Resistance to Wheat streak mosaic virus– a survey of resources and development of molecular markers

Wheat streak mosaic virus (WSMV) has been newly documented in Australia. The vulnerability of contemporary Australian elite wheat germplasm prompted a survey for effective resistance against an Australian isolate, WSMV‐ACT. This study confirms the effectiveness of previously reported sources of resistance and shows that new sources of resistance also confer protection. The resistance derived from Thinopyrum intermedium (Wsm1) as a 4D translocation and a new 4A translocation, and two bread wheat resistances, Wsm2 and the new source c2652, were effective against WSMV‐ACT in glasshouse experiments. Wsm1 was effective at lower temperatures but ineffective above 20°C, a temperature sensitivity shared with many of the derivatives of Wsm2 except for one new selection which was effective at 26°C. True wheats c2652 and Wsm2 selection CA745, and amphiploids Zhong1, Zhong2, Zhong4, Zhong5, TAF46, Summer1, Ot38 and OK7211542 were uniformly resistant at 20, 25 and 28°C. New sources of resistance were identified in a Th. scirpeum‐wheat amphiploid, B84‐994, and in chromosome addition lines Z2, Z6 and TAi27, derived from wheat‐Th. intermedium partial amphiploids. Several new, tightly linked SSR, RAPD and EST‐ILP PCR markers were developed for tracking the various Th. intermedium translocations associated with Wsm1, including the smaller translocations on wheat chromosome 4AS and 4DS. Three markers for the 4A‐Wsm1 translocation were validated on a segregating breeding population.     

A myosin passenger protein gene (<Emphasis Type="Italic">FaSmy1</Emphasis>) is an essential regulator of cell development,pathogenicity, DON biosynthesis,and resistance to the fungicide phenamacril in <Emphasis Type="Italic">Fusarium asiaticum</Emphasis>

Wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) are important viruses of wheat (Triticum aestivum L.) in the Great Plains of United States. In addition to agronomic practices to prevent damage from these viruses, temperature sensitive resistance genes Wsm1, Wsm2 and Wsm3, have been identified. However, threshold temperatures for Wsm1 and Wsm3 have not been clearly defined. To better understand these two resistance genes, wheat lines C.I.15092 (Wsm1), KS96HW10–3 (Wsm1), and KS12WGGRC59 (Wsm3) were evaluated for WSMV resistance at 27, 30, 33 and 35 °C and for TriMV resistance at 18, 21, 24, 27, 30, 33 and 35 °C. The results showed that only C.I.15092 remained resistant at 30 °C for both viruses. This line also tolerated TriMV at 33 and 35 °C with less sever symptom and lower infection rates. Wheat lines KS96HW10–3 and KS12WGGRC59 hold resistance to TriMV up to 21 °C. Molecular marker results suggested that the resistance in C.I.15092 is most probably conditioned by the resistance gene Wsm1 and additional gene(s) other than Wsm2 and Wsm3.     

First occurrence of <Emphasis Type="Italic">Sugarcane streak mosaic virus</Emphasis> infecting sugarcane in Indonesia

On plants at 59 sugarcane plantations in Central and East Java, Indonesia, we found virus-like symptoms such as streak mosaic. The virus was transmitted mechanically and was sett-borne. The nucleotide sequence of the coat protein gene had the highest identity with that of Sugarcane streak mosaic virus (SCSMV) isolate Pakistani. We tentatively designate this isolate as SCSMV-Idn (Indonesia).     

A novel putative member of the family Benyviridae is associated with soilborne wheat mosaic disease in Brazil

Soilborne wheat mosaic disease (SBWMD), originally attributed to infections by Soilborne wheat mosaic virus (SBWMV) and Wheat spindle streak mosaic virus (WSSMV), is one of the most frequent virus diseases and causes economic losses in wheat in southern Brazil. This study aimed to characterize molecularly the viral species associated with wheat plants showing mosaic symptoms in Brazil. Wheat leaves and stems displaying mosaic symptoms were collected from different wheat cultivars in Passo Fundo municipality, Rio Grande do Sul State, southern Brazil. Double-stranded RNA was extracted and submitted to cDNA library synthesis and next-generation sequencing. No sequences of SBWMV and WSSMV were detected but the complete genome sequence of a putative new member of the family Benyviridae was determined, for which the name wheat stripe mosaic virus (WhSMV) is proposed. WhSMV has a bipartite genome with RNA 1 and RNA 2 organization similar to that of viruses belonging to Benyviridae. WhSMV RNA 1 has a single open reading frame (ORF) encoding a polyprotein with putative viral replicase function. WhSMV RNA 2 has six ORFs encoding the coat protein, the major protein (read-through), triple gene block movement proteins (TGB 1, 2 and 3) and ORF 6 (hypothetical protein). In addition to the genomic organization and nucleotide and amino acid sequence identities, phylogenetic analyses also corroborated that WhSMV is a virus species of the Benyviridae. However, isolates of WhSMV formed a clade distinct from members of the genus Benyvirus. It was also demonstrated that the plasmodiophorid Polymyxa graminis is associated with wheat roots showing SBWMD symptoms and infected by WhSMV.     

Incidence of viruses in <Emphasis Type="Italic">Alstroemeria</Emphasis> plants cultivated in Japan and characterization of <Emphasis Type="Italic">Broad bean wilt virus-2, Cucumber mosaic virus</Emphasis> and <Emphasis Type="Italic">Youcai mosaic virus</Emphasis>

Alstroemeria plants were surveyed for viruses in Japan from 2002 to 2004. Seventy-two Alstroemeria plants were collected from Aichi, Nagano, and Hokkaido prefectures and 54.2% were infected with some species of virus. The predominant virus was Alstroemeria mosaic virus, followed by Tomato spotted wilt virus, Youcai mosaic virus (YoMV), Cucumber mosaic virus (CMV), Alstroemeria virus X and Broad bean wilt virus-2 (BBWV-2). On the basis of nucleotide sequence of the coat protein genes, all four CMV isolates belong to subgroup IA. CMV isolates induced mosaic and/or necrosis on Alstroemeria. YoMV and BBWV-2 were newly identified by traits such as host range, particle morphology, and nucleotide sequence as viruses infecting Alstroemeria. A BBWV-2 isolate also induced mosaic symptoms on Alstroemeria seedlings.     

A new furovirus infecting barley in France closely related to the Japanese soil-borne wheat mosaic virus

In April 2001, stunted barley plants bearing mosaic symptoms were observed in a field in France (Marne Department, 51). Rod-shaped and flexuous particles were visualized by electron microscopy and positive serological reactions were detected by ELISA with Barley yellow mosaic virus (BaYMV) and Soil-borne cereal mosaic virus (SBCMV) polyclonal antisera. The tubular virus which was soil transmissible to barley cv. Esterel was separated from BaYMV by serial mechanical inoculations to barley cv. Esterel. This furo-like virus, in contrast to a French isolate of SBCMV, could be transmitted to Hordeum vulgare, Avena sativa, Beta vulgaris and Datura stramonium. RT-PCR was used to amplify the 3′-terminal 1500 nucleotides of RNA1 and the almost complete sequence of RNA2. Nucleotide and amino acid sequence analyses revealed that the French virus infecting barley is closely related to a Japanese isolate of Soil-borne wheat mosaic virus (SBWMV-JT) which was originally isolated from barley. This French isolate was named SBWMV-Mar. The 3′ UTRs of both RNAs can be folded into tRNA-like structures which are preceded by a predicted upstream pseudoknot domain with seven and four pseudoknots for RNA1 and RNA2, respectively. The four pseudoknots strongly conserved in RNAs 1 and 2 of SBWMV-Mar show strong similarities to those described earlier in SBWMV RNA2 and were also found in the 3′ UTR of Oat golden stripe virus RNAs 1 and 2 and Chinese wheat mosaic virus RNA2. Sequence analyses revealed that the RNAs 2 of SBWMV-Mar and -JT are likely to be the product of a recombination event between the 3′ UTRs of the RNAs 2 of SBWMV and SBCMV. This is the first report of the occurrence of an isolate closely related to SBWMV-JT outside of Japan.     

Molecular and biological characterization of Cowpea mild mottle virus isolates infecting soybean in Brazil and evidence of recombination

The biological and molecular characterization of six isolates of a new Cowpea mild mottle virus strain (CPMMV; Carlavirus, Betaflexiviridae) are reported. Soybean plants with mosaic and stem necrosis were collected in Bahia, Goiás, Mato Grosso and Minas Gerais states, Brazil. Complete genomes of the CPMMV isolates are 8180–8198 nucleotides (nt) long, excluding the 3′‐polyadenylated tail, and have 67–68% nt sequence identity with a Ghana isolate of CPMMV, the only CPMMV isolate for which the genome has previously been sequenced. The replicase has only 60–61% nt sequence identity with the Ghana CPMMV isolate, and the coat protein (CP) is highly conserved (79% nt sequence identity and 95–96% amino acid sequence identity). The high CP identity and the phylogenetic analyses supported the classification of the Brazilian isolates as CPMMV. Biological and molecular differences with the Ghana CPMMV isolate were found and indicated that the six isolates represent a distinct CPMMV strain denominated as CPMMV‐BR. Furthermore, it is shown that recombination occurred mainly in the polymerase gene, and may occur less frequently in other regions of the CPMMV genome.     

Sequence of the 3′-terminal region of the RNA of a mite transmitted potyvirus fromHordeum murinum L.

The 3026 nucleotides upstream of the 3-polyadenylated tract of a mite transmitted virus fromHordeum murinum L. were cloned and sequenced, and portions of the sequence were expressed inEscherichia coli. Sequence comparisons with wheat streak mosaic virus (WSMV), Agropyron mosaic virus (AgMV) and Hordeum mosaic cirus (HoMV), three mite transmitted potyviruses, and potato virus Y (PVY), the type member of the genusPotyvirus, revealed that the virus is probably a potyvirus, but distinct from WSMV, AgMV, HoMV, and PVY. Serological tests further demonstrated these differences and that the virus is serologically related to another potyvirus, brome streak mosaic virus (BrSMV). We conclude that the virus should be named as the Hordeum isolate of BrSMV.     

Sequence analyses of Wheat dwarf virus isolates from different hosts reveal low genetic diversity within the wheat strain

Wheat dwarf virus (WDV) causes disease in wheat (Triticum aestivum) and barley (Hordeum vulgare) in many parts of Europe. The host range also includes many species of the family Poaceae. WDV is only transmitted by the leafhopper Psammotettix alienus. During a five‐year period (2001–2005), grass samples were collected in central Sweden in the vicinity of fields with WDV‐infected winter wheat. Screening with ELISA and PCR identified WDV in a low number of samples (8/1098) from only three grass species: Apera spica‐venti, Avena fatua and Poa pratensis. In addition, triticale was found to be positive. Fourteen WDV isolates from Avena fatua, Apera spica‐venti, Triticum aestivum, Lolium multiflorum, Poa pratensis, triticale and the insect vector Psammotettix alienus, were partially sequenced (ca. 1200 nucleotides), providing the first published WDV sequences from the insect vector. All isolates belonged to the wheat strain of WDV and the genetic diversity was low. Phylogenetic analyses showed no clear grouping according to geographical location or host species. The results suggest that the same WDV genotypes are infecting both wheat and grasses in Sweden. Interestingly, one group of isolates (subtype B) formed a distinct clade in the phylogenetic tree. Subtype B was always found in mixed infection with the main genotype. Complete sequencing of a subtype B isolate showed that it was 98·6% identical to a typical wheat isolate from the same plant.     

Characterization of a New Barley Mild Mosaic Virus Pathotype in France

In March 2002 in a French field, severe mosaic symptoms appeared on plants of the barley cultivar Tokyo with the rym5 locus controlling resistance to all European strains of barley yellow mosaic virus (BaYMV) and barley mild mosaic virus (BaMMV). Electron microscopic examination revealed that the disease symptoms were associated with the presence of flexuous particles which resemble bymoviruses. From these observations and after enzyme-linked immunosorbent assay analysis it was first determined that the plants could be infected by BaMMV and BaYMV. Mechanical transmission of these viruses to the barley cultivar Magie susceptible to both viruses was only possible for BaMMV. This new pathotype (BaMMV-Sil) from Sillery (Marne Department, 51, France), in contrast to another mechanically transmitted French BaMMV isolate (BaMMV-MF), could be transmitted mechanically to two barley cultivars (Tokyo, Misato Golden), Arachis hypogaea, Datura stramonium and Lactuca sativa. BaMMV-Sil was indistinguishable from three BaMMV isolates from Germany (G), Japan (Ka1) and France (PF) by monoclonal antibodies in ELISA while the Japanese isolate (Na1) and BaMMV-MF were distinguishable from all. The sequence of the 3-terminal region of BaMMV-Sil RNA1 was determined. Comparison with previously published sequence data of capsid proteins indicated that BaMMV-Sil was closely related to BaMMV-Ka1, BaMMV-G and another German isolate (BaMMV-ASL1). Resistance-breaking BaMMV strains able to infect cultivars carrying the rym5 locus have also been described in Japan (BaMMV-Na1) and Korea (BaMMV-Kor). No specific amino acid differences were detected between the capsid proteins of BaMMV-Sil, BaMMV-Na1, BaMMV-Kor and those BaMMV isolates that do not overcome the rym5 resistance gene. These results indicate that BaMMV-Sil is a new pathotype of BaMMV in France and suggests that the capsid protein is not the determining factor of the pathogenicity towards the resistance gene rym5.     

Molecular and biological characterization of Potato mop‐top virus (PMTV,Pomovirus) isolates from the potato‐growing regions of Colombia

Potato mop‐top virus (PMTV) causes necrotic flecks inside and on tubers in temperate countries. In South America, these symptoms have not been observed, although the presence of the virus has been confirmed in the Andes and in Central America. To characterize PMTV isolates from the Andes, soil samples were taken from the main potato‐producing regions in Colombia and virus was recovered by planting Nicotiana benthamiana as bait plants. The complete genomes of five isolates were sequenced and three of the isolates were inoculated to four different indicator plants. Based on sequence comparisons, three types of RNA‐CP (RNA2) and RNA‐TGB (RNA3) were found. The isolates from the centre of the country (CO3 and CO4) were similar to isolates from Europe. The genomes of CO1, CO2 and CO5 differ from other PMTV isolates, placing them in a separate clade in phylogenetic trees. The three Colombian isolates (CO1, CO2 and CO5) only induced slightly different symptoms in the indicator plants. However, the isolate from the northwest of the country (CO1) induced stronger symptoms in N. benthamiana including severe stunting. A correlation between the genotype of the isolates and the symptoms they induced on indicator plants was not found.     

Molecular characterisation of <Emphasis Type="Italic">Turnip mosaic virus</Emphasis> isolates from Brassicaceae weeds

Eight provinces of Iran were surveyed during 2003–2008 to find Brassicaceae reservoir weed hosts of Turnip mosaic virus (TuMV). A total of 532 weed samples were collected from plants with virus-like symptoms. The samples were tested for the presence of TuMV by enzyme-linked immunosorbent assay using specific antibodies. Among those tested, 340 samples (64%) were found to be infected with TuMV. Rapistrum rugosum, Sisymberium loeselii, S. irio and Hirschfeldia incana were identified as the Brassicaceae weed hosts of TuMV, and the former two plant species were found to be the most important weed hosts for the virus in Iran. The full-length sequences of the genomic RNAs of IRN TRa6 and IRN SS5 isolates from R. rugosum and S. loeselii were determined. No evidence of recombination was found in both isolates using different recombination-detecting programmes. Phylogenetic analyses of the weed isolates with representative isolates from the world showed that the IRN TRa6 and IRN SS5 isolates fell into an ancestral basal-Brassica group. This study shows for the first time the wide distribution and phylogenetic relationships of TuMV from weeds in the mid-Eurasia of Iran.     

Molecular and biological characterization of <Emphasis Type="Italic">Chrysanthemum stem necrosis virus</Emphasis> isolates from distinct regions in Japan

Three isolates of Chrysanthemum stem necrosis virus (CSNV) were obtained from chrysanthemum plants in distinct regions of Japan in 2006 and 2007. All the original host plants showed severe necrotic symptoms on the leaves and stems. Amino acid sequence data of the nucleocapsid protein genes of the three isolates (CbCh07A, TcCh07A, and GnCh07S) showed high identities with those of two other CSNV isolates, HiCh06A L1 from Japan and Chry1 from Brazil. Furthermore, for the first time the complete nucleotide sequence of the S RNA was determined for CSNV (isolate HiCh06A). In phylogenetic analysis based on the non-structural protein genes from the genus Tospovirus, HiCh06A L1 was placed in the same genetic group as Tomato spotted wilt virus (TSWV) and Impatiens necrotic spot virus. Host range examination for isolates HiCh06A L1 and CbCh07A showed that green pepper (cv. ‘Kyoyutaka’, ‘Saitamawase’, ‘Tosakatsura’, ‘L3 sarara’ and ‘L3 miogi’) and tomato (cv. ‘Sekaiichitomato’) were systemically susceptible hosts, whereas TSWV-resistant Solanaceae species, Capsicum chinense, Lycopersicon peruvianum and a TSWV-resistant cultivar of green pepper (cv. TSR miogi), were resistant.     

Leonotis nepetaefolia: An important plant virus reservoir in central Mexico

The presence of viruses in the weedLeonotis nepetaefolia in central México is reported from two field surveys.L. nepetaefolia, with viral-like symptoms such as mosaic, leaf deformation and calico, was observed growing next to cultivated fields in the Valley of Atlixco, Puebla, an important agricultural region in Mexico. The viruses harbored by this plant were characterized biologically, serologically and by molecular methods. The viruses detected wereAlfalfa mosaic virus (AMV),Cucumber mosaic virus (CMV), a satellite RNA of CMV (CMV satRNA) andTobacco mosaic virus (TMV). This last one was detected only during the first survey. CMV was the predominant virus found in both surveys, and was associated mostly to mosaic symptom. Phylogenetic analysis based on the coat protein gene sequence of CMV indicated that this isolate belongs to subgroup IA and confirmed that it is a mosaic-inducing isolate, whereas AMV belongs to subgroup II. Finally, CMV satRNA was found to be a non-necrogenic ameliorative variant, both by symptomatology and by phylogenetic analysis. Our results suggest thatL. nepetaefolia is a reservoir for several viruses in central Mexico, and given its wide distribution in several parts of the world, its role as a virus reservoir could be more general. http://www.phytoparasitica.org posting Aug. 31, 2005.     

Distinct strains of the re‐emergent Cassava common mosaic virus (genus: Potexvirus) infecting cassava in Argentina

Cassava common mosaic disease (CCMD) has been reported in all regions where cassava is grown in the Americas and the causal agent, Cassava common mosaic virus (CsCMV), has been identified as a mechanically transmitted potexvirus (Alphaflexiviridae). In Argentina, cassava is grown mainly in the northeast (NEA) region that shares borders with Brazil and Paraguay. Increasing incidences of CCMD were observed during the years 2014 to 2016 associated with severe leaf mosaic symptoms and yield reductions where the occurrence of CsCMV was confirmed by RT‐PCR and sequencing. In this work, the virus has been successfully purified and a double‐antibody sandwich (DAS‐) ELISA test has been developed from an Argentinean isolate of CsCMV to extend the diagnostics of the disease. A collection of 726 samples was screened and CsCMV was detected with 100% prevalence in the NEA region. Additional co‐infecting viruses were detected in some plants (64.4%); in these, CCMD symptoms correlated with CsCMV only, although more severe symptoms could be observed in mixed infected plants. Sequence analysis of the conserved RdRp domain showed a wider diversity of CsCMV isolates. Interestingly, a separate phylogenetic cluster was formed by isolates from the NEA region that only shared 77.1% to 80.3% nucleotide identity with the other clusters. These results indicate the presence of mixed strains occurring in the NEA region and suggest the presence of geographically distinct strains of CsCMV in South America.