Some biological and genomic properties of rice tungro bacilliform badnavirus and rice tungro spherical waikavirus from Nepal

A survey of rice fields during the main growing seasons in 81 locations from 21 districts of the Southern Terai region of Nepal indicated that rice tungro was primarily restricted to the Hardinath (Janakpur) and Parwanipur (Bara) regions. The tungro incidence in Hardinath ranged from 17% to 51% and in Parwanipur from 6% to 61% causing about 89% grain yield loss in Hardinath. Both rice tungro bacilliform badnavirus (RTBV) and rice tungro spherical picornavirus (RTSV) were found in tungro isolates collected from Hardinath and Parwanipur. These isolates were transmitted by Nephotettix virescens and leaf extracts reacted to antisera against RTBV and RTSV. In a dot blot hybridisation assay, leaf extracts of 12 weed species collected from the tungro-affected area in Hardinath and Parwanipur also reacted with RTBV DNA probes. On mass inoculation of 15 popular rice cultivars most became more than 50% infected and only cv. Radha 9 had low (22.2%) infection. RTBV DNA and the coat protein region of RTSV from the Hardinath isolate were cloned and partially characterised. A comparative analyses by restriction endonuclease digestion, cross hybridisation, the polymerase chain reaction and partial sequencing indicated that the Nepalese RTBV DNA clone and the cDNA clones of the RTSV RNA were more similar to the various tungro isolates from the Indian subcontinent than to those from the Philippines.     

Evidence that the recessive bymovirus resistance locus rym4 in barley corresponds to the eukaryotic translation initiation factor 4E gene

Recent studies have shown that resistance in several dicotyledonous plants to viruses in the genus Potyvirus is controlled by recessive alleles of the plant translation initiation factor eIF4E or eIF ( iso ) 4E genes. Here we provide evidence that the barley rym 4 gene locus, controlling immunity to viruses in the genus Bymovirus , corresponds to eIF4E . A molecular marker based on the sequence of eIF4E was developed and used to demonstrate that eIF4E and rym 4 map to the same genetic interval on chromosome 3HL in barley . Another genetic marker was developed that detects a polymorphism in the coding sequence of eIF4E and consistently distinguishes between rym 4 and susceptible barley cultivars of diverse parentage. The eIF4E gene product from barley genotypes carrying rym 4 and allelic rym 5 and rym 6 genes, originating from separate exotic germplasm, and a novel resistant allele that we identified through a reverse genetics approach all contained unique amino acid substitutions compared with the wild-type protein. Three-dimensional models of the barley eIF4E protein revealed that the polymorphic residues identified are all located at or near the mRNA cap-binding pocket, similarly to recent findings from studies on recessive potyvirus resistance in dicotyledonous plants. These new data complement our earlier observations that specific mutations in bymovirus VPg are responsible for overcoming rym 4/5-controlled resistance. Because the potyviral VPg is known to interact with eIF4E in dicotyledonous plants, it appears that monocotyledonous and dicotyledonous plants have evolved a similar strategy to combat VPg-encoding viruses in the family Potyviridae .     

Molecular phylogenetics of the juno irises,Iris subgenus Scorpiris (Iridaceae), based on six plastid markers

Relationships among the roughly 55 species of Iris subgenus Scorpiris have been studied. A matrix of six plastid DNA regions (matK, rpl14‐rps8 spacer, infA‐rpl36 spacer, trnE‐trnT spacer, trnL intron and trnL‐F spacer) was produced from 57 accessions (52 taxa) and analysed with both parsimony and Bayesian methods. Five major clades are identified, of which four have strong geographical correlations, whereas the fifth corresponds to Iris section Physocaulon. In our results, several species are placed with species not previously considered to be related, although, in some cases, there are morphological characters that suggest that these newly indicated relationships are reasonable. For some of the other oddly grouped species, we can only assume that remarkable parallelisms in morphology have occurred or hybridization is involved. Presently, with plastid DNA as our only comprehensive data resource, we are not able to evaluate more thoroughly these more puzzling associations of species. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 167 , 281–300.