Prevalence of recombinant strains of potato virus Y in seed potato planted in Idaho and Washington states between 2011 and 2021

Abstract

Potato virus Y (PVY) has emerged as the main reason for potato seed lot rejections, seriously affecting seed potato production in the United States throughout the past 20 years. The dynamics of PVY strain abundance and composition in various potato growing areas of the U.S. has not been well documented and understood up to now. The objective of this study was to find out the prevalence of PVY strains in potato fields in the Pacific Northwest (PNW), including seed potato production systems in the state of Idaho, and commercial potato fields in the Columbia Basin of Washington State between 2011-2021. Based on the testing of more than 10,000 foliar samples during Idaho seed certification winter grow-out evaluations of seed potato lots and seed lot trials in Washington State, a dramatic shift in the PVY strain composition was revealed in the PNW, between 2011 and 2016. During this time period, the prevalence of the ordinary, PVYO strain in seed potato dropped 8-10 fold, concomitantly with the rise of recombinant strains PVYN-Wi and PVYNTNa, which together accounted for 98% of all PVY-positives by 2021. In Idaho seed potato, PVYNTNa strain associated with the potato tuber necrotic ringspot disease (PTNRD) was found to increase three-fold between 2011-2019, accounting for 24% of all PVY-positives in 2019. Relatively mild foliar symptoms induced by recombinant PVY strains may be partially responsible for the proliferation of PVYN-Wi and PVYNTNa in potato crops. A spike of another PTNRD-associated recombinant, PVY-NE11, was recorded in the PNW between 2012-2016, but after reaching a 7-10% level in 2012-2013 this recombinant had disappeared from the PNW potato by 2019. Whole genome sequence analysis of the PVY-NE11 suggested this recombinant was introduced in the U.S. at least three times. The data on PVY strain abundance in the PNW potato crops suggest that virus management strategies need to consider the current dominance of the two recombinant PVY strains, PVYN-Wi and PVYNTNa.