Genetic diversity and recombination analysis of grapevine leafroll-associated virus 1 from China

Abstract

Grapevine leafroll-associated virus 1 (GLRaV-1) is one of the causal agents of grapevine leafroll disease (GLD). To investigate the prevalence and genetic variation of GLRaV-1 in China, 132 grapevine samples from 14 Chinese provinces and regions were tested using reverse transcription PCR (RT-PCR) and reverse transcription nested PCR (RT-nPCR). The samples included symptomatic and asymptomatic cultivars, and 36.4% of them tested positive for GLRaV-1. 'Beida' samples, previously identified as virus-free rootstocks, were also found to be infected with GLRaV-1 with an incidence of 40 . GLRaV-1 coat protein (CP) genes and heat-shock protein 70 (HSP70) genes from 43 GLRaV-1 isolates were selected and sequenced. Phylogenetic analysis of global CP and HSP70 gene sequences showed that all variants belonged to eight and seven groups, respectively. For CP gene sequence variants, group 4 was a new group that included only Chinese isolates. The results also showed that natural selection, rather than random processes, led to the evolution of variants belonging to CP gene sequence variants in group 2 and group 8. Furthermore, three new recombination events were identified in the GLRaV-1 CP gene population. This is the first report on the genetic variation of GLRaV-1 isolates in China, and this study will benefit grape clean-plant programs in China.

High-throughput sequencing applied for the identification of viruses infecting grapevines in Brazil and genetic variability analysis

“…Although the number of GSyV-1 sequences used in the analysis is small, this virus showed the greatest number of recombination events (Supplementary Table S4). The results of the recombination analysis suggest that this variability mechanism was important for generating genetic variation of the grapevine viruses analyzed in this work, in agreement with several studies that have shown the importance of recombination in the evolution of plant viruses (Fan et al 2015;Farooq et al 2013;Garcia-Arenal et al 2001;Lima et al 2013;Simon-Loriere and Holmes 2011;Rocha et al 2013;Zanardo et al 2014b). All coding regions of the analyzed viruses showed dN/ dS ratios (non-synonymous/synonymous substitutions ratios) lower than 1.0, indicating negative or purifying selection (Table 4).…”

Development of a Full-Length Infectious cDNA Clone of the Grapevine Berry Inner Necrosis Virus

“…In inoculated plants, the presence of GINV was assessed by RT-PCR. Total RNAs of the tested plants were extracted using a previously reported method [ 41 ]. RT-PCR was used to detect GINV using primer pairs GINVCP1A/1B and GINVMP1A/1B, amplifying the CP and MP, respectively, in accordance with a previously published method [ 23 ].…”

Methods for the Diagnosis of Grapevine Viral Infections: A Review

“…PCR is used for the detection of grapevine DNA viruses, for example, the GRBaV [15,74]. To detect the RNA viruses in a plant, PCR is carried out on the complementary DNA (cDNA) matrix that results from a reverse transcription reaction on the extracted plant RNA [75][76][77][78]. PCR and RT-PCR are often used in studies of viral genetic diversity [51,[79][80][81][82].…”

“…Nested PCR underlies several protocols for the detection of Nepovirus genus viruses, and these techniques make the diagnosis possible, with the sensitivity being several times higher than that of RT-PCR [103]. This method was used for studying the genetic diversity of GLRaV-1, GLRaV-3, and GFLV [77,104,105].…”