Prevalence, genetic diversity, and phylogenetic analysis of apple stem grooving virus in low-chilling apple cultivars

Apple is one of the most important fruit crops worldwide. Due to climate change-related issues, cultivating low-chilling commercial apple cultivars has become a widespread practice among growers in the mid-hill region of India. Additionally, several biotic and abiotic factors influence apple cultivation, with viral diseases being a major biotic threat to crop productivity and nutritional quality. Among all viruses affecting apples, the apple stem grooving virus is one of the major ones. It primarily causes a latent infection, which makes its detection and management challenging. Additionally, the adoption of low-chilling cultivars has also created new niches for ASGV infection. A survey of the low-chilling apple cultivars in the states of Himachal Pradesh and Manipur was conducted, and 105 samples from five locations were analyzed. This study documented the co-infections of major apple viruses and viroids, notably apple stem grooving virus, apple chlorotic leaf spot virus, apple stem pitting virus, apple mosaic virus, and apple scar skin viroid, detected through multiplex PCR standardized primarily in our lab. Among these viruses, apple stem grooving virus showed the highest incidence, and its infection was detected in Anna, Dorsett Golden, and Michael cultivars. The complete coat protein gene sequences of thirty-seven isolates of ASGV were analyzed. The sequence identities of the characterized ASGV isolates ranged from 87.34 to 100%. Phylogenetic analysis revealed no clear correlation between cultivar and the geographic origin of the isolates. Alignment of the CP gene sequences from ASGV isolates with global isolates obtained from various host species revealed the formation of eight distinct clusters, effectively grouping the isolates. Significantly, six isolates showed little spatial clustering and were closely related to isolates from China and Canada.

The online version contains supplementary material available at 10.1007/s13337-025-00931-z.