Colonization of Serendipita indica promotes resistance against Spodoptera exigua in onion (Allium cepa L.).

Plant-endophyte symbiosis influences plant defense and growth. Serendipita indica is a root endophyte that promotes growth and induces tolerance against biotic and abiotic stress in plants. In this study, we examined the effect of S. indica colonization on herbivore (Spodoptera exigua) resistance of onion (Allium cepa L.). We found that colonization of S. indica in the roots of onion significantly reduced the feeding damage of leaves by S. exigua larvae, and also resulted in a reduction in weight gain of the larvae when fed on S. indica plants. This enhanced resistance is a result of modulation of antioxidant and defense enzymes/genes in the host by S. indica mutualism. Specifically, the activities of enzymes such as Superoxide dismutase, peroxidase, polyphenol oxidase, phenylalanine ammonia-lyase, and H2O2 content were significantly higher in the early stages of S. exigua feeding in the S. indica colonized plants compared to the non-colonized counterparts. Similarly, defense genes also showed modulation in response to this tripartite interaction of onion -S. indica mutualism and S. exigua herbivory. The hierarchical cluster analysis and principal component analysis indicated a clear difference in the onion biochemical responses, which is due to the S. indica symbiosis. Our investigation demonstrates that onion-S. indica symbiosis significantly decreases chewing injury by efficiently modulating antioxidant and defense enzyme activities and gene expression in response to S. exigua herbivory. Therefore, S. indica can be used as a potential biocontrol agent for sustainable management of this important pest of Alliums.

Role of gut symbionts of insect pests: A novel target for insect-pest control.

Insects possess beneficial and nuisance values in the context of the agricultural sector and human life around them. An ensemble of gut symbionts assists insects to adapt to diverse and extreme environments and to occupy every available niche on earth. Microbial symbiosis helps host insects by supplementing necessary diet elements, providing protection from predators and parasitoids through camouflage, modulation of signaling pathway to attain homeostasis and to trigger immunity against pathogens, hijacking plant pathways to circumvent plant defence, acquiring the capability to degrade chemical pesticides, and degradation of harmful pesticides. Therefore, a microbial protection strategy can lead to overpopulation of insect pests, which can drastically reduce crop yield. Some studies have demonstrated increased insect mortality via the destruction of insect gut symbionts; through the use of antibiotics. The review summarizes various roles played by the gut microbiota of insect pests and some studies that have been conducted on pest control by targeting the symbionts. Manipulation or exploitation of the gut symbionts alters the growth and population of the host insects and is consequently a potential target for the development of better pest control strategies. Methods such as modulation of gut symbionts via CRISPR/Cas9, RNAi and the combining of IIT and SIT to increase the insect mortality are further discussed. In the ongoing insect pest management scenario, gut symbionts are proving to be the reliable, eco-friendly and novel approach in the integrated pest management.

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.

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.

Microbiome profiling of the onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae).

The gut microbial community structure of adult Thrips tabaci collected from 10 different agro-climatically diverse locations of India was characterized by using the Illumina MiSeq platform to amplify the V3 region of the 16S rRNA gene of bacteria present in the sampled insects. Analyses were performed to study the bacterial communities associated with Thrips tabaci in India. The complete bacterial metagenome of T. tabaci was comprised of 1662 OTUs of which 62.25% belong to known and 37.7% of unidentified/unknown bacteria. These OTUs constituted 21 bacterial phyla of 276 identified genera. Phylum Proteobacteria was predominant, followed by Actinobacteria, Firmicutes, Bacteroidetes and Cyanobacteria. Additionally, the occurrence of the reproductive endosymbiont, Wolbachia was detected at two locations (0.56%) of the total known OTUs. There is high variation in diversity and species richness among the different locations. Alpha-diversity metrics indicated the higher gut bacterial diversity at Bangalore and lowest at Rahuri whereas higher bacterial species richness at T. tabaci samples from Imphal and lowest at Jhalawar. Beta diversity analyses comparing bacterial communities between the samples showed distinct differences in bacterial community composition of T. tabaci samples from different locations. This paper also constitutes the first record of detailed bacterial communities associated with T. tabaci. The location-wise variation in microbial metagenome profile of T. tabaci suggests that bacterial diversity might be governed by its population genetic structure, environment and habitat.