Annals of Applied Biology最新文献

CCR4-associated factor 1 (CAF1), a key component of the CCR4-NOT complex, plays a central role in transcriptional regulation and mRNA degradation in several plants. Despite its importance, no studies have yet explored the molecular phylogeny and expression patterns of the CAF1 gene in the stress response in common beans. Through genome-wide analysis, 27 PvCAF1 genes were identified, with gene sizes ranging from 108 to 618 amino acids and predicted molecular weights between 25.7 and 116.1 kDa. Phylogenetic analysis classified the PvCAF1 genes into four distinct groups, and their chromosomal distribution revealed that PvCAF1 genes were mostly located on chromosome 2, with 15 genes. Gene structure analysis showed that 74% of the PvCAF1 genes were intronless, while others exhibited varied exon-intron arrangements. Gene duplication analysis identified nine duplication events, with Ka/Ks ratios indicating purifying selection. Synteny analysis showed that PvCAF1 genes have the highest homology with those in Solanum lycopersicum and Arabidopsis thaliana. Cis-regulatory elements (CREs) identified in the promoters of these genes revealed that growth and development regulatory elements, particularly light-responsive elements, were the most abundant (73.36%). Stress-responsive CREs such as drought inducibility (MYB) and low-temperature responsiveness (LTR) were also found. Protein–protein interaction analysis highlighted 32 key nodes with high interaction degrees. Expression analysis of PvCAF1 genes under different growth conditions, such as in the presence of drought (PEG), salinity (NaCl), ABA, and IAA, demonstrated the upregulation of PvCAF1 genes, indicating their involvement in response to stimuli. PvCAF1-22 and PvCAF1-23 showed the highest expression under PEG and NaCl treatments, peaking at 4.9-fold and 7.2-fold at 24 h, respectively. PvCAF1-27 responded most strongly to IAA and PEG, reaching 6.1-fold at 48 and 24 h. These findings support the importance of PvCAF1 in developing drought and salinity-tolerant bean varieties, enhancing crop productivity in changing environmental conditions.

Varroa destructor is an ectoparasite that has been identified as the primary pathogen of the western honey bee, Apis mellifera, globally. Investigating the genetic variations of this mite in different geographical regions is crucial for understanding its population dynamics and evolutionary potential. Genetic diversity data are essential for tracking its spread, identifying emerging lineages, and developing effective control strategies. The objective of this study was to investigate haplotype diversity, genetic variation and population structure by in silico phylogenetic analysis of mitochondrial cox1 and cytb gene sequences of V. destructor isolates submitted to GenBank from different regions of the world. For this purpose, 509 sequences covering 399 bp of the cox1 gene region and 215 sequences covering 628 bp of the cytb gene region were used for the analyses. A total of 37 polymorphic sites and 24 haplotypes were identified in the cox1 sequences, while 31 polymorphic sites and 23 haplotypes were observed in the cytb region. Both gene regions exhibited high negative values for diversity and neutrality indices, indicating possible recent population expansion or selective pressures. This study also evaluated single nucleotide polymorphisms (SNPs) within GenBank-derived sequences and analysed their impact on haplotype differentiation and population structure. The results revealed considerable haplotype diversity, including several region-specific variants and potential signs of recent population expansion. The findings highlight ongoing microevolution within V. destructor populations, likely driven by host movement, acaricide use and ecological pressures. These insights are vital for apiculture, as the spread of genetically diverse and potentially more virulent mite lineages could undermine mite control efficacy and honey bee health. Future surveillance efforts should integrate genetic monitoring into management practices to support sustainable beekeeping worldwide.

Yellow Canopy Syndrome (YCS) is a complex that currently only affects commercial sugarcane (Saccharum sp. hybrids) in Australia. It was first detected in Far North Queensland over a decade ago and has since spread to most cane-growing areas from Far North Queensland down to Southern Queensland. YCS represents a serious challenge to not only the Australian sugarcane industry but also a potential threat to sugarcane industries worldwide. The symptoms and physiological impacts of YCS have been well described. However, despite a decade of research, the underlying causal factor(s) of YCS still need to be fully determined. Multidisciplinary research has focused on several abiotic and biotic factors to determine the symptoms and potential causes of YCS. Although not yet conclusive, the most recent research findings exploring the impact of pesticide application on YCS symptom expression levels indicate that invertebrates may play a role. Furthermore, studies have focused on optimising invertebrate sampling strategies and exploring their population dynamics in relation to YCS expression to determine which invertebrate species may be involved. Other research involves developing effective detection and surveillance approaches for YCS. This report reviews the YCS-related research published to date. It concludes that there are still some fundamental knowledge gaps that need to be addressed before the risk to other sugarcane-producing countries other than Australia can be determined and before effective YCS management strategies can be developed.

CRISPR/Cas9 technology is a widely used plant breeding innovation that employs site-directed nucleases to target and modify DNA with great accuracy. It has received significant attention in recent years due to its broad range of applications, including biological research of gene function and breeding new plant varieties. After genome editing reagents are delivered into plant cells, a fast, simple, accurate, and cost-effective method is necessary to confirm the successful occurrence of genetic changes in the samples. In this study, we explored the use of two PCR-based methods: real-time PCR (qPCR) and digital PCR (dPCR) for detecting mutations induced by CRISPR/Cas9 in transformed protoplast samples. Designed primers and probes were tested in a duplex qPCR assay, and dPCR was employed for higher sensitivity. Using the qPCR method, we confirmed mutations in 80% of the samples, while with dPCR we could confirm mutations in all tested samples. Both methods were compared with next-generation sequencing (NGS) results, and dPCR showed more comparable mutation frequencies than qPCR. Overall, both methods effectively distinguished edited from wild-type protoplasts and provide time-saving, cost-efficient alternatives to traditional molecular tools for detecting gene-edited mutations. Furthermore, they could be used to quantify induced mutations, with dPCR offering higher sensitivity but at a higher cost than qPCR.

Nematodes are among the most diverse and abundant animal groups on our planet, and play key roles in ecosystems, agriculture and human health. This review explores their contributions from a One Health perspective, highlighting their impact on environmental, plant, animal and human well-being. Free-living nematodes are essential for nutrient cycling, decomposition and microbial regulation, and their responsiveness to various types of environmental perturbations makes them invaluable bioindicators. In agriculture, nematodes play a dual role: plant-parasitic species pose serious threats to crops, whereas free-living and entomopathogenic nematodes (EPNs) support sustainable farming by promoting soil health and serving as biocontrol agents. Advances in molecular tools, such as eDNA metabarcoding, have enhanced their use in environmental biomonitoring programmes. In biomedical research, Caenorhabditis elegans has advanced studies on disease, aging and drug discovery, whereas EPNs and marine nematodes show the potential to address antibiotic resistance. This review emphasizes the need for interdisciplinary efforts to fully leverage the ecological, agricultural and biomedical potential of nematodes and to demonstrate their value within the One Health framework in tackling global challenges.

Soil-borne diseases are responsible for huge crop losses worldwide. A deeper understanding of plant–soil–microbe interactions in the presence of soil-borne pathogens is needed for the integrated management of soil-borne diseases and tailored use of rhizosphere microbiomes for plant and soil health. In this review, we examine how soil-borne pathogens influence rhizosphere microbiomes at the compositional and functional levels, and how the study of pathobiomes allows the identification of key microbial taxa that prevent or contribute to disease development. Although soil-borne pathogens induce contrasting effects on rhizosphere microbial diversity, shifts in rhizosphere microbiome structure and function have been consistently reported in a wide range of pathosystems. These shifts are induced by changes in root exudate patterns upon infection and subsequent defence response activation, and by the recruitment of beneficial microbial taxa by the infected plants. A better understanding of these alterations could help detect functional shifts linked with the plant defence response and identify resistance markers, thus opening new avenues for plant breeding or microbiome manipulation. Moreover, incorporating the pathobiome concept into the design of disease management strategies would assist in pinpointing possible biocontrol agents and identifying biomarkers for early disease detection. We advocate for future pathobiome studies to gain mechanistic insights on the interactions between pathogens and plant microbiomes in non-model pathosystems and perform validation experiments to unravel how cross-talk within the pathobiome may lead to disease development or suppression.

Subterranean clover (Trifolium subterraneum) is a legume suitable for summer dry environments in New Zealand where rainfall is <900 mm/year. However, limited knowledge of phenology of different commercially available cultivars of subterranean clover, particularly flowering time, currently restricts the development of best management practices that optimise vegetative plant growth while also ensuring adequate seed set under different environments. In a field study, four commercial, Australian cultivars (‘Antas,’ ‘Denmark,’ ‘Leura’ and ‘Woogenellup’) were compared for flowering time across sowing dates. For each cultivar, the number of days to flower decreased around 30% from 215 days as the sowing date was delayed from February to May. The thermal time to flowering averaged 1944 ± 102^oCd, or approximately 600^oCd longer than found for Australia. Flowering time was positively related (R² = 0.97) to temperature and modified by the photoperiod duration and direction. A model and historical weather data were used to predict flowering and grazing periods (GPs) for two New Zealand locations (i) Lincoln (South Island) and (ii) Hastings (North Island). Four establishment times (February–May) were considered based on the time of opening rains and the ‘safe graze’ start time. For both locations, an early subterranean clover establishment on 1 February provided the longest GP, up to 217 ± 13 days in Lincoln and 172 ± 8 days in Hastings. At Lincoln, the GP was on average 34 days longer than in Hastings because of the later flowering time. The plant establishment in May resulted in the shortest GP, 122 ± 8 days in Lincoln and 104 ± 6 days in Hastings. The coefficients calculated should allow specific dryland management strategies to be tailored for different environments to optimise the time of grazing, but still allow subterranean clover to flower and seed set.

Effective pollination management is essential for optimised yields in animal-pollinated crops. Sweet cherry (Prunus avium) is a crop with 82% of its production associated with animal pollination. Therefore, factors impacting pollination play a key role in sweet cherry production. These factors are often accounted for in pollinator management and orchard design; however, flower phenology, cultivar compatibility, and their impacts on yield are poorly understood and often not considered. We investigated how flowering overlap among cultivars and cultivar inter- and self-compatibility impact sweet cherry cultivars' suitability as pollen donors and recipients in Beira Interior, a key production region in Portugal. For this, we performed floral biology experiments in the field and under controlled greenhouse conditions. We compared the pollination success of compatible cultivars sharing one S-allele or none. We also assessed pollinator dependence and pollen limitation levels of the studied cultivars, as well as natural pollen deposition and fruit set levels. We observed that, although often overlooked, flower phenology is very important for determining suitable cultivar pairings, and flowering overlaps differ greatly from the existing literature, likely reflecting regional responses. Controlled hand pollination experiments revealed that pollen tube growth, a more straightforward and feasible pollination metric than fruit set in a mass-flowering crop with naturally low fruit set, can be effectively used to assess compatibility levels. Crossings between cultivars without common S-alleles and between cultivars sharing one S-allele resulted in similar pollen tube numbers and fruit set levels, indicating that both pairing types are suitable. Additionally, we detected pollination deficits in the studied cultivars, likely resulting from inadequate pollination services or poor pollen donor availability in the orchard. Altogether, we estimated the cultivar suitability of 81 different pairs of sweet cherry for the Beira Interior region. Our study highlights the importance of considering plant-related factors, namely flower phenology and cultivar compatibility, to develop targeted and effective management guidelines for sweet cherry producers, emphasising the significant impact these factors can have on production and the necessity of including them in orchard management and design.

Bacterial canker caused by Gram-positive Clavibacter michiganensis subsp. michiganensis (Cmm) bacteria is a devastating disease of varied plant hosts. The host selection and pathogenicity are varied among different isolates based on genomic variations. Here, the genomes of 12 Cmm and a reference (PD223) isolate were successfully sequenced, assembled, and annotated utilising next-generation sequencing and comparatively analysed. The pathogenicity screens revealed that four of the isolates possess a higher disease severity index (DSI) (75%–85%); whilst some others have a lower DSI (18%–25%). Sequencing yielded an average of 7.46 Gbp for each strain covering the genome size in 2200× depth. A reference-based genome assembly approach provided nearly complete genomes for the Cmm strains. Orthologous group analysis of the sequenced genomes revealed that 2847 (83%) clusters were conserved across all Cmm strains. Additionally, 73 clusters were shared by only three strains, indicating possible gene gain events leading to genetic divergence among Cmm strains. On average, 3280 proteins were annotated for the Cmm assemblies, which indicated the pathogenicity-associated gene families: serine proteases, cellulases (celA and celB), xylanases (xysA and xysB), pectinases (pelA1 and pelA2), and tomatinase (tomA). Phylogenetic and sequence analyses revealed their high conservation among different Cmm isolates. There was no correlation between the gene repertoire and the pathogenicity observed in the plants, and there may be other factors influencing the expression of these genes or possibly other virulence genes that have not been reported.

Common bean is an important legume largely used for its nutritional benefits. However, several factors affect its productivity, including the lack of improved varieties that produce higher yields and the optimal plant density required for better growth. Thus, during the 2019–2020 cropping season, a field trial was conducted at the Melkassa and Negele Arsi sites to evaluate the effect of intra-row spacing on the growth and yields of common bean varieties. The factors studied include three bean varieties (Dame, SER-119, and KAT-B9) and three intra-row spacings (5, 10, and 15 cm), arranged in a randomized complete block design with three replications. Intra-row spacing significantly affected leaf area, branches plant⁻¹, shoot dry weight, pods plant⁻¹, seeds pod⁻¹, and grain yield, except for leaf area index at both sites, hundred-seed weight, and harvest index at the Melkassa site. Concerning the interaction effect, the Dame variety produced the highest yield of 2495 kg ha⁻¹ at a spacing of 5 cm in the Negele Arsi site. Nevertheless, the main effect of the SER-119 variety and a spacing of 5 cm achieved a higher yield at the Melkassa site. Overall, the varieties Dame at Negele Arsi and SER-119 at Melkassa, with a 5 cm intra-row spacing, have the potential to significantly enhance common bean cultivation in these and similar agroecological zones. Therefore, this study strongly recommends using the Dame and SER-119 varieties with a 5 cm spacing between plants to enhance their productivity and adaptability to changing environmental conditions.