TUBER NECROSIS-CAUSING VIRUSES OF POTATO: GENETIC DIVERSITY AND HOST-PATHOGEN INTERACTIONS

Lindani Moyo

Potato (Solanum tuberosum L.) is an economically important staple crop. Tuber necrosis-causing viruses of potato such as Potato virus Y (PVY) and Tobacco rattle virus (TRV) threaten potato production due to qualitative and quantitative tuber losses they can cause, that have economic costs. There is need to elucidate virus-host interactions and evolutionary dynamics of the potato viruses to help develop novel diagnosis and disease management strategies. Plant defense RNA-silencing mechanisms deployed against viruses produce virus small interfering RNAs (vsiRNAs) to degrade homologous viral transcripts. Based on sequence complementarity, the vsiRNAs can potentially degrade host RNA transcripts. This study, therefore, exploited bioinformatics and genomics tools to elucidate the transcriptome level interactions between the potato transcriptome and PVY-derived vsiRNAs of three PVY strains: PVYN, PVYNTN and PVYO. The most abundant targeted, non-coding RNA transcripts, for the strain specific PVY-derived vsiRNAs were found to be small nucleolar and ribosomal RNAs. Functional annotation and qRT-PCR validation suggested that the vsiRNAs target potato genes are involved in plant hormone signaling, plant-pathogen interactions, plant defense and stress response processes. Additionally, RNA viruses are prone to rapid evolution that could result in the emergence of more virulent and resistance-breaking strains. As such, genetic diversity studies are crucial to assess the virus population structure and evolutionary dynamics. In this study, the genetic diversity of TRV isolates from potato growing regions in the USA was elucidated. The genome of TRV is segmented into two, RNA1 and RNA2. Phylogenetic analysis of RNA2 genes, coat protein and nematode transmission (2b) nucleotide sequences revealed tendency for geographical adaptation of TRV while recombination analysis on RNA1 suggested isolates from Idaho, North Dakota, Colorado and Michigan as recombinants between American and European isolates. The replicase genes were found to be largely conserved and exhibited positive diversification in non-potato TRV isolate suggesting involvement in host adaptation. The 1b gene in RNA1 was observed to be less constrained compared to other RNA1 genes, this relates to its function as suppressor of RNA-silencing and could enable it to keep up with the evolutionary war in virus-host interactions. New insights into potato-virus interaction and virus evolution were revealed.

TUBER NECROSIS-CAUSING VIRUSES OF POTATO: GENETIC DIVERSITY AND HOST-PATHOGEN INTERACTIONS

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