Comprehensive Virome Profiling of Apple Mosaic Disease-Affected Trees in Iran Using RT-PCR and Next-Generation...

Area of Science:

• Plant Pathology
• Virology
• Horticulture

Background:

• Apples (Malus domestica) are a vital economic crop in Iran.
• Assessing the health of apple orchards is crucial for maintaining productivity.
• Previous surveys of apple viruses and viroids in Iran are limited.

Purpose of the Study:

• To comprehensively assess the sanitary status of Iranian apple cultivars.
• To identify known and potentially novel viral and viroid agents affecting apple trees in Iran.
• To understand the prevalence and genetic relationships of detected pathogens.

Main Methods:

• Collection of 170 apple leaf samples from commercial cultivars across Iran.
• RT-PCR screening for five common apple viruses and two viroids.
• Next-generation sequencing (NGS) for identifying unknown or novel agents and full genome retrieval.
• Phylogenetic analysis of selected viral and viroid isolates.

Main Results:

• RT-PCR confirmed the presence of six known pathogens: ACLSV, ASPV, ASGV, AGCaV, ApMV, and HSVd.
• NGS identified three additional pathogens: CCGaV, AHVd, and AVCaV, subsequently confirmed by RT-PCR.
• Apple green crinkle-associated virus (AGCaV) was the most prevalent (47.6%), with 67% of samples showing mixed infections.
• Phylogenetic analysis indicated common origins for Iranian isolates.
• First report of AGCaV, CCGaV, ApMV, and AVCaV in apples in Iran, and the first global report of AVCaV in a non-Prunus host.

Conclusions:

• This study provides the first comprehensive assessment of apple tree sanitary status in Iran.
• Multiple viruses and viroids, including newly reported ones, are endemic in Iranian apple orchards.
• The high prevalence of mixed infections highlights a significant threat to apple production in the region.