@article {44479,
	title = {GA3 application in grapes (Vitis vinifera L.) modulates different sets of genes at cluster emergence, full bloom, and berry stage as revealed by RNA sequence-based transcriptome analysis},
	journal = {Functional \& Integrative Genomics},
	volume = {18},
	year = {2018},
	month = {JUL},
	pages = {439{\textendash}455},
	abstract = {In grapes (Vitis vinifera L.), exogenous gibberellic acid (GA3) is applied at different stages of bunch development to achieve desirable bunch shape and berry size in seedless grapes used for table purpose. RNA sequence-based transcriptome analysis was used to understand the mechanism of GA3 action at cluster emergence, full bloom, and berry stage in table grape variety Thompson Seedless. At cluster emergence, rachis samples were collected at 6 and 24 h after application of GA3, whereas flower clusters and berry samples were collected at 6, 24, and 48 h after application at full bloom and 3{\textendash}4 mm berry stages. Seven hundred thirty-three genes were differentially expressed in GA3-treated samples. At rachis and flower cluster stage respectively, 126 and 264 genes were found to be significantly differentially expressed within 6 h of GA3 application. The number of DEG reduced considerably at 24 h. However, at berry stage, major changes occurred even at 24 h and a number of DEGs at 6 and 24 h were 174 and 191, respectively. As compared to upregulated genes, larger numbers of genes were downregulated. Stage-specific response to the GA3 application was observed as evident from the unique set of DEGs at each stage and only a few common genes among three stages. Among the DEGs, 67 were transcription factors. Functional categorization and enrichment analysis revealed that several transcripts involved in sucrose and hexose metabolism, hormone and secondary metabolism, and abiotic and biotic stimuli were enriched in response to application of GA3. A high correlation was recorded for real-time PCR and transcriptome data for selected DEGs, thus indicating the robustness of transcriptome data obtained in this study for understanding the GA3 response at different stages of berry development in grape. Chromosomal localization of DEGs and identification of polymorphic microsatellite markers in selected genes have potential for their use in breeding for varieties with improved bunch architecture.},
	keywords = {Bunch architecture, GA3 response, Microsatellite markers, RNA seq, Transcription factors, Vitis vinifera},
	issn = {1438-793X},
	doi = {10.1007/s10142-018-0605-0},
	author = {Upadhyay, Anuradha and Maske, Smita and Jogaiah, Satisha and Kadoo, Narendra Y. and Gupta, Vidya S.}
}
@article {49886,
	title = {Harnessing microRNAs and their targets for salt stress tolerance in Pandanus odorifer},
	journal = {Journal of Plant Biochemistry and Biotechnology},
	volume = {34},
	year = {2025},
	month = {SEP},
	pages = {714-730},
	type = {Article},
	abstract = {<p>
	Salinity poses a formidable challenge to agriculture, detrimentally impacting plant growth and the yield of several crops globally. Pandanus odorifer (Forssk.) Kuntze is a highly salt-stress resilient plant that grows naturally along the coastal regions of Asia, Southeast Asia, and Polynesia. It is frequently found as a frontier species along the sandy shores receiving constant salt sprays. MicroRNAs (miRNAs) play essential regulatory roles in growth, development, and combating various biotic and abiotic stresses. Thus, characterizing miRNAs and their targets is critical to understanding their roles in salt stress tolerance. Through a rigorous analysis based on homology, secondary structure and signatures of other miRNA genes, we identified 52 conserved nonredundant miRNAs from the P. odorifer transcriptome data. These miRNAs were diverse and belonged to 23 miRNA phylogenetic families. Several miRNAs, including pod-MIR156a, pod-MIR164d, and pod-MIR535d, demonstrated distinct expression patterns in response to salt stress. Their target genes exhibited opposing expression trends, corroborating the intricate miRNA-target relationship. Delving deeper into their influence, we discovered that these miRNAs mainly targeted transcription factors that are known for their pivotal roles in stress responses. We also detected four miRNA-star (miRNA*) sequences (the complementary strands of functional mature miRNAs), which supports the authenticity of the identified miRNAs. This study unveils the intricate regulatory mechanism through which miRNAs may reinforce salt stress tolerance in P. odorifer, providing a promising avenue for enhancing crop resilience to various stresses through miRNA-based strategies.</p>
},
	keywords = {Abiotic stress, microRNA, miRNA targets, Salinity tolerance, salt stress, Transcription factors},
	issn = {0971-7811},
	doi = {10.1007/s13562-025-00971-y},
	author = {Rashmi, Deo and Barvkar, Vitthal T. and Nadaf, Altafhusain B. and Kadoo, Narendra Y.}
}
@article {49702,
	title = {Transcriptome analyses reveal TaWRKY41 as a potential candidate governing spot blotch resistance in wheat},
	journal = {Physiology and Molecular Biology of Plants},
	volume = {31},
	year = {2025},
	month = {APR},
	pages = {591-608},
	type = {Article},
	abstract = {<p>
	Spot blotch disease caused by Bipolaris sorokiniana poses a significant threat to wheat production. Cultivation of disease-resistant wheat genotypes appears to be the most practical approach to mitigate the impact of this devastating disease. However, the molecular responses of wheat plants during spot blotch disease progression remain poorly understood. This study employed RNA-sequencing to unravel the spatiotemporal molecular events underlying the resistance mechanism in the spot blotch susceptible and resistant wheat genotypes. This study further provides a comprehensive overview of differentially expressed transcripts through functional analysis and transcription factor identification, elucidating the biological mechanisms governing wheat-B. sorokiniana interaction. In the resistant genotype, the expression of one of the key transcription factors, TaWRKY41, was significantly induced upon pathogen inoculation. Computational studies, electrophoretic-mobility shift assay, and yeast one-hybrid assay confirmed the interaction of the recombinant TaWRKY41 protein with W-box elements present in the promoters of plant defense-related genes. Furthermore, co-expression network analyses identified downstream genes positively correlated with TaWRKY41, providing insights into their probable involvement in the defense response. Overall, our investigation suggests that TaWRKY41 contributes to spot blotch resistance in wheat. This knowledge can help develop new disease-resistant wheat varieties.</p>
},
	keywords = {Plant defense, plant-pathogen interaction, TaWRKY41, Transcription factors, Transcriptomics},
	issn = {0971-5894},
	doi = {10.1007/s12298-025-01583-5},
	author = {Dayama, Bhakti R. and Mahadik, Varsha A. and Somani, Deepika and Shinde, Balkrishna A. and Kondhare, Kirtikumar R. and Karthikeyan, Muthukumarasamy and Kadoo, Narendra Y.}
}
