The complete nucleotide sequence and its organization of the genome of Barley yellow dwarf virus-GAV

The Barley yellow dwarf disease (BYD) was firstly recognized as an aphid transmitted virus disease by Oswald and Houston[1] in 1951. Now, Barley yel-low dwarf viruses (BYDVs) belong to members of the plant virus family Luteoviridae. They are phloem- limited and obligately transmitted in the circula-tive/persistent manner by several species of cereal aphids and can cause significant economic losses worldwide because of damage to barley, wheat, and oats. In China, BYDVs cause mainly yello…     

Screening for Barley yellow dwarf virus-Resistant Barley Genotypes by Assessment of Virus Content in Inoculated Seedlings

The content of Barley yellow dwarf virus (BYDV) in roots and leaves of barley seedling plants differing in their level of resistance was assessed by quantitative ELISA 1–42 days after inoculation with the strain of BYDV (PAV). High virus accumulation in roots and low concentration in leaves was characteristic of the period 9–15 days after inoculation. In leaves, the differences in virus content between resistant and susceptible genotypes became significant after 15 days and resistance to virus accumulation was better expressed 30–39 days after inoculation. Roots of resistant materials exhibited evident retardation of virus accumulation and the greatest difference in virus content between resistant and susceptible plants was detected 9 days after inoculation. By these criteria, the selected winter and spring barley cultivars and lines (in total 44 materials) fell in to five groups according to field reactions and the presence or absence of the Yd2 resistance gene. There were highly significant and positive relations between ELISA values and 5‐year field data on symptomatic reactions and grain‐yield reductions due to infection. Using the described method, resistant and moderately resistant genotypes (both Yd2 and non‐Yd2) were significantly differentiated from susceptible genotypes. The possible use of this method in screening for BYDV resistance is discussed.     

转病毒来源发夹RNA小麦表现对大麦黄矮病毒的抗性

将大麦黄矮病毒GPV株系的复制酶基因片段和CP基因片段构建成可在植物细胞内表达含有双链复制酶RNA(茎)和反义CP RNA(环)的复合发夹RNA结构, 希望能够诱发植物体针对病毒的RNA干扰作用, 从而达到抗病毒目的。利用基因枪法将该结构导入小麦幼胚愈伤组织细胞后, 通过在幼苗再生阶段进行以叶片为模板的快速PCR来加速阳性植株的筛选过程, 最终共获得基因组整合有外源基因的小麦再生植株21株。对再生植株接种不同剂量的病毒, 其中9株对BYDV-GPV有低度抗性, 表现在低接毒量时无症状, 接毒量提高时发病且严重; 6株具中度抗性, 表现在低接毒量时无症状, 接毒量提高时局部有不严重症状; 6株具高度抗性, 两种情况下均无症状。抗性实验结果表明, hpRNA介导对BYDV的抗性可能受到BYDV含量的影响, 具有剂量效应的特点。     

The complete sequence of a sugarcane mosaic virus isolate causing maize dwarf mosaic disease in China

The complete sequence of a potyvirus from maize in Zhejiang Province was determined. The RNA was 9596 nucleotides long, excluding the 3′-poly (A) tail, and there was a single long open reading frame (ORF) of 9192 nts encoding a 346.1 ku polyprotein. The polyprotein had substantial amino acid sequence homology with those encoded by the RNAs of a Chinese isolate of sorghum mosaic virus (SrMV-C) and a Bulgarian isolate of maize dwarf mosaic virus, but it was most closely related to sugarcane mosaic virus (SCMV) isolates, for which only partial sequences have been published. According to the published criteria for distinguishing potyviruses, the sequence reported here is clearly a strain of SCMV, but it also showed a surprisingly high amino acid homology with SrMV-C in the HC-Pro, P3 and Cl proteins.     

Identification of polypeptide markers of barley yellow dwarf virus resistance and susceptibility genes in non-infected barley (Hordeum vulgare) plants

Summary Barley yellow dwarf (BYDV) is a group a closely related viruses which cause economic losses in a wide range of graminaceous species throughout the world. Barley plants can be protected from the effects of BYDV by the Yd2 resistance gene. Plants which contain the Yd2 gene also contain a constitutively expressed polypeptide which was not found in any plants without Yd2. Conversely, BYDV susceptible plants contain another constitutively expressed polypeptide which was not found in any of the BYDV-resistant lines examined. These two polypeptides appear to have the same molecular weight (as assessed by SDS-PAGE) and only slightly different iso-electric points. They also appear to contain an extensive range of similar antigenic determinants. Both polypeptides were found in F₁ hybrids made from resistant and susceptible plants. We suggest that these two polypeptides are the products of two allelic genes. Analysis of near-isogenic lines showed that the locus which controls the Yd2 resistance gene and the locus controlling the synthesis of the two polypeptides may be within ± 9 cM of each other. We have developed a Western blot technique which allows assessment of barley lines, 4-days after seed imbibition, for the presence of the Yd2 gene.     

Cloning and Phylogenetic Analysis of Coat Protein of Barley yellow dwarf virus Isolates from Different Regions of Pakistan

Barley yellow dwarf virus (BYDVs) is an emerging threat for wheat and may seriously threaten its production, especially as climate change may result in increased infestation by aphids, the insect vectors of the virus. To assess the possibility of using pathogen‐derived resistance against the virus, the genetic diversity of BYDVs originating from different wheat‐growing areas of Pakistan where its incidence has been higher was investigated. Wheat samples with suspected symptoms of BYDVs were screened for the presence of Barley yellow dwarf and Cereal yellow dwarf viruses (B/CYDVs) subgroup 1 (Barley yellow dwarf virus‐PAV, BYDV‐MAV, BYDV‐SGV) and subgroup II (BYDV‐RPV, CYDV‐RPV, BYDV‐GPV) by PCR using basic multiplex oligonucleotides designed on coat protein (CP) of the virus. Of 37 samples tested, 13 were positive for BYDV subgroup I and only one sample was positive for BYDV subgroup II. Samples positive for subgroup I were further tested by PCR, and results showed that 10 samples were positive for BYDV‐PAV and three for BYDV‐MAV. DNA sequences of CP region of nine isolates (BYDV‐PAV) were determined and compared with available sequences in databases. Sequence analysis showed that three isolates (from Fatehjang, Nowshera and Attock districts) had maximum identity (92.8–94.6%) to BYDV‐PAS, and six isolates (from Peshawar, Islamabad Swabi and Faisalabad districts) had maximum identity (99.3–99.7%) to BYDV‐PAV. Thus BYDV‐PAV species may be dominant in northern wheat‐growing areas of Pakistan. The conserved nature of the BYDVs suggests that pathogen‐derived resistance strategies targeting the coat protein of the virus are likely to provide protection under field conditions.     

Barley yellow dwarf virus: effects on carbohydrate metabolism in oat (Avena sativa) during cold hardening

Barley yellow dwarf virus (BYDV) causes significant losses in yield and in overwintering ability of winter cereals. Mechanisms by which the physiology of plants is affected by the virus are not clear. To see how carbohydrates in the crown of winter cereals were affected by BYDV, fructan isomers of degree of polymerization (DP) 3–5, fructan DP>6 and the simple sugars, glucose, fructose and sucrose, were measured before and during cold hardening in three oat ( Avena sativa L.) cultivars, 'Wintok', 'Coast Black' and 'Fulghum'. On a fresh weight basis fructan DP>6 decreased by 50% in infected 'Wintok' and 'Coast Black' and by 25% in 'Fulghum'. Two DP3, one DP4 and one DP5 isomer were significantly higher than non-infected controls. The percentages of simple sugars in infected crowns were significantly higher than controls in all three cultivars in every week except the first week of hardening. Crude enzyme extracts from BYDV infected plants incubated with sucrose suggested higher invertase and lower sucrose-sucrosyl transferase activity. When incubated with 1-kestose and neokestin, no significant difference was found in fructose fructosyl transferase or in hydrolase activity. The activity of unidentified enzymes catalysing the synthesis of larger (DP>5) fructan was altered by BYDV. The decrease of carbohydrates in the crown induced indirectly by BYDV may alter the plant's capacity to regenerate tillers in the spring. The ability of plants to prevent or tolerate carbohydrate fluctuations induced by BYDV infection may be an important genetically regulated characteristic for developing virus-resistant cultivars.     

The complete sequence of a sugarcane mosaic virus isolate causing maize dwarf mosaic disease in China

The complete sequence of a potyvirus from maize in Zhejiang Province was determined. The RNA was 9596 nucleotides long, excluding the 3'-poly (A) tail, and there was a single long open reading frame (ORF) of 9192 nts encoding a 346.1 ku polyprotein. The polyprotein had substantial amino acid sequence homology with those encoded by the RNAs of a Chinese isolate of sorghum mosaic virus (SrMV-C) and a Bulgarian isolate of maize dwarf mosaic virus, but it was most closely related to sugarcane mosaic virus (SCMV) isolates, for which only partial sequences have been published. According to the published criteria for distinguishing potyviruses, the sequence reported here is clearly a strain of SCMV, but it also showed a surprisingly high amino acid homology with SrMV-C in the HC-Pro, P3 and Cl proteins.     

Comparison of the potential rate of population increase of brown and green color morphs of Sitobion avenae (Homoptera: Aphididae) on barley infected and uninfected with Barley yellow dwarf virus

Life tables of brown and green color morphs of the English grain aphid, Sitobion avenae (Fabricius) reared on barley under laboratory conditions at 20 ± 1°C, 65% ± 5% relative humidity and a photoperiod of 16 : 8 h (L : D) were compared. The plants were either: (i) infected with the Barley yellow dwarf virus (BYDV); (ii) not infected with virus but previously infested with aphids; or (iii) healthy barley plants, which were not previously infested with aphids. Generally, both color morphs of S. avenae performed significantly better when fed on BYDV‐infected plants than on plants that were virus free but had either not been or had been previously infested with aphids. Furthermore, when fed on BYDV‐infected plants, green S. avenae developed significantly faster and had a significantly shorter reproductive period than the brown color morph. There were no significant differences in this respect between the two color morphs of S. avenae when they were reared on virus‐free plants that either had been or not been previously infested with aphids. These results indicate that barley infected with BYDV is a more favorable host plant than uninfected barley for both the color morphs of S. avenae tested, particularly the green color morph.     

Rapid and informative assays for Yd2, the barley yellow dwarf virus resistance gene, based on the nucleotide sequence of a closely linked gene

This paper describes the isolation of the cDNA encoding a protein previously shown to be indicative of the disease-resistance phenotype mediated by the Yd2 gene in barley (Hordeum vulgare L.). Amino acid sequences of four peptides obtained after isolation of the protein on two-dimensional polyacrylamide gels were completely homologous to sequences occurring within subunit E of barley vacuolar proton-translocating ATPase. Nucleotide sequence data of cloned cDNAs from both Yd2 and non-Yd2 barley varieties showed an amino acid change arising from a single-base-pair polymorphism. This was predicted to result in the shift in isoelectric point used previously to differentiate the protein in Yd2 and non-Yd2 barleys. Earlier work had indicated very close linkage between the gene from which this cDNA is derived, which we have named Ylp, and Yd2, the barley yellow dwarf virus resistance gene. We report here the development of PCR-based assays which discriminate between the two alleles of Ylp and thereby act as valuable predictors of Yd2 for barley breeders and others looking to study this important gene in cereal crops. The validity of each assay was tested with an extensive survey of over 100 barley varieties currently under cultivation in Australia or of importance to Australian barley breeding programmes. Complete agreement was observed between the allele of Ylp detected by the assay and the known Yd2 status of the barleys. A dominant PCR marker for the Yd2-associated allele of Ylp was subsequently developed using an allele-specific primer pair. This fast and economical assay will have broad application in the marker-assisted selection of Yd2-containing lines.     

The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome

The complete sequence of the carp mitochondrial genome of 16,575 base pairs has been determined. The carp mitochondrial genome encodes the same set of genes (13 proteins, 2 rRNAs, and 22 tRNAs) as do other vertebrate mitochondrial DNAs. Comparison of this teleostean mitochondrial genome with those of other vertebrates reveals a similar gene order and compact genomic organization. The codon usage of proteins of carp mitochondrial genome is similar to that of other vertebrates. The phylogenetic relationship for mitochondrial protein genes is more apparent than that for the mitochondrial tRNA and rRNA genes.Correspondence to: F. Huang     

Barley yellow dwarf virus, wheat, and Sitobion avenae: a case of trilateral interactions

We analysed interactions in the system of two Barley Yellow Dwarf Virus (BYDV) strains (MAV and PAV), and wheat (cv. Tinos) as host plant for the virus, and the cereal aphid Sitobion avenae (F.) as vector, in particular whether or not infection by the virus might alter host plant suitability in favour of vector development. By measuring the amino acid and sugar content in the phloem sap of infected and non‐infected wheat plants we found a significant reduction in the concentration of the total amount of amino acids on BYDV‐infected plants. Qualitative and quantitative analysis of honeydew and honeydew excretion indicated a lower efficiency of phloem sap utilisation by S. avenae on infected plants. In addition, S. avenae excreted less honeydew on infected plants. Both BYDV strains significantly affected aphid development by a reduction in the intrinsic rate of natural increase. Hence, infection by the virus reduced the host suitability in terms of aphid population growth potential on BYDV‐infected plants. However, more alate morphs developed on virus‐infected plants. These findings are discussed in relation to the population dynamics of S. avenae, and, as a consequence, the spread of BYDV.     

The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants

Tobacco is a valuable model system for investigating the origin of mitochondrial DNA (mtDNA) in amphidiploid plants and studying the genetic interaction between mitochondria and chloroplasts in the various functions of the plant cell. As a first step, we have determined the complete mtDNA sequence of Nicotiana tabacum. The mtDNA of N. tabacum can be assumed to be a master circle (MC) of 430,597 bp. Sequence comparison of a large number of clones revealed that there are four classes of boundaries derived from homologous recombination, which leads to a multipartite organization with two MCs and six subgenomic circles. The mtDNA of N. tabacum contains 36 protein-coding genes, three ribosomal RNA genes and 21 tRNA genes. Among the first class, we identified the genes rps1 and rps14, which had previously been thought to be absent in tobacco mtDNA on the basis of Southern analysis. Tobacco mtDNA was compared with those of Arabidopsis thaliana, Beta vulgaris, Oryza sativa and Brassica napus. Since repeated sequences show no homology to each other among the five angiosperms, it can be supposed that these were independently acquired by each species during the evolution of angiosperms. The gene order and the sequences of intergenic spacers in mtDNA also differ widely among the five angiosperms, indicating multiple reorganizations of genome structure during the evolution of higher plants. Among the conserved genes, the same potential conserved nonanucleotide-motif-type promoter could only be postulated for rrn18-rrn5 in four of the dicotyledonous plants, suggesting that a coding sequence does not necessarily move with the promoter upon reorganization of the mitochondrial genome.Electronic Supplementary Material Supplementary material is available in the online version of this article at Communicated by R. Hagemann     

The effect of temperature and inoculation access period on the transmission of barley yellow dwarf virus byRhopalosiphum padi (L.) and Sitobion avenae (F.)

Winged individuals of Rhopalosiphum padi and Sitobion avenae transmitted the PAV-like and MAV-like isolates of barley yellow dwarf virus respectively. Success of transmission after inoculation access periods of 2, 6, 12, 24, 48 and 72 h were examined and survival, reproduction and movement of the aphid vectors were recorded at these times. The experiment was done at four different temperatures: 6^oC, 12^oC, 18^oC and 23^oC. For both isolates the inoculation efficacy did not increase after a 24 h inoculation access period and there was no difference in inoculation efficiency at the three highest temperatures, that at 6^oC being significantly lower than at 12^oC to 23^oC. The results suggest that autumn temperature is a critical factor for BYDV epidemiology in Britain with a small increase in autumn temperature leading to greatly increased infection rates.     

Transmission of barley yellow dwarf virus by field collected aphids (Homoptera: Aphididae) and their relative importance in barley yellow dwarf epidemiology in southwestern Idaho

Populations of cereal aphids were sampled from 1985–1988 and assayed for transmission of barley yellow dwarf virus (BYDV), Rhopalosiphum padi, Rho-palosiphum maidis, Sitobion avenae, Metopolophium dirhodum, Schizaphis graminum and Macrosiphum euphorbiae collected from host plants transmitted BYDV in bioassays. Of the 1028 Diuraphis noxia collected from plants, one may have transmitted BYDV. The isolate involved resembled SGV in serological and biological characteristics, but since it was not recoverable by any of more than 800 D. noxia subsequently tested, we suspect it may have been a contaminant. Among those aphids collected during the autumn from a suction trap adapted for live collection, R. padi transmitted BYDV most frequently. Other trapped species which transmitted BYDV included: R. maidis, Rhopalosiphum insertum, Macrosiphum euphorbiae, Metopolophium dirhodum and Ceruraphis eriophori. An adapted Infectivity Index indicated that R. padi is by far the most important vector of BYDV during the autumn sowing season in southwestern Idaho. Male R. padi consistently transmitted BYDV more frequently than did females collected during the same period.     

The chloroplast genome of mulberry: complete nucleotide sequence, gene organization and comparative analysis

The complete nucleotide sequence of mulberry (Morus indica cv. K2) chloroplast genome (158,484 bp) has been determined using a combination of long PCR and shotgun-based approaches. This is the third angiosperm tree species whose plastome sequence has been completely deciphered. The circular double-stranded molecule comprises of two identical inverted repeats (25,678 bp each) separating a large and a small single-copy region of 87,386 bp and 19,742 bp, respectively. A total of 83 protein-coding genes including five genes duplicated in the inverted repeat regions, eight ribosomal RNA genes and 37 tRNA genes (30 gene species) representing 20 amino acids, were assigned on the basis of homology to predicted genes from other chloroplast genomes. The mulberry plastome lacks the genes infA, sprA, and rpl21 and contains two pseudogenes ycf15 and ycf68. Comparative analysis, based on sequence similarity, both at the gene and genome level, indicates Morus to be closer to Cucumis and Lotus, phylogenetically. However, at genome level, inclusion of non-coding regions brings it closer to Eucalyptus, followed by Cucumis. This may reflect differential selection pressure operating on the genic and intergenic regions of the chloroplast genome.Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.Communicated by Y. Tsumura     

Vector specificity of barley yellow dwarf virus serotypes and variants in southwestern Idaho

Plants with symptoms of barley yellow dwarf virus (BYDV) obtained in infection feeding assays of aphids collected in the field in Idaho between 1986 and 1988 were tested for virus transmissibility by possible aphid vectors. Isolates obtained during 1987–1988 were also tested with a range of polyclonal antisera which distinguished PAV, MAV, SGV, RPV and RMV serotypes. In 1989 some Idaho (ID) BYDV isolates, maintained as standards for comparison, were serotyped and tested for aphid transmissibility, using 11 species of aphids. There was not always the expected correspondence between serotype and vector specificity for ID isolates. For isolates obtained from field-collected Rhopalosiphum padi, vector transmissibility and serotype corresponded with previous reports; however, 44% of isolates which were serotyped as RMV were also transmissible by species other than Rhopalosiphum maidis. Similarly, the transmissibility of the ID laboratory standards did not always conform to the reported vector specificity of serotypes. The laboratory ID-MAV culture was transmitted by Metopolophium dirhodum and Myzus persicae as well as by Sitobion avenae. The laboratory ID-SGV culture was transmitted by R. padi and 5. avenae as well as by Schizaphis graminum. The ID-RPV culture was transmitted by S. graminum and Rhopalosiphum insertum as well as R. padi. Both of two laboratory ID-RMV cultures were transmissible by R. insertum and R. padi transmitted one of them. The results indicate that, for isolates collected in Idaho, vector specificity cannot be assumed from their serotypes.