Managing potato tuber necrotic viruses: potato virus Y and potato mop-top virus, diversity, detection and cloning methods

Abstract

Potato virus Y (PVY) and Potato mop-top virus (PMTV) are major threats to potato production globally, significantly affecting crop quality and yield. PVY, a well-known economic concern, poses a challenge due to its wide strain diversity and prevalence, particularly in the San Luis Valley (SLV), Colorado. PMTV, a single-stranded positive-sense RNA virus from the Pomovirus genus, is vectored by the soil-borne pathogen Spongospora subterranea f. sp. subterranea (S. subterranea), which also causes potato powdery scab. Despite their importance, there is still limited knowledge of PMTV genetics and the population structure of S. subterranea, as well as the combined virulence of these pathogens in the United States. This study first investigated PVY trends and diversity in the San Luis Valley, Colorado using Colorado Seed Potato Certification Program data (2017-2022). PVY incidence fluctuated between 2.6% (2017) and 6.5% (2022) in certified seed lots, with PVYN-Wi identified as the dominant strain. A field study from 2021 to 2022 further examined PVY prevalence in 600 samples collected across 30 fields, confirming PVYN-Wi as the predominant strain, followed by PVYO and PVYNTN. The study also noted an increase in dual and triple infections, and high-throughput sequencing (HTS) of inconclusive samples revealed polymorphisms that may hinder strain typing by traditional methods. Aside from PVY, potato virus S (PVS) was the only other potato-infecting virus detected. HTS additionally uncovered diverse non-plant infecting viruses, emphasizing the complexity of the potato virome. In parallel, the study addressed the knowledge gaps surrounding PMTV and its vector S. subterranea. Sequencing of seven PMTV isolates showed low genetic variability, with one strain, ND24, containing a non-synonymous SNP in the transmembrane domain at codon 289, correlating with a mild strain instead of severe. Additionally, this work is the first to suggest diversity in S. subterranea populations across the United States with the use of microsatellite markers. Moreover, the study found that PMTV's low genetic diversity had no significant effect on its virulence in controlled conditions. Instead, the origin of S. subterranea inoculation was the greatest determinant of virulence. Primers were developed for each RNA segment of PMTV's tripartite genome, with TGB being the most abundant in both plant bioassays and sequencing read counts. Interestingly, no correlation between PMTV and S. subterranea counts was found in soil samples, but a clear relationship emerged in plant bioassays, suggesting that environmental factors and potato cultivars are critical in determining field infections. This research provides valuable insights into the genetic and population structures of PVY and PMTV, highlighting the need for ongoing surveillance and improved diagnostics to manage these viral threats. The findings underscore the importance of viral diversity, vector dynamics, and environmental influences in shaping the impact of viral infections on potato production.