Prevalence and Distribution of Beet Necrotic Yellow Vein Virus Strains in North Dakota and Minnesota

Abstract

Beet necrotic yellow vein virus (BNYVV) is the causal agent of rhizomania, a disease of global importance to the sugar beet industry. The most widely implemented resistance gene to rhizomania to date is Rz1, but resistance has been circumvented by resistance-breaking (RB) isolates worldwide. In an effort to gain greater understanding of the distribution of BNYVV and the nature of RB isolates in Minnesota and eastern North Dakota, sugar beet plants were grown in 594 soil samples obtained from production fields and subsequently were analyzed for the presence of BNYVV as well as coding variability in the viral P25 gene, the gene previously implicated in the RB pathotype. Baiting of virus from the soil with sugar beet varieties possessing no known resistance to rhizomania resulted in a disease incidence level of 10.6% in the region examined. Parallel baiting analysis of sugar beet genotypes possessing Rz1, the more recently introgressed Rz2, and with the combination of Rz1 + Rz2 resulted in a disease incidence level of 4.2, 1.0, and 0.8%, respectively. Virus sequences recovered from sugar beet bait plants possessing resistance genes Rz1 and/or Rz2 exhibited reduced genetic diversity in the P25 gene relative to those recovered from the susceptible genotype while confirming the hypervariable nature of the coding for amino acids (AAs) at position 67 and 68 in the P25 protein. In contrast to previous reports, we did not find an association between any one specific AA signature at these positions and the ability to circumvent Rz1-mediated resistance. The data document ongoing virulence development in BNYVV populations to previously resistant varieties and provide a baseline for the analysis of genetic change in the virus population that may accompany the implementation of new resistance genes to manage rhizomania.

Application of a Reverse Genetic System for Beet Necrotic Yellow Vein Virus to Study Rz1 Resistance Response in Sugar Beet

“…Furthermore, the variability in absorbance values between AYPR, VCHG, and VLHG suggests that the tetrad variants are associated with a different fitness advantage in the resistant genotype. This might be an explanation for the large variability of different tetrad variants found in natural virus populations (Galein et al, 2018;Weiland et al, 2019), which is also indicative for an ongoing virus evolution. The replacement of the RNA3 in the non-resistance-breaking BNYVV clone by an RNA3 derived from a resistance-breaking virus population demonstrated that two A-type populations can exchange genome components leading to infectious reassortments overcoming Rz1 resistance.…”

RNAseq Analysis of Rhizomania-Infected Sugar Beet Provides the First Genome Sequence of Beet Necrotic Yellow Vein Virus from the USA and Identifies a Novel Alphanecrovirus and Putative Satellite Viruses

“…The most variable region of the BNYVV genome worldwide is the noted “tetrad region” encoded on RNA3 between nucleotides 645 and 656 (E12 strain, NCBI Accession #EU330455.1; [ 5 ]). The most common tetrad amino acids (AAs) observed in the samples of the present study included VCHG, ACHG, VLHG, and TLHG, the first three of which have a prior association with the breaking of Rz1-gene-based resistance in sugar beet [ 5 , 14 , 17 ]. All sequences were used to confirm the placement of the BNYVV-US within phylogenetic groupings ( Figure 2 ) previously reported by Chiba et al [ 25 ], Schirmer et al [ 34 ], and Zhuo et al [ 35 ].…”

“…An exception to this observation worldwide is nucleotides encoding the “tetrad” of AAs within the p25 protein produced from RNA 3. The nucleotides at this location are considered to be among the most hypervariable within all eukaryotic viruses [ 25 , 34 , 43 ], a feature observed in our own recent study [ 17 ]. Moreover, recent associative [ 16 , 17 , 34 ] and functional [ 5 , 44 ] evidence suggests that variability in this region may account for the ability for some strains of the virus to circumvent dominant resistance genes in the sugar beet crop.…”

“…To recover BNYVV from infested soil samples, we followed the methodology described by Weiland et al [ 17 ]. Briefly, rhizomania-susceptible sugar beet seeds of the cultivar SLC4-K583-G1C (SES VanderHave; Tienen, Belgium) were sown in 250 mL pots containing one-part infested soil to one-part sterile sand.…”

“…Thus, genes, as well as non-coding regions, have been assigned functions in virus replication, encapsidation, intra- as well as inter-plant movement, silencing suppression, and pathogen aggressiveness [ 10 , 13 ]. Recent studies on the latter of these functions have led to the discovery of a highly mutable region in the p25 gene on RNA 3, implicated in the breaking of monogenic resistance provided by the Rz1 gene [ 5 , 14 , 15 , 16 , 17 ]. The Rz1 gene was discovered in sugar beet germplasm in the 1980s and, even with the breaking of this resistance by strains of BNYVV worldwide, it remains the most widely used gene for the management of this disease [ 6 ].…”