Ecology and Epidemiology of Wheat Curl Mite and Mite-Transmissible Viruses in Colorado and Insights into the Wheat Virome

Abstract

The wheat curl mite (WCM)-transmissible wheat streak disease complex is the most serious disease of wheat in the U.S. Great Plains. In the current study, we determined the genetic variability in WCM and mite-transmitted viruses in Colorado and identified sources of resistance in Colorado wheat germplasm to wheat streak disease complex. We identified two distinct genotypes of WCM, Type 1 and Type 2 based on the ribosomal ITS1 region. Both genotypes were found to co-exist throughout the wheat producing regions of Colorado. Analysis of the whole genome and partial coat protein sequences revealed rich diversity of wheat streak mosaic virus (WSMV) and High Plains wheat mosaic virus (HPWMoV) isolates collected from Colorado, whereas triticum mosaic virus (TriMV) showed low sequence variability. Analysis of WSMV isolates revealed two novel isolates and one that was 100% similar to a new variant of WSMV from Kansas. Interestingly, between 2-4 genotypes of all 8 RNA segments of HPWMoV were identified, which suggests new variants of emaraviruses and co-occurrence of multiple strains within host populations. Several novel viruses including mycoviruses were identified for the first time in Colorado. We found variation in WSMV resistance among wheat varieties; however a variety that harbored dual resistance to mite and WSMV had lower virus titer compared to varieties that contained single resistance gene. This suggests that pyramiding genes will ensure improved and durable resistance. Future research may be aimed at elucidating the dynamics, diversity, and distribution of the new WSMV and HPWMoV isolates and their responses to wheat genotypes.

Metagenomics Analysis of the Wheat Virome Identifies Novel Plant and Fungal-Associated Viral Sequences

“…To the best of our knowledge, this is the first report of the complete genome sequence of an ulaRNA identified in cereals. In a recent metagenomics study, contigs illustrating sequence similarities to ulaRNAs have also been reported in Colorado wheat samples [57].…”

Identification of a Novel Quinvirus in the Family Betaflexiviridae That Infects Winter Wheat

“…In recent years, the RNA sequencing (RNA-seq) analyses of field-grown crops, using next-generation sequencing (NGS) techniques, have enabled a more-detailed view on viral communities in the agroecosystem, often leading to new virus discoveries ( Roossinck et al, 2015 ). Several studies have investigated the virome of wheat and barley plants using deep RNA-seq ( Jo et al, 2018 ; Golyaev et al, 2019 ; Albrecht et al, 2020 ; Hodge et al, 2020 ; Singh et al, 2020 ), and some have identified the novel or uncharacterized wheat-infecting viruses, such as wheat stripe mosaic virus (a tentative benyvirus in the Benyviridae ), wheat yellow striate virus (an alphanucleorhabdovirus in the family Rhabdoviridae ), and European wheat striate mosaic virus (a putative tenuivirus in the family Phenuiviridae ; Liu et al, 2018 ; Valente et al, 2019 ; Somera et al, 2020 ). Nevertheless, there is still very limited information concerning virome or viral agents in the wheat plants that are associated with yellow mosaic disease.…”