A review of sources of resistance to turnip yellows virus (TuYV) in Brassica species

Turnip yellows virus (TuYV; previously known as beet western yellows virus) causes major diseases of Brassica species worldwide resulting in severe yield-losses in arable and vegetable crops. It has also been shown to reduce the quality of vegetables, particularly cabbage where it causes tip burn. Incidences of 100% have been recorded in commercial crops of winter oilseed rape (Brassica napus) and vegetable crops (particularly Brassica oleracea) in Europe. This review summarises the known sources of resistance to TuYV in B. napus (AACC genome), Brassica rapa (AA genome) and B. oleracea (CC genome). It also proposes names for the quantitative trait loci (QTLs) responsible for the resistances, Turnip Yellows virus Resistance (TuYR), that have been mapped to at least the chromosome level in the different Brassica species. There is currently only one known source of resistance deployed commercially (TuYR1). This resistance is said to have originated in B. rapa and was introgressed into the A genome of oilseed rape via hybridisation with B. oleracea to produce allotetraploid (AACC) plants that were then backcrossed into oilseed rape. It has been utilised in the majority of known TuYV-resistant oilseed rape varieties. This has placed significant selection pressure for resistance-breaking mutations arising in TuYV. Further QTLs for resistance to TuYV (TuYR2-TuYR9) have been mapped in the genomes of B. napus, B. rapa and B. oleracea and are described here. QTLs from the latter two species have been introgressed into allotetraploid plants, providing for the first time, combined resistance from both the A and the C genomes for deployment in oilseed rape. Introgression of these new resistances into commercial oilseed rape and vegetable brassicas can be accelerated using the molecular markers that have been developed. The deployment of these resistances should lessen selection pressure for resistance-breaking isolates of TuYV and thereby prolong the effectiveness of each other and extant resistance.

Evaluation of Resistance of Oilseed Rape Genotypes to Turnip Yellows Virus

Turnip yellows virus (TuYV), is one of the most important pathogens of oilseed rape, which has caused enormous yield losses in all growing regions of the world in recent years. Therefore, there is a need for resistant varieties for sustainable crop protection. We have investigated the resistance of known varieties and newly developed advanced-breeding lines of oilseed rape to TuYV in greenhouse and field trials. We have analysed the TuYV titre of individual genotypes inoculated with the virus using viruliferous aphids Myzus persicae. The genotypes 'DK Temptation' and 'Rescator' had the lowest and highest virus titres, respectively, and were used as resistant and susceptible models for comparative analyses with other genotypes. In the greenhouse, the best results were obtained with the genotypes 'OP-8143 DH' (2.94 × 10⁵ copies), OP-BN-72 (3.29 × 10⁵ copies), 'Navajo' (3.58 × 10⁵ copies) and 'SG-C 21215' (4.09 × 10⁵ copies), which reached virus titres about 2 times higher than the minimum virus concentration measured in 'DK Temptation' (1.80 × 10⁵ copies). In the field trials, the genotypes 'Navajo' (3.39 × 10⁵ copies), 'OP-8148 DH' (4.44 × 10⁵ copies), 'SG-C 21215' (6.80 × 10⁵ copies) and OP-8480 (7.19 × 10⁵ copies) had the lowest virus titres and reached about 3 times the virus titre of DK Temptation (2.54 × 10⁵ copies). Both trials showed that at least two commercial varieties (e.g., DK Temptation, Navajo) and three advanced breeding lines (e.g., OP-8143 DH, OP-BN-72, SG-C 21215) had low titres of the virus after TuYV infection. This indicates a high level of resistance to TuYV in 'Navajo' or the newly developed breeding lines and the basis of resistance is probably different from R54 (as in 'DK Temptation'). Furthermore, the greenhouse trials together with RT -qPCR-based virus titre analysis could be a cost-effective and efficient method to assess the level of resistance of a given genotype to TuYV infection compared to the field trials. However, further research is needed to identify the underlying mechanisms causing this difference in susceptibility.

Genetic Diversity Analysis of Brassica Yellows Virus Causing Aberrant Color Symptoms in Oilseed Rape

The emergence of brassica yellow virus (BrYV) has increasingly damaged crucifer crops in China in recent years. In 2020, a large number of oilseed rape in Jiangsu showed aberrant leaf color. A combined RNA-seq and RT-PCR analysis identified BrYV as the major viral pathogen. A subsequent field survey showed that the average incidence of BrYV was 32.04%. In addition to BrYV, turnip mosaic virus (TuMV) was also frequently detected. As a result, two near full-length BrYV isolates, BrYV-814NJLH and BrYV-NJ13, were cloned. Based on the newly obtained sequences and the reported BrYV and turnip yellow virus (TuYV) isolates, a phylogenetic analysis was performed, and it was found that all BrYV isolates share a common root with TuYV. Pairwise amino acid identity analysis revealed that both P2 and P3 were conserved in BrYV. Additionally, recombination analysis revealed seven recombinant events in BrYV as TuYV. We also attempted to determine BrYV infection by quantitative leaf color index, but no significant correlation was found between the two. Systemic observations indicated that BrYV-infected plants had different symptoms, such as no symptom, purple stem base and red old leaves. Overall, our work proves that BrYV is closely related to TuYV and could be considered as an epidemic strain for oilseed rape in Jiangsu.

Identification of Specific Pathogen-Infected sRNA-Mediated Interactions between Turnip Yellows Virus and Arabidopsis thaliana

Virus infestation can seriously harm the host plant's growth and development. Turnip yellows virus (TuYV) infestation of host plants can cause symptoms, such as yellowing and curling of leaves and root chlorosis. However, the regulatory mechanisms by which TuYV affects host growth and development are unclear. Hence, it is essential to mine small RNA (sRNA) and explore the regulation of sRNAs on plant hosts for disease control. In this study, we analyzed high-throughput data before and after TuYV infestation in Arabidopsis using combined genetics, statistics, and machine learning to identify 108 specifically expressed and critical functional sRNAs after TuYV infection. First, comparing the expression levels of sRNAs before and after infestation, 508 specific sRNAs were significantly up-regulated in Arabidopsis after infestation. In addition, the results show that AI models, including SVM, RF, XGBoost, and CNN using two-dimensional convolution, have robust classification features at the sequence level, with a prediction accuracy of about 96.8%. A comparison of specific sRNAs with genome sequences revealed that 247 matched precisely with the TuYV genome sequence but not with the Arabidopsis genome, suggesting that TuYV viruses may be their source. The 247 sRNAs predicted target genes and enrichment analysis, which identified 206 Arabidopsis genes involved in nine biological processes and three KEGG pathways associated with plant growth and viral stress tolerance, corresponding to 108 sRNAs. These findings provide a reference for studying sRNA-mediated interactions in pathogen infection and are essential for establishing a vital resource of regulation network for the virus infecting plants and deepening the understanding of TuYV virus infection patterns. However, further validation of these sRNAs is needed to gain a new understanding.

Symptomless turnip yellows virus infection causes grain yield loss in lentil and field pea: A three-year field study in south-eastern Australia

Turnip yellows virus (TuYV) is a damaging virus that is persistently transmitted by aphids and infects a wide range of grain hosts including lentil (Lens culinaris Medik), field pea (Pisum sativum L.) and canola (Brassica napus L., oilseed rape). Although information is available about the effects of TuYV infection on grain yield in canola, data about its impact on yield in pulses is lacking. In this study, field experiments quantifying the effects of TuYV infection on the grain yield of lentil and field pea were conducted over three consecutive years (2018-2020) with varying weather conditions. Plants artificially inoculated with TuYV using viruliferous green peach aphid (Myzus persicae, Sulzer) were grown under typical field conditions in south-eastern Australia. At maturity, grain yield, along with associated grain and plant growth parameters, were measured. Compared to the non-inoculated control treatment, early TuYV infection reduced grain yield by up to 36% in lentil and 45% in field pea, while late TuYV infection had no significant impact on yield. Despite a high incidence of TuYV infection and significant yield losses recorded in inoculated plots, no obvious symptoms of virus infection were observed in the inoculated plots in any of the six experiments; this lack of visible symptoms in lentil and field pea has significant implications for crop health assessments, demonstrating the importance of testing for virus instead of relying solely on the presence of visual symptoms, and may also be leading to an underestimation of the importance of TuYV in pulses in Australia.

Weed Hosts Represent an Important Reservoir of Turnip Yellows Virus and a Possible Source of Virus Introduction into Oilseed Rape Crop

Turnip yellows virus (TuYV) is one of the most important pathogens of oilseed rape worldwide. The virus has a large host range including many crop species (e.g., oilseed rape, pea, chickpea) and weeds from more than twenty plant families. Other than oilseed rape, we detected TuYV in many commonly grown weed species that share the fields and vegetation period together with canola crops in Czech and Slovak Republics. TuYV was detected by reverse-transcription polymerase chain reaction (RT-PCR) in at least 26 species including main crop hosts (oilseed rape), intercrops and weeds such as Amaranthus retroflexus, Atriplex patula (Amaranthaceae), Arctium lappa, Lactuca serriola, Taraxacum officinale, Tripleurospermum inodorum (Asteraceae), Phacelia tanacetifolia (Boraginaceae), Brassica napus, Capsella bursa-pastoris, Descurainia Sophia, Raphanus raphanistrum, Sinapis alba, Sisymbrium officinale, Thlaspi arvense (Brassicaceae), Silene alba, Stellaria media (Caryophyllaceae), Euphorbia helioscopia (Euphorbiaceae), Geranium rotundifolium (Geraniaceae), Lamium purpureum (Lamiaceae), Fumaria officinalis, Papaver rhoeas (Papaveraceae), Veronica persica (Plantaginaceae syn. Scrophulariaceae), Fallopia convolvulus (Polygonaceae), Solanum nigrum (Solanaceae), Urtica dioica (Urticaceae) and Viola arvensis (Violaceae). The detection of TuYV was further confirmed by RT-qPCR as well as Sanger sequencing of the PCR fragments. We discovered four new weed species as hosts of TuYV such as T. inodorum, S. alba, G. rotundifolium and E. helioscopia, representing their three respective plant families. The readthrough domain (RTD) gene sequence analysis of the Czech and Slovak TuYV isolates from oilseed rape and weed species showed similar within-group nucleotide divergence (7.1% and 5.6%, respectively) and the absence of geographical- or host-based phylogenetic clustering. The high-throughput sequencing of the P. rhoeas sample enabled the obtention of a nearly complete genome of TuYV and revealed the mixed infection of TuYV with turnip mosaic virus and cucumber mosaic virus. Our results thus show that weed species are an important TuYV reservoir and play a significant role in the spread and incidence of the disease in field crops such as oilseed rape.

Phylogenetic relationship and genetic diversity of Turkish peanut viruses

BACKGROUND

Viral diseases of peanuts (Arachis hypogaea) have never been reported in Turkey. Analyzing genetic diversity using phylogenetic analysis is important to understanding disease complexes.

METHODS AND RESULTS

Samples were taken from 63 plants showing virus-like symptoms from two major cultivation regions in Turkey. These samples were tested against five different virus genera and one virus species by PCR/RT-PCR. After sequencing and subsequent RT-PCR tests using specific primers, viruses were identified at the species level. Complete protein-coding genome analyses, multiple sequence comparisons, and phylogenetic analyses of three isolates for each identified species with world isolates were performed. And, peanut mottle virus (PeMoV), peanut stripe virus (PStV), and turnip yellows virus (TuYV) infections were detected. All Turkish isolates showed high sequence homology and were phylogenetically similar to each other. Phylogenetic analyses with world isolates revealed that Turkish PeMoV and TuYV isolates were closely related to some other world isolates, while PStV isolates were in a separate phylogenetic group from other world isolates. The genetic distance values of the PeMoV, PStV, and TuYV isolates were determined to be 0.0159, 0.0325, and 0.0753, respectively.

CONCLUSIONS

PeMoV, PStV, and TuYV were reported for the first time in Turkey. Furthermore, the peanut was identified as a new host for TuYV for the first time. The first complete protein-coding genome sequences of Turkish isolates of the three viruses were also obtained.

Investigating the Pea Virome in Germany-Old Friends and New Players in the Field(s)

Peas are an important legume for human and animal consumption and are also being used as green manure or intermediate crops to sustain and improve soil condition. Pea production faces constraints from fungal, bacterial, and viral diseases. We investigated the virome of German pea crops over the course of three successive seasons in different regions of pea production to gain an overview of the existing viruses. Pools from 540 plants, randomly selected from symptomatic and asymptomatic peas, and non-crop plants surrounding the pea fields were used for ribosomal RNA-depleted total RNA extraction followed by high-throughput sequencing (HTS) and RT-PCR confirmation. Thirty-five different viruses were detected in addition to nine associated nucleic acids. From these viruses, 25 are classified as either new viruses, novel strains or viruses that have not been reported previously from Germany. Pea enation mosaic virus 1 and 2 were the most prevalent viruses detected in the pea crops, followed by pea necrotic yellow dwarf virus (PNYDV) and turnip yellows virus which was also found also in the surrounding non-legume weeds. Moreover, a new emaravirus was detected in symptomatic peas in one region for two successive seasons. Most of the identified viruses are known to be aphid transmissible. The results revealed a high virodiversity in the German pea fields that poses new challenges to diagnosticians, researchers, risk assessors and policy makers, as the impact of the new findings are currently unknown.

In-field capable loop-mediated isothermal amplification detection of Turnip yellows virus in plants and its principal aphid vector Myzus persicae

Widespread Turnip yellows virus (TuYV) infection causes severe seed yield and quality losses in rapeseed (Brassica napus) crops grown in broadacre agricultural systems worldwide. Current TuYV detection protocols are expensive and time consuming, and can have poor specificity and sensitivity. Typically, they are used as a diagnostic tool to test already symptomatic plants, limiting their practical value to reactive disease management. To improve diagnostic services so that they provide earlier, cheaper, faster, more specific and sensitive TuYV detection, novel and innovative protocols that utilise new technology are required. A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to detect TuYV in crude and total RNA extractions of leaf material and its principal aphid vector Myzus persicae. The assay was based on a set of six primers, highly sensitive and specific to TuYV, derived from a TuYV isolate originating from the south-west Australian grainbelt. TuYV was readily detected in 1 in 100 dilutions of (i) infected to uninfected leaf material, and (ii) viruliferous to non-viruliferous M. persicae. Furthermore, detection was successful in a majority of aphids stored for at least 8 weeks in various trapping and storage substances, including 30% ethylene glycol, sticky trap glue and 70% ethanol. This RT-LAMP assay protocol enables quicker and cheaper diagnosis for TuYV than currently adopted laboratory-based diagnostic techniques. Ultimately, it has the potential for earlier in-field TuYV detection in combination with aphid trapping surveillance programs.