Plant & Food Research

Rapid population growth poses a major challenge to global food security. Promoting sustainable agricultural production is necessary to ensure global food security. Horticultural plants are a high-valued part of agricultural production. Virus and viroid diseases have long been a key factor limiting horticultural production. Cultivating and distributing pathogen-free plants is currently the most efficient practice for managing virus and viroid diseases and their spread in the landscape. Cryotherapy-based methods are recently developed novel biotechnologies for the efficient production of pathogen-free plants. This review outlines updated information on the development and advances in cryotherapy-based methods for efficiently eradicating viruses and viroids in horticultural plants. Mechanisms underlining cryotherapy-based methods for improved pathogen eradication are discussed, and suggestions for further studies are proposed.

• The intergenic small open reading frames of grape genome were comprehensive identified. • Most nsORFs were transcriptionally active under stress. • This study fills the gap of neglected intergenic sORFs in grape. High-throughput sequencing has greatly deepened our understanding of genomic information. However, due to the limitation of software threshold setting, many existing short fragment genes that actually exist are missed. For example, the intergenic region, which is regarded as a ‘black box’ of the genome, contains vast amounts of information and is worthy of greater efforts to explore. This study presents a comprehensive identification of 3357,289 small open reading frames (sORFs) within the intergenic regions of grape genome, which resulted in 2884,287 novel sORFs (nsORFs) after excluding UniProt-matched sORFs. To further investigate these functions, we assessed the Codon Adaptation Index (CAI) of the nsORFs’ and selected 2433,873 with CAI ≥ 0.7 for subsequent analysis. Using the Rfam database, we identified 1312 nsORFs matching known non-coding RNA (ncRNA) families.A total of 781 nsORFs were jointly identified by both SignalP-5.0 and NLStradamus and were classified as signal peptides. Using transcriptome data from grape powdery mildew and salt stress studies, we found 236,843 and 145,938 transcriptionally active nsORFs with CAI ≥ 0.7, respectively. Gene Ontology (GO) annotation of six powdery mildew-associated nsORFs indicated their involvement in stress response. Our research focused on previously overlooked intergenic sORFs in the grape genome, enhancing genomic annotations and providing a foundation for discovering novel gene regulatory mechanisms.

Phytophthora pluvialis is a pathogen present in the United States, New Zealand, the United Kingdom, and Belgian forests. Reported hosts include Douglas-fir in the United States, New Zealand, the United Kingdom, and Belgium, as well as tanoak in the United States, radiata pine in New Zealand, and Japanese larch and western hemlock in the United Kingdom. Disease symptoms range from needle lesions and casting on radiata pine through to twig and stem cankers and crown dieback on western hemlock, Douglas-fir, and Japanese larch. Current detection methods rely on isolation and culture or PCR targeting a single-copy gene (ypt1). A qPCR assay targeting a multiple-copy mitochondrial gene (Cytochrome c oxidase subunit 2 [cox2]) was designed to increase the sensitivity of P.pluvialis detection, critical for early diagnostics. The resulting assay has a detection limit of 12.8 fg of mycelial DNA, detecting the pathogen on average 6.12 qPCR cycles before the ypt1 assay. In New Zealand samples, the assay was found to consistently detect P.pluvialis in all stages of needle disease symptoms, from early asymptomatic infection to fully cast needles. The new assay allowed for asymptomatic detection of P.pluvialis in pine needles 4 weeks before visual symptoms of disease were observed. The availability of a highly sensitive assay has enabled diagnostic support of the biosecurity response in the United Kingdom during recent detection of P.pluvialis. The assay has been used in applications requiring detection at low pathogen titer levels, including asymptomatic infection, stream baiting, cast needles, and biosecurity response, demonstrating its efficacy for early detection of P.pluvialis in affected forests.

Information on seed viability and understanding of the specific nutritional requirements for asymbiotic seed germination of orchid species are essential for successful production of plantlets for either conservation or commercial breeding programmes. We compared seed viability and in vitro seed germination of three rare and threatened neotropical epiphytic orchid species from the Lycaste genus . Viability was assessed using a Tetrazolium test (TTC) and in vitro germination was evaluated on three culture media [Murashige and Skoog (MS), Knudson C (KC) and basic culture media 1 (BM-1)]. All species exhibited high seed viability (above 70%) but relatively low germination (below 30%) across all media tested. Although seeds germinated on all media tested, MS media showed the highest germination and high-quality plantlets. However, the fact that seed germination did not reach the highest potential, as indicated by the TTC viability test, signifies that further optimisation of in vitro germination media is required. We discuss the reasons behind the gap between viability and germination and suggest avenues for future research. These findings highlight the need for species-specific media optimisation to bridge the gap between seed viability and germination, and to establish effective conservation protocols for these threatened orchids.

Abstract Projections for climate change potentially mean that tidally exposed seaweeds will experience greater air temperature extremes than those that remain immersed. This study investigated the combined effects of temperature and humidity on the relative growth rate of Fucus vesiculosus through two controlled experiments: (1) evaluating responses to various temperature and humidity regimes, and (2) assessing the impact of three consecutive days of heatwave conditions (25 °C). Samples from the upper and lower shore were subjected to 24, 30 and 40 °C at relative humidities of 30–90 % for 4 or 8 h, using an incubator oven to generate six vapour pressure deficit (VPD) levels (0.3–5.3 kPa). A VPD of 5.3 kPa proved detrimental to the seaweeds regardless of duration. In contrast, F. vesiculosus tolerated a VPD of 2.4 kPa for up to 8 h. Little difference was detected between upper and lower shore residing specimens. Heatwave conditions did not negatively affect F. vesiculosus growth irrespective of shore location. Blades could recover from proportional water biomass loss of up to 0.6 but not from a loss of 0.7 regardless of VPD. Nonetheless, greater VPD values tended to coincide with increased water biomass loss and decreased post-exposure growth. These findings suggest that increased humidity may mitigate thermal stress, enhancing resilience under projected climate scenarios.