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The effects of potato virus Y-derived virus small interfering RNAs of three biologically distinct strains on potato (Solanum tuberosum) transcriptome

September 19 2017 by INKOA
Resource image of the African potato platform

Potato virus Y (PVY) is one of the most economically important pathogen of potato that is present as biologically distinct strains. The virus-derived small interfering RNAs (vsiRNAs) from potato cv. Russet Burbank individually infected with PVY-N, PVY-NTN and PVY-O strains were recently characterized. Plant defense RNA-silencing mechanisms deployed against viruses produce vsiRNAs to degrade homologous viral transcripts. Based on sequence complementarity, the vsiRNAs can potentially degrade host RNA transcripts raising the prospect of vsiRNAs as pathogenicity determinants in virus-host interactions. This study investigated the global effects of PVY vsiRNAs on the host potato transcriptome. 

The strain-specific vsiRNAs of PVY, expressed in high copy number, were analyzed in silico for their proclivity to target potato coding and non-coding RNAs using psRobot and psRNATarget algorithms. Functional annotation of target coding transcripts was carried out to predict physiological effects of the vsiRNAs on the potato cv. Russet Burbank. The downregulation of selected target coding transcripts was further validated using qRT-PCR. Results The vsiRNAs derived from biologically distinct strains of PVY displayed diversity in terms of absolute number, copy number and hotspots for siRNAs on their respective genomes. The vsiRNAs populations were derived with a high frequency from 6 K1, P1 and Hc-Pro for PVY-N, P1, Hc-Pro and P3 for PVY-NTN, and P1, 3′ UTR and NIa for PVY-O genomic regions. The number of vsiRNAs that displayed interaction with potato coding transcripts and number of putative coding target transcripts were comparable between PVY-N and PVY-O, and were relatively higher for PVY-NTN. The most abundant target non-coding RNA transcripts for the strain specific PVY-derived vsiRNAs were found to be MIR821, 28S rRNA,18S rRNA, snoR71, tRNA-Met and U5. Functional annotation and qRT-PCR validation suggested that the vsiRNAs target genes involved in plant hormone signaling, genetic information processing, plant-pathogen interactions, plant defense and stress response processes in potato. Conclusions The findings suggested that the PVY-derived vsiRNAs could act as a pathogenicity determinant and as a counter-defense strategy to host RNA silencing in PVY-potato interactions. The broad range of host genes targeted by PVY vsiRNAs in infected potato suggests a diverse role for vsiRNAs that includes suppression of host stress responses and developmental processes. The interactome scenario is the first report on the interaction between one of the most important Potyvirus genome-derived siRNAs and the potato transcripts. Electronic supplementary material The online version of this article (doi:10.1186/s12985-017-0803-8) contains supplementary material, which is available to authorized users.


Gender-differentiated trait preferences for sweetpotato varieties in Tanzania
January 11 2022 by INKOA

This report is an update of information on gender-differentiated producer and consumer preferred characteristics of sweet potato conducted at the Lake Zone of Tanzania.

Potato-legume intercropping enhances climate resilience and adaptive capacity of smallholder farmers
February 13 2021 by INKOA

In this research brief, two potential roles of potato-legume intercropping are reported: (i) improved control of soil erosion to make potato production more sustainable in the highlands; and (ii) optimizing soil temperatures, soil water contents and soil nutrient balance thus enabling potato production in the drier midland agro-food systems. The results are derived from six separate studies conducted between the 2014 wet season and 2018 dry season in Kenya.

Individual ambient ware potato storage excels in Uganda
December 28 2020 by INKOA

Improved individual ambient storage units allow proper ware potato storage, are easy to maintain and help smallholder farmers fetch higher prices; more education and suitable financial products are needed that entice farmers to invest in these units to enable greater profitability.

Analysis of consumers’ point of view regarding sustainability issues in Kenya
October 25 2019 by INKOA

The analysis of consumers’ point of view regarding sustainability issues in Kenya is a document delivered in the context of the  Horti-Green project  (Inclusive Green Horticultural Processing Sector in Kenya).

The Crops (Irish Potato) Regulations, Kenya 2019
June 29 2019 by INKOA

The long awaited Crops (Irish Potato) Regulations, 2019 were finally officially launched by the cabinet secretary, ministry of Agriculture, Livestock, Fisheries and Irrigation, Hon. Mwangi Kiunjuri, during the Annual National Potato Conference in KARLO, Loresho organized by National Potato Council of Kenya. The Regulations will address the prevailing challenges in the Potato Sector which include: Use of extended bags – henceforth, the maximum weight per unit package shall be 50kgs, Quality assurance and marketing and Licensing of actors in the Potato value chain. Check below or download a copy of the regulation here.

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