Biology subjects

Bhalla, P. L.

Publications and source records attributed to Bhalla, P. L..

5 recordsLinked to original sources

bioRxiv2024

Heat-Triggered Transcriptional Reprogramming in Microspores Disrupts Progression of Pollen Development in Brassica napus L.

Rising temperatures due to climate change pose significant threats to global food security, particularly by impacting crop fertility and yield. Despite the known susceptibility of male reproductive development to heat stress, the specific adaptive mechanisms and critical regulatory genes involved in the stage-specific heat stress response in crops are still not well understood. This study examines the impact of acute heat stress on pollen development in Brassica napus (Canola), an essential oilseed crop, with a focus on the uninucleate microspore stage. We demonstrate that a brief exposure to 40{degrees}C during the uninucleate microspore stage results in loss of cellular polarity, failed asymmetric cell division, loss of cytoplasm, and pollen abortion, leading to a significant decline in pollen viability. Transcriptome analysis reveals the complexity of heat-induced transcriptional reprogramming in microspores, identifying 8.1% (6,245) of the expressed genes as responsive to high temperature, with a higher degree of downregulation. Fourteen differentially expressed transcription factors (TFs) belonging to diverse TF families were identified in heat-stressed microspores, with overrepresented target genes. The differential regulation of cell cycle control genes in heat-stressed microspores supports our microscopic observations and details the transcriptional reprogramming underlying the failure of heat-stressed microspores to undergo the first and second pollen mitotic divisions (PMI and PMII), resulting in aberrant pollen development in B. napus. Heat stress disrupts key biological pathways such as transcription, mRNA processing, translational control, protein homeostasis, autophagy, phytohormone signaling, and reactive oxygen species (ROS) homeostasis. Heat stress alters the intricate network of multiple signaling pathways, potentially disrupting the regulatory pathways underlying pollen development, with evident crosstalk underscoring the complexity of the heat stress response in pollen development. These findings underscore the critical vulnerability of the microspore stage to heat stress in Canola. Understanding the identified heat-responsive genes and regulatory networks provides valuable insights for breeding climate-resilient Canola varieties, thereby contributing to global food security amidst changing climatic conditions. HighlightsO_LIAcute heat stress during microspore stage in Brassica napus disrupts pollen development. C_LIO_LIHeat stress induces complex transcriptional reprogramming in microspores, with higher degree of downregulation. C_LIO_LITranscriptional control, RNA processing, coordination of protein homeostasis and translational control is altered in heat-stressed microspores C_LIO_LIMisregulation of cell cycle control genes supports the loss of cellular polarity and failure to undergo asymmetric cell division in heat stressed microspores. C_LI

plant biology↗

bioRxiv2022

Circular RNAs are Associated with Floral Fate Acquisition in soybean shoot apical meristem

Soybean (Glycine max), a major oilseed and protein source, requires a short-day photoperiod for floral induction. Though key transcription factors controlling flowering have been identified, the role of the non-coding (dark) genome is limited. circular RNAs (circRNAs) recently emerged as a novel class of RNAs with critical regulatory functions. However, a study on circRNAs during the floral transition of a crop plant is lacking. We investigated the expression and potential function of circRNAs in floral fate acquisition by soybean shoot apical meristem in response to short-day treatment. Using deep sequencing and in-silico analysis, we denoted 384 circRNAs, with 129 exhibiting short-day treatment-specific expression patterns. We also identified 38 circRNAs with predicted binding sites for miRNAs that could affect the expression of diverse downstream genes through the circRNA-miRNA-mRNA network. Notably, four different circRNAs with potential binding sites for an important microRNA module regulating developmental phase transition in plants, miR156 and miR172, were identified. We also identified circRNAs arising from hormonal signaling pathway genes, especially abscisic acid, and auxin, suggesting an intricate network leading to floral transition. This study highlights the gene regulatory complexity during the vegetative to reproductive transition and paves the way to unlock floral transition in a crop plant. HighlightA new class of regulatory RNAs, circular RNAs, modulate floral transition in a crop plant, soybean, by regulating hormonal pathways and post-transcriptional processes.

plant biology↗

bioRxiv2022

Genome-wide analysis of lncRNAs points to their roles in the modulation of developmental regulator expression during plant male germline development

LncRNAs can function in regulating of gene expression, but their roles as essential regulators of developmental processes and organismal phenotypes remain largely unclear. Especially the roles of lncRNAs in plants are largely unexplored. However, it has been proposed that plant lncRNAs act as regulators of protein-coding genes during development and that the similar roles of animal and plant lncRNAs result from convergent evolution. Since pollen development follows an established program with well-defined and characterized stages, we have used it as a model for studying plant lncRNAs and their roles in reproductive development. We investigated of lncRNA expression and function during pollen formation in field mustard (Brassica rapa). Reference-based transcriptome assembly performed to update the existing genome annotation identified novel expressed protein-coding genes and long non-coding RNAs (lncRNAs), including 4,347 long intergenic non-coding RNAs (lincRNAs, 1058 expressed) and 2,045 lncRNAs overlapping protein-coding genes on the opposite strand (lncNATs, 780 expressed). The analysis of expression profiles reveals that lncRNAs are significant and stage-specific contributors to the gene expression profile of developing pollen. Gene co-expression networks accompanied by genome location analysis identified 38 cis-acting lincRNA, 31 cis-acting lncNAT, 7 trans-acting lincRNA and 14 trans-acting lncNAT to be substantially co-expressed with target protein-coding genes involved in biological processes regulating pollen development and male lineage specification. These findings provide a foundation for future research aiming at developing strategies to employ lncRNAs as regulatory tools for gene expression control during reproductive development.

plant biology↗

bioRxiv2021

Non-coding circular RNAs repertoire and expression profile during Brassica rapa pollen development

Circular RNAs (circRNAs) are covalently closed long non-coding RNA (lncRNA) molecules generated by the back-splicing of exons from linear precursor mRNAs. Though linear lncRNAs have been shown to play important regulatory roles in diverse biological and developmental processes, little is known about the role of their circular counterparts. In this study, we have performed high-throughput RNA sequencing to delineate the expression profile and potential function of circRNAs during the five stages of pollen development in Brassica rapa. A total of 1180 circRNAs were detected in pollen development, of which 367 showed stage-specific expression patterns. Functional enrichment and metabolic pathway analysis showed that the parent genes of circRNAs were mainly involved in pollen-related molecular and biological processes such as mitotic and meiosis cell division, DNA processes, protein synthesis, protein modification, and polysaccharide biosynthesis. Moreover, by predicting the circRNA-miRNA network from our differentially expressed circRNAs, we found 88 circRNAs with potential miRNA binding sites suggesting their role in post-transcriptional regulation of the genes. Finally, we confirmed the back-splicing sites of 9 randomly selected circRNAS using divergent primers and Sanger sequencing. Our study presents the first systematic analysis of circular RNAs during pollen development and forms the basis of future studies for unlocking complex gene regulatory networks underpinning reproduction in flowering plants.

molecular biology↗

bioRxiv2018

MCRiceRepGP: a framework for identification of sexual reproduction associated coding and lincRNA genes in rice.

Sexual reproduction in plants underpins global food production and evolution. It is a complex process, requiring intricate signalling pathways integrating a multitude of internal and external cues. However, key players and especially non-coding genes controlling plant sexual reproduction remain elusive. We report the development of MCRiceRepGP a novel machine learning framework, which integrates genomic, transcriptomic, homology and available phenotypic evidence and employs multi-criteria decision analysis and machine learning to predict coding and non-coding genes involved in rice sexual reproduction.\n\nThe rice genome was re-annotated using deep sequencing transcriptomic data from reproduction-associated tissues/cell types identifying novel putative protein coding genes, transcript isoforms and long intergenic non-coding RNAs (lincRNAs). MCRiceRepGP was used for genome-wide discovery of sexual reproduction associated genes in rice; 2,275 protein-coding and 748 lincRNA genes were predicted to be involved in sexual reproduction. The annotation performed and the genes identified, especially the ones for which mutant lines with phenotypes are available provide a valuable resource. The analysis of genes identified gives insights into the genetic architecture of plant sexual reproduction. MCRiceRepGP can be used in combination with other genome-wide studies, like GWAS, giving more confidence that the genes identified are associated with the biological process of interest. As more data, especially about mutant plant phenotypes will become available, the power of MCRiceRepGP with grow providing researchers with a tool to identify candidate genes for future experiments. MCRiceRepGP is available as a web application (http://mcgplannotator.com/MCRiceRepGP/)\n\nSignificance statementRice is a staple food crop plant for over half of the worlds population and sexual reproduction resulting in grain formation is a key process underpinning global food security. Despite considerable research efforts, much remains to be learned about the molecular mechanisms involved in rice sexual reproduction. We have developed MCRiceRepGP, a novel framework which allows prediction of sexual reproduction associated genes using multi-omics data, multicriteria decision analysis and machine learning. The genes identified and the methodology developed will become a significant resource for the plant research community.

plant biology↗