بررسی پروفایل بیانی سیب‌زمینی تحت تاثیر آلودگی با Potato Virus Y با استفاده از تجزیه و تحلیل RNA-Seq

Potato Virus Y (PVY) from the genus potyvirus, is one of the most important viruses limiting potato production worldwide. The widespread transmission of PVY mechanically and also through aphids as vectors has caused the rapid spread of this virus. The interactions between plant and virus are complex and the result of them depends on the potato cultivar, virus strain and environmental conditions. Understanding how potato responds to PVY as compatible or incompatible reaction, requires the investigation of the expression pattern of plant genes under the virus infection stress. In this study, RNA sequencing (RNA-Seq) data with the project number PRJNA283609 were analyzed. After trimming raw data and alignment with the potato reference genome, differential expression of mapped transcripts and gene ontology for understanding the function of differential expressed genes were analyzed using DESeq2. In order to investigate the expression changes in target gene using real-time PCR, 14-days old potato seedlings of Khavaran cultivar were inoculated with PVY. Sampling was done within 4, 8, 10, 12 and 24 hours post inoculation. Then, RNA extraction was done in order to check the expression of target gene. According to the results, 85 genes were differentially expressed in the expression profile of PVY infected potato compared to control with 1% p-value. Out of these, 46 genes were up-regulated and 39 genes were down-regulated. The most changes in gene expression observed in 10 hours post inoculation. Studies have indicated that response of resistant plant to PVY is associated with less expression changes in compared to susceptible cultivars that confirms the results of present study. Finding the function of genes and gene ontology analysis showed that the most expressed genes are related to plant immunity through RNA silencing (such as Argonauts proteins), biotic stress responsive genes and genes involved in MAPK signaling cascade. On the other hand, stress enhanced genes, development of cell death related genes and disease resistance genes from NBS-LRR protein family had a significant decrease in expression in PVY infected plants. Also, strong repression of Soltu.DM.06G019440.1 was observed as a result of PVY infection. Studies show the role of this gene in plant protection against virus vector. Real-time PCR also confirmed a significant down-regulation in mentioned gene under PVY stress. The results of differential gene expression in PVY infected potato can be useful in predicting the compatible or incompatible interaction between plant and pathogen, and assessment the crop damage.