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Allen W Miller - One of the best experts on this subject based on the ideXlab platform.

  • Blackwell Science, LtdPathogen profile Barley Yellow Dwarf virus: Luteoviridae or Tombusviridae?
    2014
    Co-Authors: Allen W Miller, S I Jun, Randy Beckett
    Abstract:

    Barley Yellow Dwarf virus (BYDV), the most economically important virus of small grains, features highly specialised relationships with its aphid vectors, a plethora of novel translation mechanisms mediated by long–distance RNA interactions, and an ambiguous taxonomic status. The structural and movement proteins of BYDV that confer aphid transmission and phloem-limitation properties resemble those of the Luteoviridae, the family in which BYDV is classified. In contrast, many genes and cis-acting signals involved in replication and gene expression most closely resemble those of the Tombusviridae. Taxonomy: BYDV is in genus Luteovirus, family Luteoviri-dae. BYDV includes at least two serotypes or viruses: BYDV-PAV and BYDV-MAV. The former BYDV-RPV is now Cereal Yellow Dwarf virus-RPV (CYDV-RPV). CYDV is in genus Polerovirus, fam-ily Luteoviridae. Genus Luteovirus shares many features with family Tombusviridae. Physical properties: ∼25 nm icosahedral (T = 3) virions. One major (22 kDa) and one minor (50–55 kDa) coat protein. 5.6–5.8 kb positive sense RNA genome with no 5′-cap and no poly(A) tail. Host range: Most grasses. Most important in oats, Barley and wheat. Also infects maize and rice. Symptoms: Yellowing and Dwarfing in Barley, stunting in wheat; reddening, Yellowing and blasting in oats. Some isolates cause leaf notching and curling. Key attractions: Model for the study of circulative trans-mission of aphid-transmitted viruses. Plethora of unusual trans-lation mechanisms. Evidence of recombination in recent evolutionary history creates taxonomic ambiguity. Economically important virus of wheat, Barley and oats, worldwide. Useful websites/meetings: International symposium

  • structural plasticity of Barley Yellow Dwarf virus like cap independent translation elements in four genera of plant viral rnas
    Virology, 2010
    Co-Authors: Zhaohui Wang, Jelena J Kraft, Alice Hui, Allen W Miller
    Abstract:

    The 3′ untranslated regions (UTRs) of many plant viral RNAs contain cap-independent translation elements (3′ CITEs). Among the 3′ CITEs, the Barley Yellow Dwarf virus (BYDV)-like translation elements (BTEs) form a structurally variable and widely distributed group. Viruses in three genera were known to harbor 3′ BTEs, defined by the presence of a 17-nt consensus sequence. To understand BTE function, knowledge of phylogenetically conserved structure is essential, yet the secondary structure has been determined only for the BYDV BTE. Here we show that Rose spring Dwarf-associated luteovirus, and two viruses in a fourth genus, Umbravirus, contain functional BTEs, despite deviating in the 17 nt consensus sequence. Structure probing by selective 2′-hydroxyl acylation and primer extension (SHAPE) revealed conserved and highly variable structures in BTEs in all four genera. We conclude that BTEs tolerate striking evolutionary plasticity in structure, while retaining the ability to stimulate cap-independent translation.

  • Barley Yellow Dwarf virus luteoviridae or tombusviridae
    Molecular Plant Pathology, 2002
    Co-Authors: Allen W Miller, Randy J Beckett
    Abstract:

    Summary Barley Yellow Dwarf virus (BYDV), the most economically important virus of small grains, features highly specialised relationships with its aphid vectors, a plethora of novel translation mechanisms mediated by long–distance RNA interactions, and an ambiguous taxonomic status. The structural and movement proteins of BYDV that confer aphid transmission and phloem-limitation properties resemble those of the Luteoviridae , the family in which BYDV is classified. In contrast, many genes and cis -acting signals involved in replication and gene expression most closely resemble those of the Tombusviridae . Taxonomy: BYDV is in genus Luteovirus, family Luteoviridae. BYDV includes at least two serotypes or viruses: BYDV-PAV and BYDV-MAV. The former BYDV-RPV is now Cereal Yellow Dwarf virus-RPV (CYDV-RPV). CYDV is in genus Polerovirus, family Luteoviridae. Genus Luteovirus shares many features with family Tombusviridae. Physical properties: ∼25 nm icosahedral (T = 3) virions. One major (22 kDa) and one minor (50–55 kDa) coat protein. 5.6–5.8 kb positive sense RNA genome with no 5′-cap and no poly(A) tail. Host range: Most grasses. Most important in oats, Barley and wheat. Also infects maize and rice. Symptoms: Yellowing and Dwarfing in Barley, stunting in wheat; reddening, Yellowing and blasting in oats. Some isolates cause leaf notching and curling. Key attractions: Model for the study of circulative transmission of aphid-transmitted viruses. Plethora of unusual translation mechanisms. Evidence of recombination in recent evolutionary history creates taxonomic ambiguity. Economically important virus of wheat, Barley and oats, worldwide. Useful websites/meetings: International symposium: ‘Barley Yellow Dwarf Disease: Recent Advances and Future Strategies’, CIMMYT, El Batan, Mexico, 1–5 September 2002, http://www.cimmyt.cgiar.org/Research/wheat/Conf_BYD_02/invitation.htm http://www.cimmyt.org/Research/wheat/BYDVNEWS/htm/BYDVNEWS.htm Aphid transmission animation: http://www.ppws.vt.edu/~sforza/tmv/bydv_aph.html

  • the 3 terminal structure required for replication of Barley Yellow Dwarf virus rna contains an embedded 3 end
    Virology, 2002
    Co-Authors: Gennadiy Koev, Randy J Beckett, Sijun Liu, Allen W Miller
    Abstract:

    Abstract We determined the 3′-terminal primary and secondary structures required for replication of Barley Yellow Dwarf virus (BYDV) RNA in oat protoplasts. Computer predictions, nuclease probing, phylogenetic comparisons, and replication assays of specific mutants and chimeras revealed that the 3′-terminal 109 nucleotides (nt) form a structure with three to four stem-loops followed by a coaxially stacked helix incorporating the last four nt [(A/U)CCC]. Sequences upstream of the 109-nt region also contributed to RNA accumulation. The base-pairing but not the sequences or bulges in the stems were essential for replication, but any changes to the 3′-terminal helix destroyed replication. The two 3′-proximal tetraloops tolerated all changes, but the two 3′-distal tetraloops gave most efficient replication if they fit the GNRA consensus. A mutant lacking the 3′-proximal stem-loop produced elevated levels of less-than-full-length minus strands, and no (+) strand. We propose that a “pocket” structure is the origin of (−)-strand synthesis, which is negatively regulated by the inaccessible conformation of the 3′ terminus, thus favoring a high (+)/(−) ratio. This 3′ structure and the polymerase homologies suggest that genus Luteovirus is more closely related to the Tombusviridae family than to other Luteoviridae genera.

  • primary and secondary structural elements required for synthesis of Barley Yellow Dwarf virus subgenomic rna1
    Journal of Virology, 1999
    Co-Authors: Gennadiy Koev, B R Mohan, Allen W Miller
    Abstract:

    Barley Yellow Dwarf luteovirus (BYDV) generates three 3′-coterminal subgenomic RNAs (sgRNAs) in infected cells. The promoter of sgRNA1 is a putative hot spot for RNA recombination in luteovirus evolution. The sgRNA1 transcription start site was mapped previously to either nucleotide 2670 or nucleotide 2769 of BYDV genomic RNA (gRNA) in two independent studies. Our data support the former initiation site. The boundaries of the sgRNA1 promoter map between nucleotides 2595 and 2692 on genomic RNA. Computer prediction, phylogenetic comparison, and structural probing revealed two stem-loops (SL1 and SL2) in the sgRNA1 promoter region on the negative strand. Promoter function was analyzed by inoculating protoplasts with a full-length infectious clone of the BYDV genome containing mutations in the sgRNA promoter. Because the promoter is located in an essential coding region of the replicase gene, we duplicated it in a nonessential part of the genome from which a new sgRNA was expressed. Mutational analysis revealed that secondary structure, but not the nucleotide sequence, was important at the base of SL1. Regions with both RNA primary and secondary structural features that contributed to transcription initiation were found at the top of SL1. Primary sequence, but not the secondary structure, was required in SL2, which includes the initiation site. Disruption of base pairing near the sgRNA1 start site increased the level of transcription three- to fourfold. We propose that both primary and secondary structures of the sgRNA1 promoter of BYDV play unique roles in sgRNA1 promoter recognition and transcription initiation.

Stewart M Gray - One of the best experts on this subject based on the ideXlab platform.

  • a chinese isolate of Barley Yellow Dwarf virus pav represents a third distinct species within the pav serotype
    Archives of Virology, 2007
    Co-Authors: F Liu, Stewart M Gray, Guanghe Zhou, Xifeng Wang, Y Liu, J Xie, Bida Gao
    Abstract:

    The complete nucleotide sequence of Barley Yellow Dwarf virus (BYDV) PAV-CN genomic RNA was determined. This represents the seventh complete genome sequence of a BYDV-PAV serotype. The genome organization of PAV-CN was comparable to that of other BYDV-PAV serotypes, but the nucleotide sequence of full genome was only 76.9-80.3% similar. Sequence similarity of individual open reading frames and untranslated regions (UTR) between PAV-CN and other PAV isolates ranged from 37.9 to 98.2%. Overall, PAV-CN was most similar to BYDV-PAS, which belongs to one of two distinct species within the PAV serotype of BYDV, although the 5' UTR and ORF1 of PAV-CN was most similar to BYDV-GAV, another member of the genus Luteovirus that is not serologically related to BYDV-PAV. These data suggest that PAV-CN may have undergone a recombination event with GAV and that PAV-CN represents a third distinct species within the PAV serotype of BYDV.

  • vector specificity of Barley Yellow Dwarf virus bydv transmission identification of potential cellular receptors binding bydv mav in the aphid sitobion avenae
    Virology, 2001
    Co-Authors: Diana L Coxfoster, Stewart M Gray, F E Gildow
    Abstract:

    Two proteins (SaM35 and SaM50) isolated from head tissues of the aphid vector, Sitobion avenae, were identified as potential receptors for Barley Yellow Dwarf virus MAV isolate (Luteoviridae) based on MAV virus overlay assays and immunoblots of urea SDS 2-D gels. An anti-idiotypic antibody (MAV4 anti-ID) that mimics an epitope on MAV virions and competes with MAV in antibody binding assays also bound to SaM50 and SaM35 and to six additional proteins including a GroEL homolog. No MAV-binding proteins were detected from the nonvector aphid, Rhopalosiphum maidis, although MAV4 anti-ID did react with four proteins from R. maidis. It is hypothesized that SaM35 and SaM50 may be MAV receptors involved in MAV transmission based on their high affinity for MAV and their unique association with the vector, S. avenae. The additional aphid proteins binding the MAV4 anti-ID may represent less specific virus-binding proteins facilitating transmission through different aphid tissues.

  • seasonal abundance of aphids homoptera aphididae in wheat and their role as Barley Yellow Dwarf virus vectors in the south carolina coastal plain
    Journal of Economic Entomology, 2001
    Co-Authors: Jay W Chapin, Dawn M Smith, James S Thomas, Stewart M Gray, Susan E Halbert
    Abstract:

    Aphid (Homoptera: Aphididae) seasonal flight activity and abundance in wheat, Triticum aestivum L., and the significance of aphid species as vectors of Barley Yellow Dwarf virus were studied over a nine-year period in the South Carolina coastal plain. Four aphid species colonized wheat in a consistent seasonal pattern. Greenbug, Schizaphis graminum (Rondani), and rice root aphid, Rhopalosiphum rufiabdominalis (Sasaki), colonized seedling wheat immediately after crop emergence, with apterous colonies usually peaking in December or January and then declining for the remainder of the season. These two aphid species are unlikely to cause economic loss on wheat in South Carolina, thus crop managers should not have to sample for the subterranean R. rufiabdominalis colonies. Bird cherry-oat aphid, Rhopalosiphum padi (L.), was the second most abundant species and the most economically important. Rhopalosiphum padi colonies usually remained below 10/row-meter until peaking in February or March. Barley Yellow Dwarf incidence and wheat yield loss were significantly correlated with R. padi peak abundance and aphid-day accumulation on the crop. Based on transmission assays, R. padi was primarily responsible for vectoring the predominant virus serotype (PAV) we found in wheat. Pest management efforts should focus on sampling for and suppressing this aphid species. December planting reduced aphid-day accumulation and Barley Yellow Dwarf incidence, but delayed planting is not a practical management option. English grain aphid, Sitobion avenae (F.), was the last species to colonize wheat each season, and the most abundant. Sitobion avenae was responsible for late-season virus transmission and caused direct yield loss by feeding on heads and flag leaves during an outbreak year.

  • Barley Yellow Dwarf luteoviruses and their predominant aphid vectors in winter wheat grown in south carolina
    Plant Disease, 1998
    Co-Authors: Stewart M Gray, Jay W Chapin, Dawn M Smith, Nanditta Banerjee, James S Thomas
    Abstract:

    Barley Yellow Dwarf is recognized as an important disease problem in winter wheat production in the southeastern United States, but there is relatively little known about the ecology and epidemiology of Barley Yellow Dwarf virus (BYDV) in this region. From 1991 to 1993, and in 1996 and 1997, winter wheat was sampled for BYDV throughout the principal wheat production areas in South Carolina. In addition, in 1997, a small number of samples were collected from fields in North Carolina and Kentucky. Plant samples were assayed to determine the BYDV serotype and, subsequently, coat protein sequences of isolates within the same serotype were compared using restriction fragment length polymorphisms. Representative BYDV isolates from South Carolina and type isolates from New York were compared in aphid transmission experiments using aphid species collected from South Carolina and laboratory colonies maintained in New York. The predominant BYDV serotype in South Carolina (in all years) was PAV, accounting for 94% of the total BYDV-infected samples analyzed. The RPV serotypes were more abundant in samples collected from western North Carolina and Kentucky. PAV isolates from all regions were identical to the New York BYDV-PAV in terms of serology and restriction fragment patterns. Furthermore, the aphid transmission phenotypes were similar for South Carolina and New York BYDV isolates. The predominant aphids colonizing winter wheat in South Carolina included Schizaphis graminum, Rhopalosiphum rufiabdominalis, R. padi, and Sitobion avenea. The South Carolina clones of R. padi and S. avenae were similar to the New York laboratory clones in their abilities to transmit various BYDV isolates from New York and South Carolina. In contrast to the New York clone of Schizaphis graminum that can vector SGV, PAV, and RPV, the S. graminum clone from South Carolina was not a vector of any BYDV serotype tested. R. rufiabdominalis was found to be an efficient vector of PAV, RPV, and RMV isolates, but did not transmit MAV or SGV.

  • characterization of wheatgrass derived Barley Yellow Dwarf virus resistance in a wheat alien chromosome substitution line
    Phytopathology, 1998
    Co-Authors: J Anderson, Stewart M Gray, H W Ohm, Dennis L Bucholtz, Ann E Greene, Michael G Francki, H C Sharma, Keith L Perry
    Abstract:

    Wheatgrass (Thinopyrum intermedium) possesses a high level of resistance to Barley Yellow Dwarf virus (BYDV) subgroup I and subgroup II strains. A wheat line (P29), in which the 7D chromosome has been substituted with a group 7 chromosome from T. intermedium, was examined for the level of resistance to two subgroup I and two subgroup II BYDV strains. In P29 plants inoculated with the subgroup I PAV strains, the titer of virus in leaf and stem tissue was typically reduced 42 to 52% when compared with the BYDV-susceptible cv. Abe. P29 and ‘Abe’ had the same content of PAV in roots. These results and the absence of detectable virus in inoculated T. intermedium plants indicate that the complete resistance to subgroup I possessed by the wheatgrass has not been introgressed into P29. In contrast, P29 was completely resistant throughout the plant to the subgroup II strains, NY-RPV and NY-RMV, demonstrating that the complete resistance to subgroup II in T. intermedium was incorporated into P29. Further analysis of this resistance to NY-RPV showed that NY-RPV can replicate in mesophyll protoplasts of P29 and ‘Abe’, suggesting that this resistance is not operating at the single-cell level. Molecular marker analysis confirmed that the T. intermedium chromosome present in P29 is a different group 7 wheatgrass chromosome than that present in L1, a wheat line with BYDV resistance properties similar to those of P29.

Philip J. Larkin - One of the best experts on this subject based on the ideXlab platform.

  • genome wide association study reveals novel qtl for Barley Yellow Dwarf virus resistance in wheat
    BMC Genomics, 2019
    Co-Authors: Philip J. Larkin, Shormin Choudhury, Holger Meinke, Meixue Zhou, Matthew Hayden, Kerrie Forrest, Yun Fan
    Abstract:

    Barley Yellow Dwarf (BYD) is an important virus disease that causes significant reductions in wheat yield. For effective control of Barley Yellow Dwarf virus through breeding, the identification of genetic sources of resistance is key to success. In this study, 335 geographically diverse wheat accessions genotyped using an Illumina iSelect 90 K single nucleotide polymorphisms (SNPs) bead chip array were used to identify new sources of resistance to BYD in different environments. A genome-wide association study (GWAS) performed using all the generalised and mixed linkage models (GLM and MLM, respectively) identified a total of 36 significant marker-trait associations, four of which were consistently detected in the K model. These four novel quantitative trait loci (QTL) were identified on chromosomes 2A, 2B, 6A and 7A and associated with markers IWA3520, IWB24938, WB69770 and IWB57703, respectively. These four QTL showed an additive effect with the average visual symptom score of the lines containing resistance alleles of all four QTL being much lower than those with less favorable alleles. Several Chinese landraces, such as H-205 (Baimazha) and H-014 (Dahongmai) which have all four favorable alleles, showed consistently higher resistance in different field trials. None of them contained the previously described Bdv2, Bdv3 or Bdv4 genes for BYD resistance. This study identified multiple novel QTL for BYD resistance and some resistant wheat genotypes. These will be useful for breeders to generate combinations with and/or without Bdv2 to achieve higher levels and more stable BYD resistance.

  • Comparison of Thinopyrum intermedium derivatives carrying Barley Yellow Dwarf virus resistance in wheat
    Genome, 2009
    Co-Authors: L. Ayala-navarrete, A A Mechanicos, E Tourton, Philip J. Larkin
    Abstract:

    Resistance to both Barley Yellow Dwarf virus (BYDV) and cereal Yellow Dwarf virus (CYDV) has been demonstrated in wheat genetic stocks with Thinopyrum intermedium chromatin. A number of resistance-...

  • molecular characterization of a thinopyrum intermedium group 2 chromosome 2ai 2 conferring resistance to Barley Yellow Dwarf virus
    Genome, 2001
    Co-Authors: Zengyan Zhang, Z Y Xin, Philip J. Larkin
    Abstract:

    The wheat – Thinopyrum intermedium addition lines Z1 and Z2 carry 21 pairs of wheat chromosomes and one pair of Th. intermedium chromosomes (2Ai-2) conferring resistance to Barley Yellow Dwarf virus (BYDV). GISH results using the genomic DNA of Pseudoroegneria strigosa (S genome) as the probe indicated that the 2Ai-2 chromosome in Z1 and Z2 is an S–J intercalary translocation. Most of the 2Ai-2 chromosome belongs to the S genome, except for about one third in the middle region of the long arm that belongs to the J genome. The results of detailed RFLP analyses confirmed that the 2Ai-2 chromosome is extensively homoeologous to wheat group 2 chromosomes. Some new RFLP markers specific to the 2Ai-2 chromosome were identified. A RAPD marker, OP-R16340, specific to the 2Ai-2 chromosome, was screened. We converted the RAPD marker into a sequence-characterized amplified region (SCAR) marker (designated SC-R16). The study establishes the basis for selecting translocation lines with small segments of the 2Ai-2 chro...

  • molecular characterization of a thinopyrum intermedium group 2 chromosome 2ai 2 conferring resistance to Barley Yellow Dwarf virus
    Genome, 2001
    Co-Authors: Zengyan Zhang, Z Y Xin, Philip J. Larkin
    Abstract:

    The wheat--Thinopyrum intermedium addition lines Z1 and Z2 carry 21 pairs of wheat chromosomes and one pair of Th. intermedium chromosomes (2Ai-2) conferring resistance to Barley Yellow Dwarf virus (BYDV). GISH results using the genomic DNA of Pseudoroegneria strigosa (S genome) as the probe indicated that the 2Ai-2 chromosome in Z1 and Z2 is an S-J intercalary translocation. Most of the 2Ai-2 chromosome belongs to the S genome, except for about one third in the middle region of the long arm that belongs to the J genome. The results of detailed RFLP analyses confirmed that the 2Ai-2 chromosome is extensively homoeologous to wheat group 2 chromosomes. Some new RFLP markers specific to the 2Ai-2 chromosome were identified. A RAPD marker, OP-R16(340), specific to the 2Ai-2 chromosome, was screened. We converted the RAPD marker into a sequence-characterized amplified region (SCAR) marker (designated SC-R16). The study establishes the basis for selecting translocation lines with small segments of the 2Ai-2 chromosome and localizing the BYDV resistance gene when introgressed into a wheat background.

  • disomic thinopyrum intermedium addition lines in wheat with Barley Yellow Dwarf virus resistance and with rust resistances
    Genome, 1995
    Co-Authors: Philip J. Larkin, P M Banks, E S Lagudah, R Appels, Chen Xiao, Xin Zhiyong, H W Ohm, R A Mcintosh
    Abstract:

    Zhong 5 is a partial amphiploid (2n = 56) between Triticum aestivum (2n = 42) and Thinopyrum intermedium (2n = 42) carrying all the chromosomes of wheat and seven pairs of chromosomes from Th. intermedium. Following further backcrossing to wheat, six independent stable 2n = 44 lines were obtained representing 4 disomic chromosome addition lines. One chromosome confers Barley Yellow Dwarf virus (BYDV) resistance, whereas two other chromosomes carry leaf and stem rust resistance; one of the latter also confers stripe rust resistance. Using RFLP and isozyme markers we have shown that the extra chromosome in the Zhong 5-derived BYDV resistant disomic addition lines (Z1, Z2, or Z6) belongs to the homoeologous group 2. It therefore carries a different locus to the BYDV resistant group 7 addition, L1, described previously. The leaf, stem, and stripe rust resistant line (Z4) carries an added group 7 chromosome. The line Z3 has neither BYDV nor rust resistance, is not a group 2 or group 7 addition, and is probably...

Randy J Beckett - One of the best experts on this subject based on the ideXlab platform.

  • Barley Yellow Dwarf virus luteoviridae or tombusviridae
    Molecular Plant Pathology, 2002
    Co-Authors: Allen W Miller, Randy J Beckett
    Abstract:

    Summary Barley Yellow Dwarf virus (BYDV), the most economically important virus of small grains, features highly specialised relationships with its aphid vectors, a plethora of novel translation mechanisms mediated by long–distance RNA interactions, and an ambiguous taxonomic status. The structural and movement proteins of BYDV that confer aphid transmission and phloem-limitation properties resemble those of the Luteoviridae , the family in which BYDV is classified. In contrast, many genes and cis -acting signals involved in replication and gene expression most closely resemble those of the Tombusviridae . Taxonomy: BYDV is in genus Luteovirus, family Luteoviridae. BYDV includes at least two serotypes or viruses: BYDV-PAV and BYDV-MAV. The former BYDV-RPV is now Cereal Yellow Dwarf virus-RPV (CYDV-RPV). CYDV is in genus Polerovirus, family Luteoviridae. Genus Luteovirus shares many features with family Tombusviridae. Physical properties: ∼25 nm icosahedral (T = 3) virions. One major (22 kDa) and one minor (50–55 kDa) coat protein. 5.6–5.8 kb positive sense RNA genome with no 5′-cap and no poly(A) tail. Host range: Most grasses. Most important in oats, Barley and wheat. Also infects maize and rice. Symptoms: Yellowing and Dwarfing in Barley, stunting in wheat; reddening, Yellowing and blasting in oats. Some isolates cause leaf notching and curling. Key attractions: Model for the study of circulative transmission of aphid-transmitted viruses. Plethora of unusual translation mechanisms. Evidence of recombination in recent evolutionary history creates taxonomic ambiguity. Economically important virus of wheat, Barley and oats, worldwide. Useful websites/meetings: International symposium: ‘Barley Yellow Dwarf Disease: Recent Advances and Future Strategies’, CIMMYT, El Batan, Mexico, 1–5 September 2002, http://www.cimmyt.cgiar.org/Research/wheat/Conf_BYD_02/invitation.htm http://www.cimmyt.org/Research/wheat/BYDVNEWS/htm/BYDVNEWS.htm Aphid transmission animation: http://www.ppws.vt.edu/~sforza/tmv/bydv_aph.html

  • the 3 terminal structure required for replication of Barley Yellow Dwarf virus rna contains an embedded 3 end
    Virology, 2002
    Co-Authors: Gennadiy Koev, Randy J Beckett, Sijun Liu, Allen W Miller
    Abstract:

    Abstract We determined the 3′-terminal primary and secondary structures required for replication of Barley Yellow Dwarf virus (BYDV) RNA in oat protoplasts. Computer predictions, nuclease probing, phylogenetic comparisons, and replication assays of specific mutants and chimeras revealed that the 3′-terminal 109 nucleotides (nt) form a structure with three to four stem-loops followed by a coaxially stacked helix incorporating the last four nt [(A/U)CCC]. Sequences upstream of the 109-nt region also contributed to RNA accumulation. The base-pairing but not the sequences or bulges in the stems were essential for replication, but any changes to the 3′-terminal helix destroyed replication. The two 3′-proximal tetraloops tolerated all changes, but the two 3′-distal tetraloops gave most efficient replication if they fit the GNRA consensus. A mutant lacking the 3′-proximal stem-loop produced elevated levels of less-than-full-length minus strands, and no (+) strand. We propose that a “pocket” structure is the origin of (−)-strand synthesis, which is negatively regulated by the inaccessible conformation of the 3′ terminus, thus favoring a high (+)/(−) ratio. This 3′ structure and the polymerase homologies suggest that genus Luteovirus is more closely related to the Tombusviridae family than to other Luteoviridae genera.

James S Thomas - One of the best experts on this subject based on the ideXlab platform.

  • seasonal abundance of aphids homoptera aphididae in wheat and their role as Barley Yellow Dwarf virus vectors in the south carolina coastal plain
    Journal of Economic Entomology, 2001
    Co-Authors: Jay W Chapin, Dawn M Smith, James S Thomas, Stewart M Gray, Susan E Halbert
    Abstract:

    Aphid (Homoptera: Aphididae) seasonal flight activity and abundance in wheat, Triticum aestivum L., and the significance of aphid species as vectors of Barley Yellow Dwarf virus were studied over a nine-year period in the South Carolina coastal plain. Four aphid species colonized wheat in a consistent seasonal pattern. Greenbug, Schizaphis graminum (Rondani), and rice root aphid, Rhopalosiphum rufiabdominalis (Sasaki), colonized seedling wheat immediately after crop emergence, with apterous colonies usually peaking in December or January and then declining for the remainder of the season. These two aphid species are unlikely to cause economic loss on wheat in South Carolina, thus crop managers should not have to sample for the subterranean R. rufiabdominalis colonies. Bird cherry-oat aphid, Rhopalosiphum padi (L.), was the second most abundant species and the most economically important. Rhopalosiphum padi colonies usually remained below 10/row-meter until peaking in February or March. Barley Yellow Dwarf incidence and wheat yield loss were significantly correlated with R. padi peak abundance and aphid-day accumulation on the crop. Based on transmission assays, R. padi was primarily responsible for vectoring the predominant virus serotype (PAV) we found in wheat. Pest management efforts should focus on sampling for and suppressing this aphid species. December planting reduced aphid-day accumulation and Barley Yellow Dwarf incidence, but delayed planting is not a practical management option. English grain aphid, Sitobion avenae (F.), was the last species to colonize wheat each season, and the most abundant. Sitobion avenae was responsible for late-season virus transmission and caused direct yield loss by feeding on heads and flag leaves during an outbreak year.

  • Barley Yellow Dwarf luteoviruses and their predominant aphid vectors in winter wheat grown in south carolina
    Plant Disease, 1998
    Co-Authors: Stephen K Gray, Jay W Chapin, Dawn M Smith, Nanditta Banerjee, James S Thomas
    Abstract:

    ABSTRACT Barley Yellow Dwarf is recognized as an important disease problem in winter wheat production in the southeastern United States, but there is relatively little known about the ecology and epidemiology of Barley Yellow Dwarf virus (BYDV) in this region. From 1991 to 1993, and in 1996 and 1997, winter wheat was sampled for BYDV throughout the principal wheat production areas in South Carolina. In addition, in 1997, a small number of samples were collected from fields in North Carolina and Kentucky. Plant samples were assayed to determine the BYDV serotype and, subsequently, coat protein sequences of isolates within the same serotype were compared using restriction fragment length polymorphisms. Representative BYDV isolates from South Carolina and type isolates from New York were compared in aphid transmission experiments using aphid species collected from South Carolina and laboratory colonies maintained in New York. The predominant BYDV serotype in South Carolina (in all years) was PAV, accounting ...

  • Barley Yellow Dwarf luteoviruses and their predominant aphid vectors in winter wheat grown in south carolina
    Plant Disease, 1998
    Co-Authors: Stewart M Gray, Jay W Chapin, Dawn M Smith, Nanditta Banerjee, James S Thomas
    Abstract:

    Barley Yellow Dwarf is recognized as an important disease problem in winter wheat production in the southeastern United States, but there is relatively little known about the ecology and epidemiology of Barley Yellow Dwarf virus (BYDV) in this region. From 1991 to 1993, and in 1996 and 1997, winter wheat was sampled for BYDV throughout the principal wheat production areas in South Carolina. In addition, in 1997, a small number of samples were collected from fields in North Carolina and Kentucky. Plant samples were assayed to determine the BYDV serotype and, subsequently, coat protein sequences of isolates within the same serotype were compared using restriction fragment length polymorphisms. Representative BYDV isolates from South Carolina and type isolates from New York were compared in aphid transmission experiments using aphid species collected from South Carolina and laboratory colonies maintained in New York. The predominant BYDV serotype in South Carolina (in all years) was PAV, accounting for 94% of the total BYDV-infected samples analyzed. The RPV serotypes were more abundant in samples collected from western North Carolina and Kentucky. PAV isolates from all regions were identical to the New York BYDV-PAV in terms of serology and restriction fragment patterns. Furthermore, the aphid transmission phenotypes were similar for South Carolina and New York BYDV isolates. The predominant aphids colonizing winter wheat in South Carolina included Schizaphis graminum, Rhopalosiphum rufiabdominalis, R. padi, and Sitobion avenea. The South Carolina clones of R. padi and S. avenae were similar to the New York laboratory clones in their abilities to transmit various BYDV isolates from New York and South Carolina. In contrast to the New York clone of Schizaphis graminum that can vector SGV, PAV, and RPV, the S. graminum clone from South Carolina was not a vector of any BYDV serotype tested. R. rufiabdominalis was found to be an efficient vector of PAV, RPV, and RMV isolates, but did not transmit MAV or SGV.