Biology subjects

McCabe, P. F.

Publications and source records attributed to McCabe, P. F..

8 recordsLinked to original sources

bioRxiv2024

FT-like genes in Cannabis and hops: sex specific expression and copy-number variation may explain flowering time variation

Cannabis sativa is a fascinating, yet under-researched, species. To facilitate the global expansion of C. sativa cultivation a greater understanding of flowering time control is crucial. The PEBP gene family consists of universal promoters and repressors of flowering, with homologs of FLOWERING LOCUS T (FT) being highly conserved key regulators of flowering. FT encodes florigen, and balancing the florigen and anti-florigen signals is key for fine-tuning a crops flowering to local climatic conditions. Here, we provide an in-depth characterisation of the PEBP gene family in C. sativa and the closely related species H. lupulus. Phylogenetic analysis reveals expansion of FT and TFL1/CEN clades in the Cannabaceae. The retention of the duplicated PEBP genes likely has functional significance with divergent sequences and expression patterns hinting at signatures of sub-functionalisation. We speculate that duplicated PEBP genes have been crucial to the evolution of photoperiod insensitivity and sexually dimorphic flowering in C. sativa and harnessing the available genetic variation for these traits will be key for establishing this future crop.

plant biology↗

bioRxiv2023

The polyamines spermine and spermidine inhibit or induce programmed cell death in Arabidopsis thaliana in vitro and in vivo in a dose dependent manner.

Polyamines are ubiquitous biomolecules with a number of established functions in eukaryotic cells. In plant cells, polyamines have previously been linked to abiotic and biotic stress tolerance, as well as to the modulation of programmed cell death (PCD), with contrasting reports on their pro-PCD and pro-survival effects. Here, we used two well established platforms for the study of plant PCD; Arabidopsis thaliana suspension cultures cells and the root hair assay, to examine the roles of the polyamines spermine and spermidine in the regulation of PCD. We demonstrate that both polyamines can trigger PCD when applied exogenously at higher doses, whereas at lower concentrations they inhibit PCD induced by both biotic and abiotic stimuli. Furthermore, we show that concentrations of polyamines resulting in inhibition of PCD generated a transient ROS burst in our experimental system, and activated the expression of oxidative stress- and pathogen response-associated genes. Finally, we examined PCD responses in existing Arabidopsis polyamine synthesis mutants, and identified a subtle PCD phenotype in Arabidopsis seedlings deficient in thermo-spermine. The presented data show that polyamines can have a role in PCD regulation, however that role is dose-dependent and consequently they may act as either inhibitors, or inducers, of PCD in Arabidopsis.

plant biology↗

bioRxiv2023

Exploring phenotypic and genetic variability in hemp (Cannabis sativa)

Hemp (Cannabis sativa L.) is a high-value multi-purpose crop with applications ranging from the medicinal use of its secondary metabolites to carbon-sequestering building materials. To fully capitalise on the potential of hemp as a crop for more sustainable agriculture, detailed phenotypic and genotypic characterizations are required in order to inform targeted breeding programmes. Here, we present a detailed morphological and genomic analysis of 10 hemp cultivars. We found high variability in agronomically important traits such as flowering time, plant height, and biomass in most of the hemp cultivars tested. Additionally, genotyping by sequencing demonstrates that genetic differences are pervasive, both between hemp cultivars as well as between individuals of a single cultivar. The significant genetic and phenotypic variability we observe in hemp contrasts with other crops, where cultivars are often phenotypically and genetically relatively uniform. We argue that the variability of hemp is an asset for breeding and increases the potential for further improvement of the crop but is also a challenge for todays highly automated agriculture that relies on phenotypic uniformity. Author summaryHemp (Cannabis sativa L.) stands as one of the earliest domesticated crops. This remarkable plant is a sustainable crop with high carbon sequestration capacity which can be cultivated for soil remediation. Furthermore, hemp oil and fibre are used for many applications ranging from cooking to manufacturing bioplastics, textiles, or building materials of superb characteristics, and its secondary metabolites are sought after because of their medicinal properties. However, in contrast to many modern crops, hemp exhibits extensive variability in key agricultural traits, such as plant height and flowering time. This variability presents a challenge for both farmers and processors. To unravel the fundamentals of hemp diversity we conducted a comprehensive study of phenotypic and genetic characterisation of ten diverse hemp cultivars. We present findings confirming substantial variability not only among individuals of different cultivars but also within the same cultivar. Additionally, we explore heterozygosity in the context of other hemp studies and other crops. Understanding this variability in the context of a single hemp cultivar and across multiple cultivars is paramount for breeding novel, more uniform hemp varieties which will allow us to unlock the full potential of hemp as a crop of the future.

plant biology↗

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

A FLOWERING LOCUS T ortholog is associated with photoperiod-insensitive flowering in hemp (Cannabis sativa L.)

Hemp (Cannabis sativa L.) is an extraordinarily versatile crop, with applications ranging from medicinal compounds to seed oil and fibre products. Cannabis sativa is a short-day plant, and its flowering is tightly controlled by photoperiod. However, substantial genetic variation exists for photoperiod sensitivity in C. sativa, and photoperiod-insensitive ("autoflower") cultivars are available. Using a bi-parental mapping population and bulked segregant analysis, we identified Autoflower2, a 0.5 Mbp locus significantly associated with photoperiod-insensitive flowering in hemp. Autoflower2 contains an ortholog of the central flowering time regulator FLOWERING LOCUS T (FT) from Arabidopsis thaliana which we termed CsFT1. Extensive sequence divergence between alleles of CsFT1 was identified between photoperiod-sensitive and insensitive cultivars of C. sativa, including a duplication of CsFT1 and sequence differences especially in introns. Genotyping of several mapping populations and a diversity panel confirmed a strong correlation between CsFT1 alleles and photoperiod response as well as affirming that at least two independent loci for this agriculturally important trait, Autoflower1 and Autoflower2, exist in the C. sativa gene pool. This study reveals the multiple independent origins of photoperiod insensitivity in C. sativa, supporting the likelihood of a complex domestication history in this species. By integrating the genetic relaxation of photoperiod sensitivity into novel C. sativa cultivars, expansion to higher latitudes will be permitted, thus allowing the full potential of this versatile crop to be reached.

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↗

bioRxiv2022

A protocol for rapid generation cycling (speed breeding) of hemp (Cannabis sativa) for research and agriculture

Hemp (Cannabis sativa) is a highly versatile multi-purpose crop with a multitude of applications, from textiles, biofuel and building material to high-value food products for consumer markets. Furthermore, non-hallucinogenic cannabinoids like cannabidiol (CBD), which can be extracted from female hemp flowers, are potentially valuable pharmacological compounds. In addition, hemp has high carbon sequestration potential due to its rapid growth rate. Therefore, the hemp industry is gaining more traction and breeding hemp cultivars adapted to local climate conditions or bred for specific applications is becoming increasingly important. Here, we present a method for rapid generation cycling (speed breeding) for hemp. The speed breeding protocol makes use of the photoperiod sensitivity of Cannabis. It encompasses vegetative growth of the plants for two weeks under continuous light, followed by flower induction, pollination and seed development for four weeks under short-day conditions and a seed ripening phase under continuous light and water stress. With the protocol introduced here, a generation time of under nine weeks (61 days) from seed to seed can be achieved. Our method furthermore synchronises flowering time of different hemp cultivars, thus facilitating crosses between cultivars. The extremely short generation time will enable hemp researchers and breeders to perform crosses in a time-efficient way and generate new hemp cultivars with defined genetic characteristics in a shorter amount of time.

plant biology↗

bioRxiv2020

The nitrogen-fixing symbiotic cyanobacterium, Nostoc punctiforme can regulate plant programmed cell death

Cyanobacteria such as Nostoc spp. can form nitrogen-fixing symbioses with a broad range of plant species. Unlike other plant-bacteria symbioses, little is understood about the immunological and developmental signalling events induced by Nostoc cyanobionts (symbiotic cyanobacteria). Here, we used suspension cell cultures to elucidate the early molecular mechanisms underpinning the association between cyanobionts and plants by studying the effects of conditioned medium (CM) from Nostoc punctiforme cultures on plant programmed cell death (PCD), a typical immune response activated during incompatible interactions. We showed that N. punctiforme-CM could suppress PCD induced by a temperature stress. Interestingly, this was preceded by significant transcriptional reprogramming, as evidenced by the differential regulation of a network of defence-associated genes, as well as genes implicated in regulating cell growth and differentiation. This work is the first to show that cyanobionts can regulate PCD in plants and provides a valuable transcriptome resource for the early immunological and developmental signalling events elicited by Nostoc cyanobionts.

plant biology↗