Prevalence and Strain Composition of Potato virus Y Circulating in Potato Fields in China’s North-Central Province of Shanxi

Abstract

Potato is an important crop in Shanxi province located in north-central China. During 2019-2020, 319 potato leaf samples were collected from eight locations distributed in three major potato production areas in Shanxi. Bio-chip detection kit revealed the presence of several potato viruses, and among them potato virus Y (PVY) was the most common one, reaching the incidence of 87.8% of all symptomatic samples. The immuno-captured multiplex reverse transcription (RT)-PCR was used to identify strains for all 280 PVY-positive samples, unveiling 242 samples infected with a single strain of PVY (86.4%) and 38 (13.6%) with a mixed infection. Of samples with a single-strain infection, PVY -SYR-II accounted for 102 (42.1%), followed by PVYN-Wi (33, 13.6%) , PVY -SYR-I (28, 11.6%), 261-4 (22, 9.1%), PVYNTNa (20, 8.3%), PVYNTNb (19, 7.9%), and PVY -SYR-III (18, 7.4%). Seven isolates representing different recombinants were selected for whole genome sequencing. Phylogenetic and recombination analyses confirmed the RT-PCR based strain typing for all seven strains of PVY found in Shanxi. SXKL-12 is the first SYR-III strain from potato reported from China. However, unlike that in other known SYR-III isolates, the region positioned from 1,764 to1,902 nt in SXKL-12 shared the highest sequence identity of 82.2% with an uncharacterized PVY isolate, JL-23, from China. Interestingly, the PVYN-Wi isolate SXZY-40 also possessed a more divergent sequence for the region positioned from 6,156 to 6,276 nt than other N-Wi isolates known to date, sharing the highest identity of 86.6% with an uncharacterized Chinese PVY isolate, JL-11. Pathogenicity analysis of dominant strains PVY -SYR-II and PVYN-Wi in six local popular potato cultivars revealed that Kexin 13, Helan 15 and Jizhangshu 12 were susceptible to these two strains with mild mottling or mosaic symptoms expression, while three cultivars, Jinshu 16, Qingshu 9, Xisen 6 were found fully resistant.

Genome sequences of six recombinant variants of potato virus Y identified in North American potato cultivars grown in China

“…Three recombinant types were revealed among the six sequenced PVY genomes ( Fig. 1 ), one PVY N-Wi , three PVY-SYR-II, and two PVY-SYR-I, in general agreement with the PVY strain composition determined for local Chinese potato cultivars ( 10 – 12 ). Examination of the sequences around the two main recombinant junctions, RJ2 and RJ3, revealed the shifts for the RJ breakpoint locations in Chinese PVY recombinants which may be responsible for the unusual banding patterns observed for the RT-PCR typing ( Table 1 ).…”

“…PVY belongs to the genus Potyvirus (family Potyviridae ) ( 2 – 5 ) and exists as a complex of strains and genetic variants including multiple, more than 35, recombinants ( 2 , 6 – 9 ). China is one of the potato-growing countries with a great diversity of PVY recombinants described ( 10 – 12 ) but this diversity was addressed primarily for the local potato cultivars ( 10 – 12 ), and not studied in cultivars of North American origin.…”

Development of an attenuated potato virus Y mutant carrying multiple mutations in helper-component protease for cross-protection

“…Group O induces mosaic and mottle symptoms, while group N causes systemic veinal necrosis symptoms on tobacco leaves ( Karasev and Gray, 2013 ; McDonald and Singh, 1996 ; Nie et al, 2012 ; Tian and Valkonen, 2013 ), resulting in significant yield losses to tobacco production ( Faurez et al, 2012 ; Hu et al, 2009 ; Tsedaley, 2015 ). A growing number of PVY recombinant strains emerged in China, such as PVY SYR-I , PVY SYR-II , PVY SYR-III , PVY N-Wi , PVY NTN , and PVY N:O ( Bai et al, 2019 ; Ding et al, 2022 ; Gao et al, 2024 ).…”