Understanding the plant-pathogen interactions is of out most importance to design strategies for minimizing the economic deficits caused by pathogens in crops. With an aim to identify genes underlying resistance to downy mildew, a major disease responsible for productivity loss in pearl millet, transcriptome analysis was performed in downy mildew resistant and susceptible genotypes upon infection and control on 454 Roche NGS platform. A total of ~685 Mb data was obtained with 1 575 290 raw reads. The raw reads were pre-processed into high-quality (HQ) reads making to ~82% with an average of 427 bases. The assembly was optimized using four assemblers viz. Newbler, MIRA, CLC and Trinity, out of which MIRA with a total of 14.10 Mb and 93787 transcripts proved to be the best for assembling reads. Differential expression analysis depicted 1396 and 936 and 1000 and 1591 transcripts up and down regulated in resistant inoculated/resistant control and susceptible inoculated/susceptible control respectively with a common of 3644 transcripts. The pathways for secondary metabolism, specifically the phenylpropanoid pathway was up-regulated in resistant genotype. Transcripts up-regulated as a part of defence response included classes of R genes, PR proteins, HR induced proteins and plant hormonal signalling transduction proteins. The transcripts for skp1 protein, purothionin, V type proton ATPase were found to have the highest expression in resistant genotype. Ten transcripts, selected on the basis of their involvement in defence mechanism were validated with qRT-PCR and showed positive co-relation with transcriptome data. Transcriptome analysis evoked potentials of hypersensitive response and systemic acquired resistance as possible mechanism operating in defence mechanism in pearl millet against downy mildew infection.

Background/Objectives: Abiotic stresses such as salinity and drought significantly constrain crop cultivation and affect productivity. Quinoa (Chenopodium quinoa Willd.), a facultative halophyte, exhibits remarkable tolerance to drought and salinity stresses, making it a valued model for understanding stress adaptation mechanisms. The objective of this study was to identify and characterize Sodium/Hydrogen antiporter (NHX) genes from the quinoa genome and study their role in stress tolerance. Methods: We identified and characterized 10 NHX genes from the quinoa genome, which belong to the monovalent cation/proton antiporter 1 (CPA1) superfamily. Comprehensive analysis, including phylogenetic relationships, motif patterns, and structural characteristics, was performed to classify these genes into three subfamilies. Physicochemical properties such as isoelectric point (pI), GRAVY, and transmembrane domains were examined. Promoter analysis was conducted to identify cis-elements linked to abiotic stress responses, phytohormone signalling, and light regulation. qPCR analysis was used to assess the differential expression patterns of CqNHX genes under salt and drought stress. Results: The analysis revealed that the NHX genes were divided into three subfamilies localized to vacuolar, plasma, and endosomal membranes. These genes exhibited structural and functional diversity. Promoter analysis indicated the presence of cis-elements associated with abiotic stress responses, phytohormone signalling, and light regulation, suggesting diverse regulatory roles. qPCR analysis revealed differential expression patterns of CqNHX genes under salt and drought stress, with vacuolar NHXs showing higher induction in leaf tissues under salinity. This underscores their critical role in sodium sequestration and ion homeostasis. Evolutionary analysis indicated a high degree of conservation within subfamilies, alongside evidence of purifying selection. Conclusions: The findings enhance our understanding of the molecular basis of stress tolerance in quinoa and provide valuable targets for genetic engineering to improve crop resilience to environmental challenges.