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Small RNA profiling of virus-infected grapevines: evidences for virus infection-associated and variety-specific miRNAs

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Abstract

Grapevine is one of the economically and culturally important perennial fruit crops. More than 60 viruses infect grapevines and adversely affect their growth and development. Latent infection of most viruses in grapevines leads to chronic modulation of gene expression at transcriptional and post-transcriptional levels. Plant small RNAs (sRNAs) consist of microRNA (miRNA) and small interfering RNA (siRNA). miRNAs are expressed from the plant genome while most siRNAs are derived from double-stranded RNA molecules which are intermediates during virus replication. In a previous study, we constructed four cDNA libraries of sRNAs that were enriched from three virus-infected grapevines and one virus-free grapevine. Majority of siRNAs align most closely with the genomes of DNA viruses in the genus Badnavirus, family Caulimoviridae that led to the discovery of a new Grapevine vein clearing virus in grapevines. In this study, we conducted a comprehensive analysis of miRNAs in the four cDNA libraries and identified novel and stress-related miRNAs. The results indicated that miRNA abundance was influenced by virus infection. A total of 54 new miRNAs were identified and characterized, six of which, VITIS-MIR17, 18, 19, 20, 21, and 22, were detected only in virus-infected samples. One target of VITIS-MIR18 is the gene coding a non-apical meristem protein (GSVIVT00035370001), a transcription factor in the regulation of plant development and stress responses. Among the virus infection-induced known miRNAs, miRNA168 and miRNA3623 likely regulate grapevine’s defense response, miRNA319 and miRNA395 modulate the expression of genes that are involved in nutrient metabolisms while miRNA396 plays a role in the regulation of cell division and cell cycle. The abiotic stress-induced miR169 and mi398 were negatively regulated by virus infection in grapevines. In addition, variety-specific miRNAs were discovered and compiled. The newly discovered miRNAs expand the miRNA profiles in the Vitis species. The characteristics of variety-specific and virus infection-associated miRNAs help understand the biology underlying the development and defense response of grapevines.

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Acknowledgments

This project was supported by USDA-CSREES (2009-38901-19962) grant to WQ. We thank Chin-Feng Hwang for critical reviewing of the manuscript. We are indebted to Brian Dalley in the Microarray and Genomic Analysis Core Facility at the University of Utah, Salt Lake City, UT, USA, for technical assistance with construction of small RNA libraries and deep sequencing.

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  1. Kashmir Singh

    Present address: Department of Biotechnology, Panjab University, Chandigarh, 160014, Punjab, India

Authors and Affiliations

  1. Center for Grapevine Biotechnology, William H. Darr School of Agriculture, Missouri State University, Mountain Grove, MO, 65711, USA

    Kashmir Singh, Aarthi Talla & Wenping Qiu

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  1. Kashmir Singh
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  2. Aarthi Talla
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  3. Wenping Qiu
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Correspondence to Wenping Qiu.

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Supplemental Table 1

List of new miRNAs and their predicted target genes (DOCX 25 kb)

Supplemental Table 2

Read count of novel miRNA in each grapevine and their detailed annotations and predicted target genes (XLSX 30 kb)

Supplemental Table 3

Predicted target genes of virus-induced miRNAs in grapevine (DOCX 24 kb)

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Singh, K., Talla, A. & Qiu, W. Small RNA profiling of virus-infected grapevines: evidences for virus infection-associated and variety-specific miRNAs. Funct Integr Genomics 12, 659–669 (2012). https://doi.org/10.1007/s10142-012-0292-1

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