Response of bitter and sweet Chenopodium quinoa varieties to cucumber mosaic virus: Transcriptome and small RNASeq perspective

Nourolah Soltani; Margaret Staton; Kimberly D Gwinn

doi:10.1371/journal.pone.0244364

Response of bitter and sweet Chenopodium quinoa varieties to cucumber mosaic virus: Transcriptome and small RNASeq perspective

PLoS One. 2021 Feb 23;16(2):e0244364. doi: 10.1371/journal.pone.0244364. eCollection 2021.

Authors

Nourolah Soltani^{1

2}, Margaret Staton¹, Kimberly D Gwinn¹

Affiliations

¹ Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America.
² Department of Plant Pathology, University of California-Davis, Davis, California, United States of America.

Abstract

Saponins are secondary metabolites with antiviral properties. Low saponin (sweet) varieties of quinoa (Chenopodium quinoa) have been developed because seeds high in saponins taste bitter. The aim of this study was to elucidate the role of saponin in resistance of quinoa to Cucumber mosaic virus (CMV). Differential gene expression was studied in time-series study of CMV infection. High-throughput transcriptome sequence data were obtained from 36 samples (3 varieties × +/- CMV × 1 or 4 days after inoculation × 3 replicates). Translation, lipid, nitrogen, amino acid metabolism, and mono- and sesquiterpenoid biosynthesis genes were upregulated in CMV infections. In 'Red Head' (bitter), CMV-induced systemic symptoms were concurrent with downregulation of a key saponin biosynthesis gene, TSARL1, four days after inoculation. In local lesion responses (sweet and semi-sweet), TSARL1 levels remained up-regulated. Known microRNAs (miRNA) (81) from 11 miR families and 876 predicted novel miRNAs were identified. Differentially expressed miRNA and short interfering RNA clusters (24nt) induced by CMV infection are predicted to target genomic and intergenic regions enriched in repetitive elements. This is the first report of integrated RNASeq and sRNASeq data in quinoa-virus interactions and provides comprehensive understanding of involved genes, non-coding regions, and biological pathways in virus resistance.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Chenopodium quinoa / genetics*
Chenopodium quinoa / virology
Cucumovirus*
Genes, Plant*
MicroRNAs
Plant Diseases / genetics*
Plant Diseases / virology
Transcriptome*

Substances

MicroRNAs

Grants and funding

This work was supported in part by the USDA National Institute of Food and Agriculture, Hatch project TEN0048 (K.D.G.). Research on small RNA was also supported by a grant to N.S. and K.D.G. from the University of Tennessee Graduate School. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.