Biology subjects

Whelan, C. V.

Publications and source records attributed to Whelan, C. V..

3 recordsLinked to original sources

bioRxiv2023

Transcriptional signatures associated with waterlogging stress responses and aerenchyma formation in barley root tissue

The negative impact of soil waterlogging on crop production is expected to increase due higher frequencies of extreme rainfall events arising from climate change. Consequently, understanding the molecular mechanisms that enable plants to mitigate waterlogging stress is critical for breeding programmes, particularly in the case of waterlogging-susceptible crop species, such as barley (Hordeum vulgare). Aerenchyma formation is a key morphological adaptation allowing plants to cope with waterlogging stress and hypoxic conditions, however, the genetic regulation of its development in barley remains largely unresolved. In this study, two barley cultivars with contrasting waterlogging tolerance (Franklin and Yerong) were subjected to waterlogging stress, followed by analysis of phenotypic traits including root aerenchyma formation, and transcriptomic profiling of root tissue samples. Differential expression analyses identified genes transcriptionally responsive to 24 and 72 h of waterlogging in both cultivars, and highlighted metabolic adaptations, regulation of ROS signalling and management of stress responses as key elements of the waterlogging response. The results revealed large intra-individual variations in root aerenchyma formation, and these variations were exploited to isolate 81 candidate aerenchyma-associated genes from the generated RNA-seq datasets. Network analyses suggest the involvement of the DNA damage response gene, DRT100 and cell wall modifying genes, XHT16 and XHT15 as regulatory hub genes in aerenchyma formation. Collectively, the generated data provide insights into transcriptional signatures associated with the barley root responses to waterlogging and aerenchyma formation, informing our understanding of strategies that plants employ to cope with the negative impacts of heavy rainfall.

plant biology↗

bioRxiv2023

Arabidopsis cell suspension culture and RNA sequencing reveal regulatory networks underlying plant programmed cell death.

Programmed cell death (PCD) facilitates targeted elimination of redundant, damaged, or infected cells via genetically controlled pathways. In plants, PCD is often an essential component of normal development and can also mediate responses to abiotic and biotic stress stimuli. However, studying the transcriptional regulation of this fundamental process is hindered by difficulties in sampling small groups of cells undergoing PCD that are often buried within the bulk of living plant tissue. We addressed this challenge by using RNA sequencing (RNA-Seq) of Arabidopsis thaliana suspension cells, a system that allows precise monitoring of PCD activation and progression. The use of three PCD-inducing treatments (salicylic acid, heat and critical dilution), in combination with three cell death modulators (3- methyladenine, lanthanum chloride and conditioned medium), allowed isolation of candidate core and stimuli-specific PCD genes, inference of underlying gene regulatory networks and identification of putative transcriptional regulators. This analysis underscored cell cycle disturbance and the repression of both pro-survival stress responses and mitochondrial retrograde signalling as key elements of the PCD-associated transcriptional signature in plants. Further, phenotyping of twenty Arabidopsis T-DNA insertion mutants in selected candidate genes confirmed a role for several in PCD and stress tolerance regulation, and validated the potential of these generated resources to identify novel genes involved in plant PCD pathways and/or stress tolerance in plants.

plant biology↗

bioRxiv2017

Population level mitogenomics of the long-lived Greater Mouse-eared bat, Myotis myotis, reveals dynamic heteroplasmy and challenges the Free Radical Theory of Ageing

BackgroundBats are the only mammals capable of true, powered flight, which drives an extremely high metabolic rate. The \"Free Radical Theory of Ageing\" (FTRA) posits that a high metabolic rate leads to mitochondrial heteroplasmy and the progressive ageing phenotype. Contrary to this, bats are the longest lived order of mammals despite their small size and high metabolic rate. To investigate if bats exhibit increased mitochondrial heteroplasmy with age as predicted by the FRTA, we performed targeted, deep sequencing of mitogenomes and measured point heteroplasmy in wild, long lived Myotis myotis as they age.\n\nResultsIn total, blood was sampled from 195 individuals, aged between <1 and at 6+ years old, and whole mitochondria were sequenced, with a subset sampled over multiple years. The majority of heteroplasmies, 77.6%, were at a frequency below 5%. Oxidative mutations were not the primary source of heteroplasmies and present in only a small number of individuals, likely representing local oxidative stress events. There was a significant positive correlation between age and heteroplasmy, with a rate of increase of 0.13 sites per year. Longitudinal data from recaptured individuals show heteroplasmy is dynamic, and does not increase uniformly over time.\n\nConclusionsWe show that bats do not suffer from the predicted, inevitable increase in heteroplasmy which underscores the FRTA. Most heteroplasmies were at low frequency and are primarily transitions. Heteroplasmy increased with age, however how this contributes to ageing is unclear, as heteroplasmy was dynamic, questioning its presumed role as a primary driver of ageing.

genomics↗