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ARS Home » Southeast Area » Charleston, South Carolina » Vegetable Research » Research » Publications at this Location » Publication #349619

Research Project: Biological, Genetic and Genomic Based Disease Management for Vegetable Crops

Location: Vegetable Research

Title: Survey of potato viruses and viroids in Heilongjiang province of China by sRNA deep sequencing and VirusDetect

item Shamimuzzaman, Md - Shamim
item Ling, Kai-Shu

Submitted to: International Congress of Plant Pathology Abstracts and Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 5/31/2018
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Heilongjiang province is one of the most important potato production areas in China. Frequent outbreaks of virus and viroid diseases in production fields have significantly decreased potato yield and quality. However, we still do not have a clear understanding on the composition and genetic diversity of viruses and viroids in the field. In order to investigate the occurrence of known and novel viruses and viroids infecting potato plants in Heilongjiang, we performed this survey to identify viruses and viroids using small RNA (sRNA) deep sequencing. In this study, we used VirusDetect pipeline to analyze a total of 20 sRNA libraries generated from symptomatic potato samples collected throughout Heilongjiang. The results showed a total of six viruses and one viroid infecting potatoes, with 100% incidence for Potato virus Y (PVY), 55% for Potato spindle tuber viroid (PSTVd), 30% for Potato virus H (PVH), 25% for Potato virus S, 15% for Potato virus M, 5% for Potato virus X, and 5% for Potato leafroll virus. Complete or near complete genomes of the six viruses and PSTVd were assembled successfully by VirusDetect, with or without RT-PCR gap filling. Although the high incidence of PVY and PSTVd were somewhat expected, PVH which was only first discovered from Inner Mongolia in China in 2013 was detected in 30% of samples analyzed. PVH is not included in routine test of seed potato in China, with the results obtained here, we recommend to include PVH in the test.