Poleroviruses of legume vegetable crops : abundance, diversity, and impact

Vegetable and pulse legumes are very important sources of human and animal nutrition and are known to be susceptible to many plant viruses including members of the genus Polerovirus. Thirteen species or tentative species have been reported from vegetable or pulse legume crops of which Turnip yellows virus (TuYV) is the most abundant and economically important virus, infecting pulses, canola and various vegetable crops worldwide and causing significant losses. Pea and weed samples were collected during 2019-2020 between October to January, from thirty-four sites across three different regions (far North-West, North, and Midlands) of Tasmania and tested by RT-PCR assay with selected samples subject to next-generation sequencing. Results revealed the presence of poleroviruses infection and the prevalence of TuYV in both weeds and pea crops varied across the three Tasmanian cropping regions with TuYV infection levels in pea crops ranging between 0 to 27.5% of tested plants. Significant genetic diversity was found within isolates of TuYV across different parts of their genome with P0 displaying higher genetic variability. Phylogenetic inconsistency in the P0 and P3 ORFs supports the concept that recombination may have played a role in TuYV evolution in Tasmania. Results of the evolutionary analysis showed that the selection pressure was higher in the P0 gene than P3 gene and the majority of the codons for each gene are evolving under purifying selection. Overall, two species member from each genus Polerovirus and Potyvirus, and one member from each Luteovirus, Potexvirus, and Carlavirus, and an unclassified virus from family Partitiviridae were also found as a result of NGS data analysis.
Among these viruses we further studied Brassica yellows virus (BrYV) which is a tentative species in the genus Polerovirus, and is closely related to, but distinct from TuYV in terms of the P0, P3, P4, and P5 cistrons sequences. BrYV isolates have at least three genotypes (A, B, and C), have not been previously described from Tasmania, and its genetic variability remains unknown. Here, we describe a near complete genome sequence of BrYV (genotype A) isolated from Raphanus raphanistrum in Tasmania using next-generation sequencing and Sanger sequencing of RT-PCR products. The BrYV-Tas isolate (Accession no. OM469309) possesses a genome of 5516 nucleotides (nt) and shares high sequence identities (about 90%) with other BrYV isolates. Phylogenetic analyses further showed variability in the clustering patterns of individual genes of BrYV-Tas. Recombination analysis revealed the beginning and ending breakpoints at nucleotide positions 1922 to 5234 nt, with BrYV isolate LC428359 as a major parent and BrYV isolate KY310572 as a minor parent. Moreover, results of the evolutionary analysis showed that the majority of the codons for each gene are evolving under purifying selection, though a few codons were also detected to have positive selection pressure.
During the spring-summer cropping season of 2020−2021, the transmission, epidemiology, and impact, of TuYV with regards to Tasmanian pea crops were assessed at three sites in Poatina, Cressy and Longford. Across all fields, twenty-two aphid species were identified along with some unidentified species off which ten are known vectors of TuYV including Myzus persicae. The population and activity of aphids in the field influenced virus transmission events and were found to be associated with rainfall. When comparing two known vectors, M. persicae was found to have a 1.7-fold greater efficiency in transmitting TuYV into peas than Acyrthosiphon pisum. Moreover, M. persicae displayed a variable efficiency to transmit different isolates of TuYV with the range of 10−75%. Overall, TuYV incidence ranged from 16.7−45% in all three regions which increased as the cropping season progressed. However, TuYV infections had no significant impact on growth or pea yield when heathy and infected plants were compared, nor on the nutrient parameters of harvested peas from infected and healthy plants, although a trend for reduced yield and protein content was indicated.
By combining several biological and molecular techniques, this study has increased understanding of the diversity of polerovirus species in general and genomic diversity of TuYV in particular, associated with Tasmanian pea crops. It also provides a qualitative and quantitative information about the impact of TuYV on pea crops. This project also contributed to a better understanding of the pathogen/vector relationship, which is necessary for limiting pathogen/vector spread. In a broader spectrum, the outcomes of this project will facilitate to improve the resilience of vegetable growers to impacts from viral diseases, by developing appropriate management and control strategies that can be implemented on an area-wide scale to combat the challenges of commercial vegetable production.