ROS) generation. Many wild tomato species have drought tolerance gene(s); however, their exploitation is very difficult because of high genetic distance and pre- and post-transcriptional barriers for embryo development. To overcome these issues, biotechnological methods, including transgenic technology and CRISPR-Cas, are used to enhance drought tolerance in tomato. Transgenic technology permitted the exploitation of non-host gene/s. On the other hand, CRISPR-Cas9 technology facilitated the editing of host tomato gene(s) for drought stress tolerance. The present review provides updated information on biotechnological intervention in tomato for drought stress management and sustainable agriculture.

Unfolding the mitochondrial genome structure of green semilooper (Chrysodeixis acuta Walker): An emerging pest of onion (Allium cepa L.).

Onion is the most important crop challenged by a diverse group of insect pests in the agricultural ecosystem. The green semilooper (Chrysodeixis acuta Walker), a widespread tomato and soybean pest, has lately been described as an emergent onion crop pest in India. C. acuta whole mitochondrial genome was sequenced in this work. The circular genome of C. acuta measured 15,743 base pairs (bp) in length. Thirteen protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one control region were found in the 37 sequence elements. With an average 395 bp gene length, the maximum and minimum gene length observed was 1749 bp and 63 bp of nad5 and trnR, respectively. Nine of the thirteen PCGs have (ATN) as a stop codon, while the other four have a single (T) as a stop codon. Except for trnS1, all of the tRNAs were capable of producing a conventional clover leaf structure. Conserved ATAGA motif sequences and poly-T stretch were identified at the start of the control region. Six overlapping areas and 18 intergenic spacer regions were found, with sizes ranged from 1 to 20 bp and 1 to 111 bp correspondingly. Phylogenetically, C. acuta belongs to the Plusiinae subfamily of the Noctuidae superfamily, and is closely linked to Trichoplusia ni species from the same subfamily. In the present study, the emerging onion pest C. acuta has its complete mitochondrial genome sequenced for the first time.

Anthracnose of Onion (Allium cepa L.): A Twister Disease.

The onion (Allium cepa L.) is a lucrative and high-value vegetable-spice crop in India, but it is sensitive to several of diseases caused by fungi, bacteria, viruses, and nematodes, of which a fungal disease, anthracnose, caused by Colletotrichum spp., is a major issue for both onion producers and researchers since it severely affects the bulb production. Twister disease is currently one of the most common problems in onion production, particularly in humid regions, and it reduces productivity while also lowering the value and profitability. Twister disease is visualised by white or pale-yellow water-soaked oval depressed lesions on leaf blades, which are the first symptoms. Lesions expand as the disease advances, and numerous black-coloured, slightly elevated structures/fruiting bodies appear in the middle area, arranged in concentric rings. Curling, twisting, chlorosis of the leaves, and aberrant extension of the neck or pseudo-stem occurs, followed by rotting of the bulb. In an unmanaged crop, an excess gibberellin production by Colletotrichum gloeosporioides and Gibberella moniliformis is suspected to induce twisting and aberrant neck elongation, which will ruin onion productivity. It is difficult and environmentally unfriendly to control these infections. Since, to the best of our knowledge, this is the first review on onion anthracnose, we tried to consolidate information. This review updates our knowledge of the pathogen, including the disease cycle, infection pathways, and disease management techniques. As a result, growers will be benefit from the application of cultural, biological, and chemical measures and the use of resistant varieties.

Comparative Transcriptome Analysis of Onion in Response to Infection by Alternaria porri (Ellis) Cifferi.

Purple blotch (PB) is one of the most destructive foliar diseases of onion and other alliums, caused by a necrotrophic fungal pathogen Alternaria porri. There are no reports on the molecular response of onion to PB infection. To elucidate the response of onion to A. porri infection, we consequently carried out an RNAseq analysis of the resistant (Arka Kalyan; AK) and susceptible (Agrifound rose; AFR) genotype after an artificial infection. Through differential expression analyses between control and pathogen-treated plants, we identified 8,064 upregulated and 248 downregulated genes in AFR, while 832 upregulated and 564 downregulated genes were identified in AK. A further significant reprogramming in the gene expression profile was also demonstrated by a functional annotation analysis. Gene ontology (GO) terms, which are particularly involved in defense responses and signaling, are overrepresented in current analyses such as "oxidoreductase activity," "chitin catabolic processes," and "defense response." Several key plant defense genes were differentially expressed on A. porri infection, which includes pathogenesis-related (PR) proteins, receptor-like kinases, phytohormone signaling, cell-wall integrity, cytochrome P450 monooxygenases, and transcription factors. Some of the genes were exclusively overexpressed in resistant genotype, namely, GABA transporter1, ankyrin repeat domain-containing protein, xyloglucan endotransglucosylase/hydrolase, and PR-5 (thaumatin-like). Antioxidant enzyme activities were observed to be increased after infection in both genotypes but higher activity was found in the resistant genotype, AK. This is the first report of transcriptome profiling in onion in response to PB infection and will serve as a resource for future studies to elucidate the molecular mechanism of onion-A. porri interaction and to improve PB resistance in onions.

Piriformospora indica Primes Onion Response against Stemphylium Leaf Blight Disease.

The root-endophytic fungus Piriformospora indica (=Serendipita indica) has been revealed for its growth-promoting effects and its capacity to induce resistance in a broad spectrum of host plants. However, the bioefficacy of this fungus had not yet been tested against any pathogen affecting onion (Allium cepa). In this study, the biocontrol potency of P. indica against onion leaf blight, an impacting disease caused by the necrotrophic fungal pathogen Stemphylium vesicarium, was evaluated. First, it was proved that colonisation of onion roots by P. indica was beneficial for plant growth, as it increased leaf development and root biomass. Most relevantly, P. indica was also effective in reducing Stemphylium leaf blight (SLB) severity, as assessed under greenhouse conditions and confirmed in field trials in two consecutive years. These investigations could also provide some insight into the biochemical and molecular changes that treatment with P. indica induces in the main pathways associated with host defence response. It was possible to highlight the protective effect of P. indica colonisation against peroxidative damage, and its role in signalling oxidative stress, by assessing changes in malondialdehyde and H2O2 content. It was also showed that treatment with P. indica contributes to modulate the enzymatic activity of superoxide dismutase, catalase, phenylalanine ammonia-lyase and peroxidase, in the course of infection. qPCR-based expression analysis of defence-related genes AcLOX1, AcLOX2, AcPAL1, AcGST, AcCHI, AcWRKY1, and AcWRKY70 provided further indications on P. indica ability to induce onion systemic response. Based on the evidence gathered, this study aims to propose P. indica application as a sustainable tool for improving SLB control, which might not only enhance onion growth performance but also activate defence signalling mechanisms more effectively, involving different pathways.

A simple flow cytometry-based assay to study global methylation levels in onion, a non-model species.

DNA methylation is an important epigenetic mark and global methylation dynamics regulate plant developmental processes. Even though genome sequencing technologies have made DNA methylation studies easier, it is difficult in non-model species where genome information is not available. Therefore in this study, we developed a simple assay for analysing global methylation levels in plants by washless immunolabelling of unfixed nuclei using flow cytometry. Onion leaf tissue was used as a model system, and mean fluorescence intensity due to anti-5- methyl cytosine (5-mC) antibodies were used as a measure of global methylation levels. Among three nuclear isolation buffers evaluated, the highest nuclear yield with the low background was obtained with LB01. To maintain a balance between high DNA fluorescence value and low coefficient of variation of DNA peaks, 45 min of hydrolysis with 0.2 N hydrochloric acid was used for chromatin denaturation resulting in six-fold increase in 5-mC fluorescence compared to control. This method was used successfully to detect 5-Azacytidine induced DNA hypomethylation in onion leaf tissues. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01047-6.

Genetic diversity of Indian garlic core germplasm using agro-biochemical traits and SRAP markers.

The characterization of garlic germplasm improves its utility, despite the fact that garlic hasn't been used much in the past. Garlic has an untapped genetic pool of immense economic and medicinal value in India. Hence, using heuristic core collection approach, a core set of 46 accessions were selected from 625 Indian garlic accessions based on 13 quantitative and five qualitative traits. The statistical measures (CV per cent, CR per cent, VR per cent) were used to sort the core set using Shannon-Wiener diversity index and the Nei diversity index. In addition, the variation within the core set was tested for 18 agro-morphological and six biochemical characteristics (allicin, phenol content, pyruvic acid, protein, allyl methyl thiosulfinate (AMTHS), and methyl allyl thiosulfinate (MATHS)). Further study of the core set's molecular diversity was performed using sequence related amplified polymorphism (SRAP) markers, which revealed a wide range of diversity among the core set's accessions, with an average polymorphism efficiency (PE) of 80.59 percent, polymorphism information content (PIC) of 0.29, effective multiplex ratio (EMR) of 3.51, and marker index (MI) of 0.99. The findings of this study will be useful in identifying high-yielding, elite garlic germplasm lines with the trait of interest. Since this core set is indicative of total germplasm, these selected breeding lines will be used for genetic improvement of garlic in the future.

Overexpression of AtDREB1 and BcZAT12 genes confers drought tolerance by reducing oxidative stress in double transgenic tomato (Solanum lycopersicum L.).

KEY MESSAGE: Double transgenic tomato developed by AtDREB1A and BcZAT12 genes pyramiding showed significant drought tolerance by reducing oxidative stress with enhanced yield. Although a large number of efforts have been made by different researchers to develop abiotic stress tolerance tomato for improving yield using single gene, however, no reports are available which targets AtDREB1 and BcZAT12 genes together. Hence, in the present study, double transgenic plants were developed using AtDREB1 and BcZAT12 genes to improve yield potential with better drought tolerance. Double transgenic (DZ1-DZ5) tomato lines showed enhanced drought tolerance than their counterpart non-transgenic and single transgenic plants at 0, 07, 14, and 21 days of water deficit, respectively. Double transgenic plants showed increased activity of antioxidant enzymes, like catalase (CAT), superoxide dismutase (SOD), glutathione reductase (GR), ascorbate peroxidase (APX), dehydroascorbate reductase (DHAR), monodehydroascorbate reductase (MDHAR) and guaiacol peroxidase (POD), and accumulation of non-enzymatic antioxidants like ascorbic acid, glutathione as compared to non-transgenic and single transgenic. Additionally, the transcript analysis of antioxidant enzymes revealed the increased level of gene expression in double transgenic tomato lines. Developed double-transgenic tomato plants co-over-expressing both genes exhibited more enzymatic and non-enzymatic anti-oxidative activities as compared to the non-transgenic and single transgenic control, respectively. This is the preliminary report in tomato, which forms the basis for a multigene transgenic approach to cope with drought stress.

Engineered BcZAT12 gene mitigates salt stress in tomato seedlings.

In salt-prone areas, plant growth and productivity is adversely affected. In the present study, the ZT1-ZT6 transgenic tomato lines having BcZAT12 gene under the regulatory control of the stress inducible Bclea1 promoter were exposed to three salinity levels (50, 100 and 200 mM) at the four leaf stage for 10 days. The transgenic lines showed improved growth in stem height, leaf area, root length and shoot length under saline conditions, as compared to control. Moreover, ZT1 and ZT5 lines showed lower electrolyte leakage and decreased hydrogen peroxide formation, in combination with elevated relative water content, proline and chlorophyll levels. The enzyme activity of catalase was also enhanced in ZT1 and ZT5. These results poses the present lines as an attractive alternative for tomato cultivation in salinity-affected areas.

Screening of Onion (Allium cepa L.) Genotypes for Drought Tolerance Using Physiological and Yield Based Indices Through Multivariate Analysis.

Drought is a leading abiotic constraints for onion production globally. Breeding by using unique genetic resources for drought tolerance is a vital mitigation strategy. With a total of 100 onion genotypes were screened for drought tolerance using multivariate analysis. The experiment was conducted in a controlled rainout shelter for 2 years 2017-2018 and 2018-2019 in a randomized block design with three replications and two treatments (control and drought stress). The plant was exposed to drought stress during the bulb development stage (i.e., 50-75 days after transplanting). The genotypes were screened on the basis of the drought tolerance efficiency (DTE), percent bulb yield reduction, and results of multivariate analysis viz. hierarchical cluster analysis by Ward's method, discriminate analysis and principal component analysis. The analysis of variance indicated significant differences among the tested genotypes and treatments for all the parameters studied, viz. phenotypic, physiological, biochemical, and yield attributes. Bulb yield was strongly positively correlated with membrane stability index (MSI), relative water content (RWC), total chlorophyll content, antioxidant enzyme activity, and leaf area under drought stress. The genotypes were categorized into five groups namely, highly tolerant, tolerant, intermediate, sensitive, and highly sensitive based on genetic distance. Under drought conditions, clusters II and IV contained highly tolerant and highly sensitive genotypes, respectively. Tolerant genotypes, viz. Acc. 1656, Acc. 1658, W-009, and W-085, had higher DTE (>90%), fewer yield losses (<20%), and performed superiorly for different traits under drought stress. Acc. 1627 and Acc. 1639 were found to be highly drought-sensitive genotypes, with more than 70% yield loss. In biplot, the tolerant genotypes (Acc. 1656, Acc. 1658, W-085, W-009, W-397, W-396, W-414, and W-448) were positively associated with bulb yield, DTE, RWC, MSI, leaf area, and antioxidant enzyme activity under drought stress. The study thus identified tolerant genotypes with favorable adaptive traits that may be useful in onion breeding program for drought tolerance.

Screening of Onion (Allium cepa L.) Genotypes for Waterlogging Tolerance.

Onion production is severely affected by waterlogging conditions, which are created due to heavy rainfall. Hence, the identification of waterlogging-tolerant onion genotypes is crucial for increasing onion production. In the present study, 100 distinct onion genotypes were screened for waterlogging tolerance under artificial conditions by using the phenotypic approach in the monsoon season of 2017. Based on plant survival and recovery and changes in bulb weight, we identified 19 tolerant, 27 intermediate tolerant, and 54 highly sensitive onion genotypes. The tolerant genotypes exhibited higher plant survival and better recovery and bulb size, whereas sensitive genotypes exhibited higher plant mortality, poor recovery, and small bulb size under waterlogging conditions. Furthermore, a subset of 12 contrasting genotypes was selected for field trials during monsoon seasons 2018 and 2019. Results revealed that considerable variation in the morphological, physiological, and yield characteristics were observed across the genotypes under stress conditions. Waterlogging-tolerant genotypes, namely, Acc. 1666, Acc. 1622, W-355, W-208, KH-M-2, and RGP-5, exhibited higher plant height, leaf number, leaf area, leaf length, chlorophyll content, membrane stability index (MSI), pyruvic acid, antioxidant content, and bulb yield than sensitive genotypes under stress conditions. Furthermore, the principal component analysis biplot revealed a strong association of leaf number, leaf area, chlorophyll content, MSI, and bulb yield with tolerant genotypes under stress conditions. The study indicates that the waterlogging-tolerant onion genotypes with promising stress-adaptive traits can be used in plant breeding programs for developing waterlogging-tolerant onion varieties.

Identification of genes involved in phosphate solubilization and drought stress tolerance in chickpea symbiont Mesorhizobium ciceri Ca181.

Chickpea plant root colonizing bacteria Mesorhizobium ciceri Ca181 promotes plant growth and development through symbiotic association with root nodules. The potentially beneficial effects on plants generated due to this bacterium are mineral nutrient solubilization, abiotic stress tolerance, and nitrogen-fixation, though the molecular mechanisms underlying these probiotic capacities are still largely unknown. Hence, this study aims to describe the molecular mechanism of M. ciceri Ca181 in drought stress tolerance and phosphorus solubilization. Here we have developed the transposon inserted mutant library of strain Ca181 and further screened it to identify the phosphorous solubilization and PEG-induced drought stress tolerance defective mutants, respectively. Resultantly, a total of four and three mutants for phosphorous solubilization and drought stress tolerance were screened and identified. Consequently, Southern blot confirmation was done for the cross verification of insertions and stability in the genome. Through the sequencing of each mutant, the interrupted gene was confirmed, and the finding revealed that the production of gluconic acid is necessary for phosphorus solubilization, while otsA, Auc, and Usp genes were involved in the mechanism of drought stress tolerance in M. ciceri Ca181.

First Report of Garlic virus B infecting Garlic in India.

Garlic (Allium sativum L.) is an economically important spice and vegetable crop grown throughout the world. Garlic viral disease complex caused by multiple virus infections is an important constraint in exploiting the potential yield of garlic. Among these viral pathogens, allexivirus (family Alphaflexiviridae) is the genus of viruses known for their degenerative effect on garlic yield. Their coexistence with other viruses, particularly potyviruses, has an adverse effect on garlic yield and quality (Perotto et al. 2010). During Sept 2018, while screening garlic germplasm accessions for the presence of allexiviruses, symptoms like foliar mosaic and curling were observed on accession G-204, planted at an experimental plot of ICAR-DOGR, Pune, India. A total of five samples comprised of five randomly selected G-204 garlic plants were collected from the experimental plot. Each sample contained leaves from the top, middle, and bottom portion of the individual garlic plants. These samples were subjected to RNA extraction using the RNeasy Plant Mini Kit (Qiagen, Germany) followed by reverse transcription (RT) using the Transcriptor cDNA synthesis kit (Roche Diagnostics, GmbH, Germany). The extracted RNA was then tested for allexiviruses such as garlic virus A (GarV-A), garlic virus B (GarV-B), garlic virus C (GarV-C), garlic virus D (GarV-D), and garlic virus X (GarV-X) by polymerase chain reaction (PCR) (Gawande et al. 2015; Roylawar et al. 2019; Baranwal et al. 2011; Gieck et al. 2009). Leaf samples tested through RT-PCR were found positive for garlic viruses GarV-A, GarV-B, GarV-C, GarV-D, and GarV-X. Allexiviruses other than GarV-B had been previously reported in India and hence further tests were conducted to confirm GarV-B infection. RT-PCR using primers, CF 5'- ATGGGAGACAGGTCGCAA-3' and CR5'- CTAAAATGTAAGCATGAGCGGT-3' designed specific to the coat protein yielded a 735-bp amplicon from all five G-204 plants. The amplified product was purified using QIAquick PCR Purification Kit (Qiagen, Germany) and cloned in pJET1.2 vector (Thermo Scientific, Lithuania). Two clones containing the CP gene were bidirectionally sequenced, and a consensus sequence was submitted to GenBank (MN650206). BLASTn results indicated that this consensus sequence showed 97.96% nucleotide (KP657919.1) and 100% amino acid sequence (AKN19940.1) identity with the CP sequence of GarV-B isolate from Poland. The presence of GarV-B was confirmed by enzyme-linked immunosorbent assay (ELISA) using a double-antibody sandwich ELISA kit (Arsh Biotech, Delhi, India) as per the manufacturer's protocol. An absorbance of reaction was read using a microplate reader at 405 nm. The mean OD values of negative and positive controls were 0.034 and 0.373, respectively. The OD values of five samples tested ranged from 0.210 to 0.296 indicating a positive reaction for GarV-B. To assess the presence of GarV-B in the available genetic stock, we tested 30 garlic germplasm accessions for GarV-B using RT-PCR. Out of these, 17 accessions were found positive for GarV-B. GarV-B has been reported from many countries (Gieck et al. 2009). This is the first report of GarV-B from India. Globally, allexiviruses are known for their adverse impact on garlic production (Oliveira et al. 2014). GarV-B together with other viruses can be a potential threat to garlic production in India. Further, detailed evaluations are needed to study the impact of GarV-B on garlic production in India.

Omics approaches in Allium research: Progress and way ahead.

BACKGROUND: The genus Allium (Family: Amaryllidaceae) is an economically important group of crops cultivated worldwide for their use as a vegetable and spices. Alliums are also well known for their nutraceutical properties. Among alliums, onion, garlic, leek, and chives cultivated worldwide. Despite their substantial economic and medicinal importance, the genome sequence of any of the Allium is not available, probably due to their large genome sizes. Recently evolved omics technologies are highly efficient and robust in elucidating molecular mechanisms of several complex life processes in plants. Omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, metagenomics, etc. have the potential to open new avenues in research and improvement of allium crops where genome sequence information is limited. A significant amount of data has been generated using these technologies for various Allium species; it will help in understanding the key traits in Allium crops such as flowering, bulb development, flavonoid biosynthesis, male sterility and stress tolerance at molecular and metabolite level. This information will ultimately assist us in speeding up the breeding in Allium crops. METHOD: In the present review, major omics approaches, and their progress, as well as potential applications in Allium crops, could be discussed in detail. RESULTS: Here, we have discussed the recent progress made in Allium research using omics technologies such as genomics, transcriptomics, micro RNAs, proteomics, metabolomics, and metagenomics. These omics interventions have been used in alliums for marker discovery, the study of the biotic and abiotic stress response, male sterility, organ development, flavonoid and bulb color, micro RNA discovery, and microbiome associated with Allium crops. Further, we also emphasized the integrated use of these omics platforms for a better understanding of the complex molecular mechanisms to speed up the breeding programs for better cultivars. CONCLUSION: All the information and literature provided in the present review throws light on the progress and potential of omics platforms in the research of Allium crops. We also mentioned a few research areas in Allium crops that need to be explored using omics technologies to get more insight. Overall, alliums are an under-studied group of plants, and thus, there is tremendous scope and need for research in Allium species.

Comparative transcriptome analyses in contrasting onion (Allium cepa L.) genotypes for drought stress.

Onion (Allium cepa L.) is an important vegetable crop widely grown for diverse culinary and nutraceutical properties. Being a shallow-rooted plant, it is prone to drought. In the present study, transcriptome sequencing of drought-tolerant (1656) and drought-sensitive (1627) onion genotypes was performed to elucidate the molecular basis of differential response to drought stress. A total of 123206 and 139252 transcripts (average transcript length: 690 bases) were generated after assembly for 1656 and 1627, respectively. Differential gene expression analyses revealed upregulation and downregulation of 1189 and 1180 genes, respectively, in 1656, whereas in 1627, upregulation and downregulation of 872 and 1292 genes, respectively, was observed. Genes encoding transcription factors, cytochrome P450, membrane transporters, and flavonoids, and those related to carbohydrate metabolism were found to exhibit a differential expression behavior in the tolerant and susceptible genotypes. The information generated can facilitate a better understanding of molecular mechanisms underlying drought response in onion.

Insight in the transcriptome data of hairy root disease-causing bacterium-Agrobacterium rhizogenes.

Agrobacterium rhizogenes induce the production of the hairy root through the transformation of plant genomes. In this article, we executed the transcriptome of A. rhizogenes through RNA-sequencing. RNA-sequencing of A. rhizogenes generated a total of 2.6 Gb raw data with a 75 bp paired-end sequence. The raw data has been submitted to the SRA database of NCBI with accession number SRR5641651. Reads were generated 2946 unigenes and all unigenes were annotated in the database. The length of transcripts ranged from 90 to 6369 bp, with a median transcript length of 968. The transcripts were annotated through the number of databases to obtain information about SSRs, SNPs, Gene Ontology, Transcription factors, and pathways analysis .