Transcriptome analysis provides insights into the responses of sweet potato to sweet potato virus disease (SPVD)

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Transcriptome responses in sweet potato infected with SPCSV and/or SPFMV were studied.

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Numerous genes, miRNAs and phasiRNAs were responsive mainly to the dual infection.

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Salicylic acid-mediated pathways play important roles in antiviral defense responses.

Sweet potato (Ipomoea batatas) ranks among the most important crops in the world and provides nutritional and economic sustainability for subsistence farmers in sub-Saharan Africa. Its production is mainly constrained by sweet potato virus disease (SPVD) caused by the coinfection of two positive-sense single-stranded RNA viruses, sweet potato chlorotic stunt virus (SPCSV) and sweet potato feathery mottle virus (SPFMV). Current understanding of sweet potato responses to SPCSV and SPFMV at the molecular level remains very limited. In this study, we performed deep sequencing of both messenger RNA (mRNA) and small RNA (sRNA) populations in an SPVD-susceptible cultivar ‘Beauregard’ upon viral infection, to identify biological pathways that contribute to both general and specific host responses to these important viral pathogens. We found that pathways related to stress response and signaling were significantly affected by viral infection. sRNA components of these pathways were predominantly affected in late stages of the coinfection by SPCSV and SPFMV. We identified several novel microRNAs that were responsive to viral infection, some of which were predicted to target nucleotide-binding site leucine-rich repeat (NBS-LRR) disease resistance genes. The downregulation of the salicylic acid-mediated defense response pathway in particular seems to be a result of the viral infection process, and can in part explain the susceptible nature of the ‘Beauregard’ cultivar.

Synergistic interactions of begomoviruses with Sweet potato chlorotic stunt virus (genus Crinivirus) in sweet potato (Ipomoea batatas L.)

Three hundred and ninety-four sweet potato accessions from Latin America and East Africa were screened by polymerase chain reaction (PCR) for the presence of begomoviruses, and 46 were found to be positive. All were symptomless in sweet potato and generated leaf curling and/or chlorosis in Ipomoea setosa. The five most divergent isolates, based on complete genome sequences, were used to study interactions with Sweet potato chlorotic stunt virus (SPCSV), known to cause synergistic diseases with other viruses. Co-infections led to increased titres of begomoviruses and decreased titres of SPCSV in all cases, although the extent of the changes varied notably between begomovirus isolates. Symptoms of leaf curling only developed temporarily in combination with isolate StV1 and coincided with the presence of the highest begomovirus concentrations in the plant. Small interfering RNA (siRNA) sequence analysis revealed that co-infection of SPCSV with isolate StV1 led to relatively increased siRNA targeting of the central part of the SPCSV genome and a reduction in targeting of the genomic ends, but no changes to the targeting of StV1 relative to single infection of either virus. These changes were not observed in the interaction between SPCSV and the RNA virus Sweet potato feathery mottle virus (genus Potyvirus), implying specific effects of begomoviruses on RNA silencing of SPCSV in dually infected plants. Infection in RNase3-expressing transgenic plants showed that this protein was sufficient to mediate this synergistic interaction with DNA viruses, similar to RNA viruses, but exposed distinct effects on RNA silencing when RNase3 was expressed from its native virus, or constitutively from a transgene, despite a similar pathogenic outcome.

Control of sweet potato virus diseases

Sweet potato (Ipomoea batatas) is ranked seventh in global food crop production and is the third most important root crop after potato and cassava. Sweet potatoes are vegetative propagated from vines, root slips (sprouts), or tubers. Therefore, virus diseases can be a major constrain, reducing yields markedly, often more than 50%. The main viruses worldwide are Sweet potato feathery mottle virus (SPFMV) and Sweet potato chlorotic stunt virus (SPCSV). Effects on yields by SPFMV or SPCSV alone are minor, or but in complex infection by the two or other viruses yield losses of 50%. The orthodox way of controlling viruses in vegetative propagated crops is by supplying the growers with virus-tested planting material. High-yielding plants are tested for freedom of viruses by PCR, serology, and grafting to sweet potato virus indicator plants. After this, meristem tips are taken from those plants that reacted negative. The meristems were grown into plants which were kept under insect-proof conditions and away from other sweet potato material for distribution to farmers after another cycle of reproduction.