Transcriptomic responses under combined bacterial blight and drought stress in rice reveal potential genes to improve multi-stress tolerance

BACKGROUND

The unprecedented drought and frequent occurrence of pathogen infection in rice is becoming more due to climate change. Simultaneous occurrence of stresses lead to more crop loss. To cope up multiple stresses, the durable resistant cultivars needs to be developed, by identifying relevant genes from combined biotic and abiotic stress exposed plants.

RESULTS

We studied the effect of drought stress, bacterial leaf blight disease causing Xanthomonas oryzae pv. oryzae (Xoo) pathogen infection and combined stress in contrasting BPT5204 and TN1 rice genotypes. Mild drought stress increased Xoo infection irrespective of the genotype. To identify relevant genes that could be used to develop multi-stress tolerant rice, RNA sequencing from individual drought, pathogen and combined stresses in contrasting genotypes has been developed. Many important genes are identified from resistant genotype and diverse group of genes are differentially expressed in contrasting genotypes under combined stress. Further, a meta-analysis from individual drought and Xoo pathogen stress from public domain data sets narrowed- down candidate differentially expressed genes. Many translation associated genes are differentially expressed suggesting their extra-ribosomal function in multi-stress adaptation. Overexpression of many of these genes showed their relevance in improving stress tolerance in rice by different scientific groups. In combined stress, many downregulated genes also showed their relevance in stress adaptation when they were over-expressed.

CONCLUSIONS

Our study identifies many important genes, which can be used as molecular markers and targets for genetic manipulation to develop durable resistant rice cultivars. Strategies should be developed to activate downregulated genes, to improve multi-stress tolerance in plants.

Identification of major candidate genes for multiple abiotic stress tolerance at seedling stage by network analysis and their validation by expression profiling in rice (Oryza sativa L.)

A wealth of microarray and RNA-seq data for studying abiotic stress tolerance in rice exists but only limited studies have been carried out on multiple stress-tolerance responses and mechanisms. In this study, we identified 6657 abiotic stress-responsive genes pertaining to drought, salinity and heat stresses from the seedling stage microarray data of 83 samples and used them to perform unweighted network analysis and to identify key hub genes or master regulators for multiple abiotic stress tolerance. Of the total 55 modules identified from the analysis, the top 10 modules with 8-61 nodes comprised 239 genes. From these 10 modules, 10 genes common to all the three stresses were selected. Further, based on the centrality properties and highly dense interactions, we identified 7 intra-modular hub genes leading to a total of 17 potential candidate genes. Out of these 17 genes, 15 were validated by expression analysis using a panel of 4 test genotypes and a pair of standard check genotypes for each abiotic stress response. Interestingly, all the 15 genes showed upregulation under all stresses and in all the genotypes, suggesting that they could be representing some of the core abiotic stress-responsive genes. More pertinently, eight of the genes were found to be co-localized with the stress-tolerance QTL regions. Thus, in conclusion, our study not only provided an effective approach for studying abiotic stress tolerance in rice, but also identified major candidate genes which could be further validated by functional genomics for abiotic stress tolerance.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03182-7.

RiceMetaSysB: a database of blast and bacterial blight responsive genes in rice and its utilization in identifying key blast-resistant WRKY genes

Nearly two decades of revolution in the area of genomics serves as the basis of present-day molecular breeding in major food crops such as rice. Here we report an open source database on two major biotic stresses of rice, named RiceMetaSysB, which provides detailed information about rice blast and bacterial blight (BB) responsive genes (RGs). Meta-analysis of microarray data from different blast- and BB-related experiments across 241 and 186 samples identified 15135 unique genes for blast and 7475 for BB. A total of 9365 and 5375 simple sequence repeats (SSRs) in blast and BB RGs were identified for marker development. Retrieval of candidate genes using different search options like genotypes, tissue, developmental stage of the host, strain, hours/days post-inoculation, physical position and SSR marker information is facilitated in the database. Search options like 'common genes among varieties' and 'strains' have been enabled to identify robust candidate genes. A 2D representation of the data can be used to compare expression profiles across genes, genotypes and strains. To demonstrate the utility of this database, we queried for blast-responsive WRKY genes (fold change ≥5) using their gene IDs. The structural variations in the 12 WRKY genes so identified and their promoter regions were explored in two rice genotypes contrasting for their reaction to blast infection. Expression analysis of these genes in panicle tissue infected with a virulent and an avirulent strain of Magnaporthe oryzae could identify WRKY7, WRKY58, WRKY62, WRKY64 and WRKY76 as potential candidate genes for resistance to panicle blast, as they showed higher expression only in the resistant genotype against the virulent strain. Thus, we demonstrated that RiceMetaSysB can play an important role in providing robust candidate genes for rice blast and BB.

Whole Genome Characterization of a Few EMS-Induced Mutants of Upland Rice Variety Nagina 22 Reveals a Staggeringly High Frequency of SNPs Which Show High Phenotypic Plasticity Towards the Wild-Type

The Indian initiative, in creating mutant resources for the functional genomics in rice, has been instrumental in the development of 87,000 ethylmethanesulfonate (EMS)-induced mutants, of which 7,000 are in advanced generations. The mutants have been created in the background of Nagina 22, a popular drought- and heat-tolerant upland cultivar. As it is a pregreen revolution cultivar, as many as 573 dwarf mutants identified from this resource could be useful as an alternate source of dwarfing. A total of 541 mutants, including the macromutants and the trait-specific ones, obtained after appropriate screening, are being maintained in the mutant garden. Here, we report on the detailed characterizations of the 541 mutants based on the distinctness, uniformity, and stability (DUS) descriptors at two different locations. About 90% of the mutants were found to be similar to the wild type (WT) with high similarity index (>0.6) at both the locations. All 541 mutants were characterized for chlorophyll and epicuticular wax contents, while a subset of 84 mutants were characterized for their ionomes, namely, phosphorous, silicon, and chloride contents. Genotyping of these mutants with 54 genomewide simple sequence repeat (SSR) markers revealed 93% of the mutants to be either completely identical to WT or nearly identical with just one polymorphic locus. Whole genome resequencing (WGS) of four mutants, which have minimal differences in the SSR fingerprint pattern and DUS characters from the WT, revealed a staggeringly high number of single nucleotide polymorphisms (SNPs) on an average (16,453 per mutant) in the genic sequences. Of these, nearly 50% of the SNPs led to non-synonymous codons, while 30% resulted in synonymous codons. The number of insertions and deletions (InDels) varied from 898 to 2,595, with more than 80% of them being 1-2 bp long. Such a high number of SNPs could pose a serious challenge in identifying gene(s) governing the mutant phenotype by next generation sequencing-based mapping approaches such as Mutmap. From the WGS data of the WT and the mutants, we developed a genic resource of the WT with a novel analysis pipeline. The entire information about this resource along with the panicle architecture of the 493 mutants is made available in a mutant database EMSgardeN22 (http://14.139.229.201/EMSgardeN22).

RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement

Background

Genome-wide microarray has enabled development of robust databases for functional genomics studies in rice. However, such databases do not directly cater to the needs of breeders. Here, we have attempted to develop a web interface which combines the information from functional genomic studies across different genetic backgrounds with DNA markers so that they can be readily deployed in crop improvement. In the current version of the database, we have included drought and salinity stress studies since these two are the major abiotic stresses in rice.

Results

RiceMetaSys, a user-friendly and freely available web interface provides comprehensive information on salt responsive genes (SRGs) and drought responsive genes (DRGs) across genotypes, crop development stages and tissues, identified from multiple microarray datasets. ‘Physical position search’ is an attractive tool for those using QTL based approach for dissecting tolerance to salt and drought stress since it can provide the list of SRGs and DRGs in any physical interval. To identify robust candidate genes for use in crop improvement, the ‘common genes across varieties’ search tool is useful. Graphical visualization of expression profiles across genes and rice genotypes has been enabled to facilitate the user and to make the comparisons more impactful. Simple Sequence Repeat (SSR) search in the SRGs and DRGs is a valuable tool for fine mapping and marker assisted selection since it provides primers for survey of polymorphism. An external link to intron specific markers is also provided for this purpose. Bulk retrieval of data without any limit has been enabled in case of locus and SSR search.

Conclusions

The aim of this database is to facilitate users with a simple and straight-forward search options for identification of robust candidate genes from among thousands of SRGs and DRGs so as to facilitate linking variation in expression profiles to variation in phenotype.

Database URL: http://14.139.229.201

Electronic supplementary material

The online version of this article (10.1186/s12859-017-1846-y) contains supplementary material, which is available to authorized users.

Concurrent syringomyelia and intradural extramedullary tuberculoma as late complications of tuberculous meningitis

Tuberculous meningitis (TBM) is a common presentation of extrapulmonary tuberculosis. TBM is associated with many complications. However, concurrent syringomyelia and intradural extramedullary tuberculoma occurring in a patient treated for TBM is rare. Only one such case has been reported earlier. A 27-year-old woman presented with paraparesis of 2 months duration. She had been treated for TBM 8 months earlier. She was found to have an extensive syringomyelia from C2 to the conus medullaris and an intradural extramedullary tuberculoma at the lower thoracic levels. At surgery, a thick, granulomatous lesion was found in the intradural extramedullary plane. Following excision of the granulomatous lesion, a syringostomy was done. The patient was treated with antituberculous drugs and steroids. Six months after treatment, there was no significant change in her neurological status. Concurrent syringomyelia and intradural extramedullary tuberculoma should be entertained in the differential diagnosis when a patient presents with myelopathy following TBM. The pathogenesis of syringomyelia in this condition is discussed.

Interaction between enrofloxacin and monensin in broiler chickens

Enrofloxacin, a fluoroquinolone, and its interaction with monensin, an ionophore drug, was studied to explore the influence of enrofloxacin on drug metabolizing enzymes that can lead to physiological and toxicological consequences upon coadministration with monensin in broiler chickens. Group I, treated with 100 mg monesin/kg feed from 1 d old to 41st d of age, did not show any influence on aniline hydroxylase and cytochrome b5 levels. Group II, treated with 10 mg enrofloxacin/kg body weight per os for three consecutive days on 33rd, 34th, 35th d of age, had a highly significant decrease in aniline hydroxylase on 38th d (ie on 3rd d post-treatment with enrofloxacin); a reversal effect was noticed on the 41st day (ie on 6th d post-treatment with enrofloxacin). There was no alteration in cytochrome b5 level. Group III with monensin and enrofloxacin coadministration 100 mg monensin/kg feed from 1 d old to the 41st day + 10 mg enrofloxacin/kg body weight, per os for 3 consecutive days on the 33rd, 34th, 35th d of age) had a significant decrease in aniline hydroxylase level on the 3rd d post-treatment with enrofloxacin, but an elevation tending to reach normal on the 6th d post-treatment with enrofloxacin. Monensin + enrofloxacin coadministration did not produce any alteration in cytochrome b5 level. Creatine kinase (CK) and alanine amino transferase (ALT) levels significantly increased on the 3rd d post-treatment with enrofloxacin, but on the 6th d post-treatment with enrofloxacin the increase declined. Aspartate amino transferase (AST) significantly increased on the 6th d post enrofloxacin treatment. This study demonstrated the reversible competitive type of inhibition of enrofloxacin on CYP450 enzymes, and with coadministration with monensin produced increased CK, AST and ALT serum enzymes suggesting heart and liver injury. Simultaneous administration of enrofloxacin and monensin even at recommended levels could result in adverse interactions.

Hepatotoxic alterations induced by subchronic exposure of rats to formulated fenvalerate (20% EC) by nose only inhalation

OBJECTIVE

Fenvalerate (20% EC) is a synthetic pyrethroid, which is commonly used in India by farmers for the protection of many food and vegetable crops against a wide variety of insects. However, its inhalation toxicity data is very limited in the literature due to the fact that the exposure levels associated with these effects were usually not reported. Hence, inhalation exposure was carried out to investigate the hepatotoxic effects.

METHOD

Adult male rats were exposed to fen for 4 h/day, 5 days a week for 90 days by using Flow Past Nose Only Inhalation Chamber. Sham treated control rats were exposed to compressed air in the inhalation chamber for the same period.

RESULTS

The results indicated hepatomegaly, increased activities of serum clinical enzymes (indicative of liver damage/dysfunction) along with pronounced histopathological damage of liver.

CONCLUSION

The hepatotoxic potential of formulated Fen (20% EC) in rats exposed by nose only inhalation is being reported for the first time and warrant adequate safety measures for human beings exposed to this insecticide, particularly by inhalation route.