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Detection of tomato brown rugose fruit virus is influenced by infection at different growth stages and sampling from different plant parts

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Detection of tomato brown rugose fruit virus is influenced by infection at different growth stages and sampling from different plant parts

Detection of tomato brown rugose fruit virus is influenced by plant age at time of infection. Regardless of plant age, sepals and young leaves, where present, give the best chance of detection.


Abstract

Since the first report of the virus in 2014, tomato brown rugose fruit virus (ToBRFV) has spread widely through Europe, the Americas and Asia. Within Europe there is currently a requirement for annual surveillance for the virus. However, little is known about the relative impact of sampling strategy with respect to timing of infection and the detection of virus from different plant parts. To test reliably for ToBRFV in crops of unknown infection status, this issue needed to be addressed. To do this, two different approaches were followed: (1) inoculation experiments were conducted at two institutes to look at the relative effects of time of infection, plant parts, cropping season and cultivar on detection of the virus; and (2) sampling and testing various plant parts were carried out during active outbreaks from two tomato production sites in the Netherlands to look at the effect of sampling plant parts on detection of the virus. In inoculation experiments, the greatest impact on detection was timing of infection, with plants infected early in the growth cycle showing a predictable development of infection. In plants infected later, infection was detectable in sepals (calyx) earlier than in older leaves. In the studies carried out on commercial crops during ToBRFV outbreaks, the highest virus concentrations were obtained from testing sepals and young leaves. Thus, in a young crop where sepals and fruit are not yet developed, sampling should focus on the young leaves; in a mature crop it may be better to sample sepals and/or fruit.

Double trouble: Co‐infection of potato with the causal agents of late and early blight

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Double trouble: Co-infection of potato with the causal agents of late and early blight

Alternaria solani directly inhibits Phytophthora infestans growth in vitro and co-inoculation of potato with both pathogens favours A. solani, even when P. infestans arrives first/simultaneously.


Abstract

Global potato production is plagued by multiple pathogens, amongst which are Phytophthora infestans and Alternaria solani, the causal agents of potato late blight and early blight, respectively. Both these pathogens have different lifestyles and are successful pathogens of potato, but despite observations of both pathogens infecting potato simultaneously in field conditions, the tripartite interactions between potato and these two pathogens are so far poorly understood. Here we studied the interaction of A. solani and P. infestans first in vitro and subsequently in planta both in laboratory and field settings. We found that A. solani can inhibit P. infestans in terms of growth in vitro and also infection of potato in both laboratory experiments and in an agriculturally relevant field setting. A. solani had a direct inhibitory effect on P. infestans in vitro and compounds secreted by A. solani had both an inhibitory and disruptive effect on sporangia and mycelium of P. infestans in vitro. In planta infection bioassays revealed that simultaneous co-inoculation of both pathogens resulted in larger necrotic lesions than single inoculations; however, consecutive inoculations only resulted in larger lesions when A. solani was inoculated after P. infestans. These results indicate that the order in which these pathogens attempt to colonize potato is important for the disease outcome and that the influence of plant pathogens on each other should be accounted for in the design of future disease control strategies in crops such as potato.

Damage on grapevine cv. Niagara Rosada leaves caused by the combined effect of temperature and Asian grapevine leaf rust (Neophysopella tropicalis)

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Damage on grapevine cv. Niagara Rosada leaves caused by the combined effect of temperature and Asian grapevine leaf rust (Neophysopella tropicalis)

Inoculated plants kept at 30°C presented cell alterations that blocked colonization, reducing lesion density and severity. However, accelerated leaf senescence due to temperature raise may increase leaf damage and reduce yield.


Abstract

Asian grapevine leaf rust (AGLR), caused by Neophysopella tropicalis, is a problem for viticulture, especially in latitudes lower than 25° S, which include the most significant production regions in Brazil. Climate change has raised new concerns in agriculture as temperature can affect the resistance of plants to pathogens. With the aim of understanding how air temperature rise affects the AGLR pathosystem, measurements of leaf gas exchange and epidemiological and histopathological analyses were carried out on control and inoculated leaves of Vitis labrusca ‘Niagara Rosada’ grown at 25°C and 30°C. The lesion density and rust severity were higher at 25°C than 30°C, and the ratio between adaxial surface necrosis and the abaxial surface area occupied by pustules was >1 only at 30°C, presenting a necrosis not associated to the pathogen lesion. In fact, leaf necrosis was identified on control plants kept at 30°C and associated with gerontoplasts, representing accelerated leaf senescence. The AGLR pathogen reduced gas exchange and photosystem II activities at 25°C, with no difference between control and inoculated plants at 30°C. Our results indicate that AGLR is sensitive to increasing air temperature. However, the accelerated leaf senescence caused by the combination of N. tropicalis infection and temperature on Niagara Rosada can lead to high leaf damage.

Transmission of Furcraea necrotic streak virus (FNSV) by Olpidium virulentus

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Transmission of Furcraea necrotic streak virus (FNSV) by Olpidium virulentus

Fique plants are source of natural fibre. Furcraea necrotic streak virus (FNSV) causes the most detrimental disease in fique plants, affecting fibre production, and is transmitted by Olpidium virulentus.


Abstract

Furcraea necrotic streak virus (FNSV) is the causative agent of necrotic streak disease, also known as macana in fique crops (Furcraea spp.) resulting in damage to leaf fibres and economic losses. The rhizospheric fungus Olpidium spp. is present in the roots of affected plants and may play a role in the disease transmission. FNSV infection and the role of fungi were examined in macanavirus-diseased plants in Colombia. Spherical, and icosahedral (24.7 ± 1.98 nm), non-enveloped virions with a granular surface were isolated from field fique plants showing signs of macana disease, and the viral genome was completely sequenced. Taxonomic status was assigned through sequence analysis (Macanavirus genus in Tombusviridae family). The variability of the virus pangenome was evaluated in diseased fique plants from ecologically different Andean regions that showed low gene flow. Olpidium virulentus zoospores, identified by internal transcribed spacer (ITS) sequencing and microscopic analysis, were associated with viral particles and resting spores in diseased fique roots. An in vitro virion–zoospore binding assay showed that FNSV and O. virulentus zoospores interacted. Transmission assays in lettuce (Lactuca sativa), a model plant used to study this virus, showed 100% infection when a preincubated mixture of zoospores and FNSV was added to roots, whereas only 33% infection occurred when FNSV was added alone. This demonstrated the ability of O. virulentus to act as a vector for FNSV, potentially enhancing viral transmissibility in field fique crops. This is the first report of FNSV being transmitted by O. virulentus, a rhizosphere fungus.

Genetic loci associated with Fusarium wilt resistance in tomato (Solanum lycopersicum L.) discovered by genome‐wide association study

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Abstract

Fusarium wilt (FW), caused by Fusarium oxysporum f. sp. lycopersici (Fol), has impacted global tomato production. This study aims to identify single nucleotide polymorphisms (SNPs) and candidate genes associated with FW resistance against different Fol isolates in tomato accessions using genome-wide association studies (GWAS). Ninety-four tomato accessions were evaluated for FW resistance and subjected to GWAS analysis. Broad-spectrum tomato accessions demonstrated resistance to Fol in at least two isolates, exhibiting a disease severity index (DSI) of 0%. Thirty-two SNP loci were significantly linked to the DSI of Fol isolates TFPK401, BK2269 and NP-T4, clustering on chromosome 6. Among these, 12 common significant SNPs were associated with the DSI of at least two Fol isolates, while four unique SNPs were specific to TFPK401 or NP-T4. Furthermore, candidate genes associated with disease response to Fol infection were identified within a 37.9–41 Mb region flanking the SNPs. These findings contribute to a deeper understanding of resistance mechanisms against Fol infection in tomatoes, potentially aiding the development of effective breeding strategies for Fusarium wilt resistance.

Varietal effects on Greenhouse Gas emissions from rice production systems under different water management in the Vietnamese Mekong Delta

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Abstract

Rice production accounts for 15% of the national Greenhouse Gas (GHG) emissions and Vietnam aims at reducing emissions from rice production by focusing on changing farming practices. However, the potential for mitigation through the selection of different rice varieties is still poorly understood. A two-year field screening of 20 rice varieties under continuous flooding (CF) and alternate wetting and drying (AWD) irrigation was conducted in the Vietnamese Mekong Delta (VMD), Vietnam, employing the closed chamber method for assessing GHG emissions. The results confirmed that varietal variation was the largest for methane (CH4) emissions under CF. Across the varietal spectrum, CH4 emissions were more important than nitrous oxide (N2O) (accounts for less than 2% of the CO2e) with the lowest emitting variety showing 243 kg CH4 ha−1 and the highest emitting variety showing 398 kg CH4 ha−1 emissions as compared to 0.07 kg N2O ha−1 and 0.76 kg N2O ha−1 emissions, respectively. Under AWD, CH4 emissions were generally strongly reduced with the varietal effect being of minor importance. Compared with IPCC default values, the data set from the two seasons yielded higher Emission Factors (EFs) under CF (2.92 and 3.00 kg ha−1 day−1) as well as lower Scaling Factors (SFs) of AWD (0.41 and 0.38). In the context of future mitigation programs in the VMD, the dry season allows good control of the water table, so varietal selection could maximize the mitigation effect of AWD that is either newly introduced or practised in some locations already. In the wet seasons, AWD may be difficult to implement whereas other mitigation options could be implemented such as selecting low-emitting cultivars.

Pioneers of post‐agricultural forest successions are adapted for herbivory avoidance but not biotic seed dispersal

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Pioneers of post-agricultural forest successions are adapted for herbivory avoidance but not biotic seed dispersal

Natural reforestation through secondary succession in marginal agricultural land is an important component of climate mitigation and adaptation, but the fundamental ecological processes promoting or constraining it are poorly understood. This study provides national-scale evidence that species accumulation in post-agricultural forest successions may be slowed by intense mammalian herbivory and low rates of biotic seed dispersal. Naturally reforesting post-agricultural land, South Island, New Zealand.


Abstract

Question

Natural reforestation is an important component of climate mitigation and adaptation, but the ecological processes promoting or constraining it are poorly understood. In this study we employ a stand reconstruction approach (which uses ages of extant trees to estimate year of establishment for each individual tree) to test for general trait-based effects on tree species arrival order in post-agricultural forest successions.

Location

Naturally reforesting post-agricultural landscapes throughout New Zealand.

Methods

Ages were obtained for 2434 individuals spanning 30 tree species across a nationwide network of 128 plots in 14 naturally reforesting post-agricultural sites. These ages were used to calculate individual-level arrival times (relative to the oldest individual in each plot). We estimated species-level arrival times by fitting linear mixed-effects (LME) regressions (with species identity as the fixed effect, and plots nested within sites as the random effects) to individual arrival time data. We used back-casting (where arrival time data are used to document individual-level presence in plots through time) to track annual changes in species abundance and community-weighted mean (CWM) trait values.

We used standardised major axis (SMA) regressions to examine the effect of traits related to resource use strategy, herbivory avoidance, seed dispersal and disturbance response on species-level arrival times. We used LME regressions to test for changes in CWM trait values with stand age.

Results

The earliest-arriving species had traits associated with herbivory avoidance, were abiotically dispersed and had short predicted dispersal distances. There was no evidence that traits linked to resource use strategy or disturbance response affected species arrival times. Every significant species-level relationship was recovered in community-level LME analyses.

Conclusions

Our findings suggest that mammalian herbivore control and enhancement of biotic (bird) seed dispersal may be key management interventions in realising the full climate mitigation and adaptation potential of natural reforestation in post-agricultural landscapes.

Development of KASP fingerprinting panel for clonal identification in red raspberry (Rubus idaeus L.)

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Abstract

Red raspberry is an economically important horticultural crop that is known for its fruit's sweet flavour and nutritional value. A reliable and economic genotyping platform is needed to facilitate clonal/variety identification. Previous attempts for clonal identification utilized morphological traits or low-throughput, difficult to score dinucleotide-containing simple sequence repeat molecular markers. Single nucleotide polymorphisms (SNPs), despite having lower allelic diversity, are numerous across the genome and more easily converted to high-throughput assays restoring differential power. In this study, we use the kompetitive allele-specific PCR (KASP™) chemistry, an affordable and high-throughput platform, to develop a panel of SNPs to distinguish a diverse collection of red raspberry accessions for clonal identification. The panel consists of 48 KASP assays that show high concordance with whole genome sequencing, allelic balance, and recovery rate and a minimal set of 24 assays that distinguished the same accessions differentiated by the larger panel.