Abstract
Viruses are considered of major importance in strawberry (Fragaria × ananassa Duchesne) production given their negative impact on plant vigor and growth. Strawberry accessions from the National Clonal Germplasm Repository were screened for viruses using high throughput sequencing (HTS). Analyses of sequence information from 45 plants identified multiple variants of 14 known viruses, comprising strawberry mottle virus (SMoV), beet pseudo yellows virus (BPYV), strawberry pallidosis-associated virus (SPaV), tomato ringspot virus (ToRSV), strawberry mild yellow edge virus (SMYEV), strawberry vein banding virus (SVBV), strawberry crinkle virus (SCV), strawberry polerovirus 1 (SPV-1), apple mosaic virus (ApMV), strawberry chlorotic fleck virus (SCFaV), strawberry crinivirus 4 (SCrV-4), strawberry crinivirus 3 (SCrV-3), Fragaria chiloensis latent virus (FClLV) and Fragaria chiloensis cryptic virus (FCCV). Genetic diversity of sequenced virus isolates was investigated via sequence homology analysis, and partial-genome sequences were deposited into GenBank. To confirm the HTS results and expand the detection of strawberry viruses, new reverse transcription quantitative PCR (RT-qPCR) assays were designed for the above-listed viruses. Further in silico and in vitro validation of the new diagnostic assays indicated high efficiency and reliability. Thus, the occurrence of different viruses, including divergent variants, among the strawberries was verified. This is the first viral metagenomic survey in strawberry, additionally, this study describes the design and validation of multiple RT-qPCR assays for strawberry viruses, which represent important detection tools for clean plant programs.
Highlights
The garden or commercial strawberry (Fragaria × ananassa Duchesne) is a widely grown hybrid species of the genus Fragaria, which is cultivated as a source of food in many parts of the world [1]
The occurrence of different viruses, including divergent variants, among the strawberries was verified. This is the first viral metagenomic survey in strawberry, this study describes the design and validation of multiple reverse transcription quantitative PCR (RT-qPCR) assays for strawberry viruses, which represent important detection tools for clean plant programs
Forty-five strawberry plants originating from the National Clonal Germplasm Repository (NCGR) were screened for viruses via high throughput sequencing (HTS)
Summary
The garden or commercial strawberry (Fragaria × ananassa Duchesne) is a widely grown hybrid species of the genus Fragaria (family Rosaceae), which is cultivated as a source of food in many parts of the world [1]. This plant was first bred in Europe around 1750 and is a hybrid between F. virginiana from North America and F. chiloensis from South America [2,3]. An important resource of genetic material from Fragaria is the US Department of Agriculture, ARS National Clonal Germplasm Repository (NCGR) located in Corvallis (OR, USA). Besides having foundational material for horticultural distribution, the NCGR separately houses pathogen-positive accessions for virology research
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