Sequence Variations Among 17 New Radish Isolates of Turnip mosaic virus Showing Differential Pathogenicity and Infectivity in Nicotiana benthamiana, Brassica rapa, and Raphanus sativus

Abstract

Infectious clones were generated from 17 new Korean radish isolates of Turnip mosaic virus (TuMV). Phylogenetic analysis indicated that all new isolates, and three previously characterized Korean radish isolates, belong to the basal-BR group (indicating that the pathotype can infect both Brassica and Raphanus spp.). Pairwise analysis revealed genomic nucleotide and polyprotein amino acid identities of >87.9 and >95.7%, respectively. Five clones (HJY1, HJY2, KIH2, BE, and prior isolate R007) had lower sequence identities than other isolates and produced mild symptoms in Nicotiana benthamiana. These isolates formed three distinct sequence classes (HJY1/HJY2/R007, KIH2, and BE), and several differential amino acid residues (in P1, P3, 6K2, and VPg) were present only in mild isolates HJY1, HJY2, and R007. The remaining isolates all induced systemic necrosis in N. benthamiana. Four mild isolates formed a phylogenetic subclade separate from another subclade including all of the necrosis-inducing isolates plus mild isolate KIH2. Symptom severity in radish and Chinese cabbage genotypes was not correlated with pathogenicity in N. benthamiana; indeed, Chinese cabbage cultivar Norang was not infected by any isolate, whereas Chinese cabbage cultivar Chusarang was uniformly susceptible. Four isolates were unable to infect radish cultivar Iljin, but no specific amino acid residues were correlated with avirulence. These results may lead to the identification of new resistance genes against TuMV.

Resistance to Turnip Mosaic Virus in the Family Brassicaceae

“…The phylogenetic analysis showed three distinct groups that generally correlated with geographical and/or the host plant origin of the isolates (Lehmann et al, 1997). With the increase, initially in partial and later in complete, sequence determination of TuMV isolates, other more recent approaches used have involved sequence analysis of the CP coding region (Farzadfar and Pourrahim, 2014;Parmar et al, 2017;Sánchez et al, 2003), the CP and P1 regions , the NIb and CP regions (Korkmaz et al, 2020), or using either most or all of the entire genome (Farzadfar et al, 2009;Gong et al, 2019;Hu et al, 2019;Korkmaz et al, 2008;Tomimura et al, 2003Tomimura et al, , 2004Tomitaka and Ohshima, 2006;Wang et al, 2009a;Yasaka et al, 2017), to examine either variation in sequence and infection of particular brassica species or specific changes that affect Palukaitis et al 4 infection of differential hosts.…”

“…Other studies have examined similar sequence variations associated with local host types and various groupings from isolates in Asia Minor (or most of Turkey) (Korkmaz et al, 2008(Korkmaz et al, , 2020, West Asia (Iran) (Farzadfar and Pourrahim, 2014;Farzadfar et al, 2009), South Asia (India) (from radish; Parmar et al, 2017), Vietnam (Nguyen et al, 2013b), Korea (from radish; Gong et al, 2019), and Australia (Nyalugwe et al, 2015b). The Turkish isolates fell into the basal-B, world-B, and Asian-BR groups; the Iranian isolates were in the basal-B and Asian-BR groups; the Indian (radish) isolates were in the basal-BR group; the Vietnamese isolates were in the world-B group; the Korean (radish) isolates were in the basal-BR group; and the Australian isolates were in the basal-B and world-B groups.…”

Five Newly Collected Turnip Mosaic Virus (TuMV) Isolates from Jeju Island, Korea are Closely Related to Previously Reported Korean TuMV Isolates but Show Distinctive Symptom Development

“… Phylogenetic tree constructed by the maximum-likelihood method with 1,000 bootstrap replicates, based on the complete genome sequences of 58 TuMV isolates including twenty other Korean isolates ( Gong et al, 2019 ) and the five new isolates from Jeju (indicated by arrows to the right of the isolate/accession number/country label). …”

“…TuMV together with cucumber mosaic virus (CMV) and radish mosaic virus (RaMV) were also reported from a nationwide survey of radish fields conducted in South Korea in 2014 ( Chung et al, 2015 ). Recently, Gong et al (2019) collected new TuMV isolates from South Korea that showed symptoms of varying severity on Chinese cabbage, Nicotiana benthamiana and radish. Although new TuMV isolates were reported from Korea recently, a detailed genetic analysis has not been conducted of TuMV isolates from Jeju Island where 30% of Korea’s vegetables including carrots, Chinese cabbage, and radish are produced ( Kim et al, 2012 ).…”

“…Additional TuMV sequences were obtained from NCBI Genbank. Phylogenetic relationship of TuMV isolates in this work were analyzed together with twenty previously reported Korean TuMV isolates ( Gong et al, 2019 ; Han et al, 2016 ) and 33 previously characterized TuMV isolates ( Nguyen et al, 2013a ) from NCBI. All isolates were compared based on aa and nt sequences.…”