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

Nourolah Soltani,Kimberly D Gwinn,Margaret Staton,Basavaprabhu L Patil

doi:10.1371/journal.pone.0244364

Nourolah Soltani, Kimberly D Gwinn + Show 2 more

Open Access

https://doi.org/10.1371/journal.pone.0244364

Copy DOI

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.

Highlights

Quinoa (Chenopodium quinoa Willd.) is a pseudocereal crop with high nutritional value [1, 2]
By 4 days after inoculation with cucumber mosaic virus (CMV), chlorotic local lesions developed across all replicates of ‘QQ74’ and ‘Jessie’, whereas all replicates of the bitter variety ‘Red Head’ had local systemic chlorosis that was not spread throughout the plant (Fig 1A, S2 Fig)
Infection was confirmed in vivo by immunoassay and in silico, with all CMV genomic RNAs detected in RNASeq and small RNASeq datasets (Fig 1B)

Summary

Introduction

Quinoa (Chenopodium quinoa Willd.) is a pseudocereal crop with high nutritional value [1, 2]. Quinoa varieties are classified as bitter or sweet depending upon saponin content of the seed. Mechanical abrasion or water rinsing is typically used to remove saponin from the seed of bitter varieties [6, 7]. Because these methods are costly and reduce nutritional value of the seeds [6, 8], quinoa cultivars with low seed saponin content (sweet cultivars) are desired [9]. Saponins from quinoa are active against several plant pathogens including viruses and are pre-existing defense factors in other pathosystems [10,11,12,13,14]

Objectives

Methods

Results

Discussion

Conclusion