Use of Degenerate Primers in a RT-PCR Assay for the Identification and Analysis of Some Filamentous Viruses, with Special Reference to Clostero- and Vitiviruses of the Grapevine

RT-PCR with degenerate primers was used for the screening of the genome of some members of the Closterovirus, Vitivirus and Trichovirus genera. Two sets of primers, targeted to conserved sequences of the heat shock protein 70 homologue of closteroviruses or to the RNA dependent RNA polymerase genes of tricho- and vitiviruses, amplified the expected fragments from total RNA extracts or double-stranded RNAs of infected plants. Amplified cDNAs were cloned, sequenced and phylogenetically analyzed. Results support the allocation of grapevine viruses A, B, D and heracleum latent virus (HLV) in the genus Vitivirus, whereas, the detection of a HSP70 homologue in grapevine leafroll-associated viruses agrees with their assignment in the genus Closterovirus. The use of degenerate primers for the identification of grapevine viruses belonging to Vitivirus and Closterovirus genera is envisaged.     

Synergy between grapevine vitiviruses and grapevine leafroll viruses

An interactive relationship between vitiviruses and grapevine leafroll viruses was characterized in grapevine. Grapevine viruses A and B (GVA and GVB) were found more frequently in the presence of co-infecting Grapevine leafroll associated viruses (GLRaV-1, ?2 or ?3) than in their absence. The titers of the vitiviruses in co-infection with leafroll viruses were found to be higher than were their titers in the absence of leafroll virus infection. The occurrence of vitivirus-associated stem-pitting symptoms was correlated with leafroll virus co-infection. Specific pairing associations on the species level were found between different viti- and leafroll virus species: GVB was associated preferentially with GLRaV-2; GVA was associated preferentially with GLRaV-1 and GLRaV-3. In contrast to the increase in vitivirus titer seen with leafroll virus co-infection, the incidence and titer of grapevine leafroll virus appeared to be unaltered by vitivirus co-infection. The potential for a synergistic enhancement of grapevine disease in co-infected vines is discussed.     

Landscape-wide changes in land use and land cover correlate with,but rarely explain local biodiversity change

Landscape Ecology - There is an ongoing debate whether local biodiversity is declining and what might drive this change. Changes in land use and land cover (LULC) are suspected to impact local...     

Genetic variability and population structure of <Emphasis Type="Italic">Grapevine virus A</Emphasis> coat protein gene from naturally infected Italian vines

Grapevine virus A (GVA) is considered one of the viruses associated with rugose wood (RW), one of the most economically important diseases of grapevine. Thirty-seven GVA isolates collected from grapevine cultivars from Marche (central-eastern Italy), Apulia and Campania (southern Italy), were subjected to molecular characterization. The genetic and population diversity was studied in the coat protein (CP) gene by RT-PCR-RFLP analysis with three restriction enzymes (MseI, AluI, and AciI), and nucleotide sequencing. A new primer pair (CP1F/R) allowing amplification of the whole CP gene (621 bp) was developed. RFLP with AciI yielded the highest number of variants in GVA isolates, showing seven different ‘simple’ profiles (A, B, C, D, E, F, and G). ‘Complex’ profiles were also found, and the most common variant combination was A + B in 39% of isolates. The analysis of GVA sequences confirmed the presence of plants infected with more than one GVA variant and suggested that RT-PCR-RFLP is suitable for evaluating population diversity of GVA enabling a screening of different haplotypes. The distribution of RFLP profiles and the phylogenetic analysis were not correlated with the location of infected plants, showing the presence of a GVA population with genetic diversity in the average with those of RNA viruses.     

Climate variability and crop production in Tanzania

Improved understanding of the influence of climate on agricultural production is needed to cope with expected changes in temperature and precipitation, and an increasing number of undernourished people in food insecure regions. Many studies have shown the importance of seasonal climatic means in explaining crop yields. However, climate variability is expected to increase in some regions and have significant consequences on food production beyond the impacts of changes in climatic means. Here, we examined the relationship between seasonal climate and crop yields in Tanzania, focusing on maize, sorghum and rice. The impacts of both seasonal means and variability on yields were measured at the subnational scale using various statistical methods and climate data. The results indicate that both intra- and interseasonal changes in temperature and precipitation influence cereal yields in Tanzania. Seasonal temperature increases have the most important impact on yields. This study shows that in Tanzania, by 2050, projected seasonal temperature increases by 2 °C reduce average maize, sorghum, and rice yields by 13%, 8.8%, and 7.6% respectively. Potential changes in seasonal total precipitation as well as intra-seasonal temperature and precipitation variability may also impact crop yields by 2050, albeit to a lesser extent. A 20% increase in intra-seasonal precipitation variability reduces agricultural yields by 4.2%, 7.2%, and 7.6% respectively for maize, sorghum, and rice. Using our preferred model, we show that we underestimate the climatic impacts by 2050 on crop yields in Tanzania by 3.6%, 8.9%, and 28.6% for maize, sorghum and rice respectively if we focus only on climatic means and ignore climate variability. This study highlights that, in addition to shifts in growing season means, changes in intra-seasonal variability of weather may be important for future yields in Tanzania. Additionally, we argue for a need to invest in improving the climate records in these regions to enhance our understanding of these relationships.