In vivo virulence and genomic comparison of infectious Salmon Anaemia Virus isolates from Atlantic Canada

The infectious salmon anaemia virus (ISAV) is capable of causing a significant disease in Atlantic salmon, which has resulted in considerable financial losses for salmon farmers around the world. Since the first detection of ISAV in Canada in 1996, it has been a high priority for aquatic animal health management and surveillance programmes have led to the identification of many genetically distinct ISAV isolates of variable virulence. In this study, we evaluated the virulence of three ISAV isolates detected in Atlantic Canada in 2012 by doing in vivo‐controlled disease challenges with two sources of Atlantic salmon. We measured viral loads in fish tissues during the course of infection. Sequences of the full viral RNA genomes of these three ISAV isolates were obtained and compared to a high‐virulence and previously characterized isolate detected in the Bay of Fundy in 2004, as well as a newly identified ISAV NA‐HPR0 isolate. All three ISAV isolates studied were shown to be of low to mid‐virulence with fish from source A having a lower mortality rate than fish from source B. Viral load estimation using an RT‐qPCR assay targeting viral segment 8 showed a high degree of similarity between tissues. Through genomic comparison, we identified various amino acid substitutions unique to some isolates, including a stop codon in the segment 8 ORF2 not previously reported in ISAV, present in the isolate with the lowest observed virulence.     

A novel aphid resistance locus in cowpea identified by combining SSR and SNP markers

The utility of combining simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) marker genotyping was determined for genetically mapping a novel aphid (Aphis craccivora) resistance locus in cowpea breeding line SARC 1‐57‐2 and for introgressing the resistance into elite cultivars by marker‐assisted backcrossing (MABC). The locus was tagged with codominant SSR marker CP 171F/172R with a recombination fraction of 5.91% in an F₂ population from ‘Apagbaala’ x SARC 1‐57‐2. A SNP‐genotyped biparental recombinant inbred line population was genotyped for CP 171F/172R, which was mapped to position 11.5 cM on linkage group (LG) 10 (physical position 30.514 Mb on chromosome Vu10). Using CP 171F/172R for foreground selection and a KASP‐SNP‐based marker panel for background selection in MABC, the resistance from SARC 1‐57‐2 was introduced into elite susceptible cultivar ‘Zaayura’. Five BC₄F₃ lines of improved ‘Zaayura’ that were isogenic except for the resistance locus region had phenotypes similar to SARC 1‐57‐2. This study identified a novel aphid resistance locus and demonstrated the effectiveness of integrating SSR and SNP markers for trait mapping and marker‐assisted breeding.     

Quantitative trait loci associated with trichomes in the <Emphasis Type="Italic">Solanum galapagense</Emphasis> accession LA1401

Pest resistance in Solanum galapagense has been associated with the presence of type IV glandular trichomes and allelochemicals. Knowledge of the genetic factors involved in determining the presence and type of trichomes may assist in the process of gene introgression for development of pest resistant tomato cultivars. In this study, we sought to identify QTLs associated with the presence of type IV trichomes in an F₂ population derived from the interspecific cross of Solanum lycopersicum TOM-684?×?S. galapagense accession LA1401. Two QTLs contributing to type IV trichome occurrence and density were detected, one major QTL (gal.IV-2), responsible for 35.22% of phenotypic variation, was located on chromosome 2. The other QTL (gal.IV-3) was located on chromosome 3, and explained 23.35% of the phenotypic variation in the F₂ population. These QTLs were responsible for 26.44 and 3.37% of the variation observed in a progeny derived from a backcross to TOM-684. The same QTLs were also associated with type II?+?III non-glandular trichomes, whose densities were negatively correlated to those of type IV trichomes, suggesting that the loci found may have pleiotropic effects for high type IV/low type II?+?III trichome densities. Our results indicate that the inheritance for type IV trichomes can be explained by a few genetic factors affecting the presence of a gland and the density of trichomes. These results further suggest a revision to trichome classification used for tomato may be appropriate.     

Socio-economic factors influencing household dependence on forests and its implication for forest-based climate change interventions§

In most African countries, forest-based climate change intervention initiatives such as nationally appropriate mitigation actions (NAMAs) and national adaptation programmes of action (NAPAs) are widely accepted. This is mainly due to the fact that they are relevant in addressing multiple challenges associated with rural development, mitigation and adaptation to climate change, and sustainable forest management. However, there are concerns about the implications of strategic and practical steps taken in this context on forest-dependent communities. Thus, there is need to reconcile local socio-economic vulnerabilities and forest-based climate change intervention initiatives. In the current study, socio-economic factors influencing households’ dependence on forest resources and associated implications on climate change interventions were investigated. Proportionate stratified random sampling was used to select 366 households from forest-based rural communities in Vhembe District of South Africa. A structured questionnaire was administered to household heads in 21 villages. The Pearson’s chi-square test was used to analyse the factors that influence household dependence on forest. The effects of household socio-economic characteristics on households’ forest dependence influencing factor were determined using the binary logit model. Up to 97% of the respondents depended on the forest resources predominantly because of low costs associated with using them. It was observed that socio-economic characteristics of households such as farm husbandry skills, years of residence (53–65) in the community and age of respondents (≤38–65) significantly (P < 0.05) influenced use of the forest resources. Thus, effectiveness and sustainability of forest-based climate change intervention initiatives can be promoted if the socio-economic conditions prevailing within households in areas next to forests are improved.     

Characterization of the urogenital microbiome in Miniature Schnauzers with and without calcium oxalate urolithiasis

BackgroundCalcium oxalate (CaOx) uroliths are common in dogs. Humans with CaOx urolithiasis exhibit alterations of the urinary and urogenital microbiomes that might mediate urolith formation. Detection of urogenital microbes associated with CaOx in dogs could inform disease pathophysiology.ObjectiveTo identify compositional differences in the urogenital microbiome of Miniature Schnauzers with and without CaOx uroliths.AnimalsNineteen midstream, voided urine samples from Miniature Schnauzers with (n = 9) and without (n = 10) a history of CaOx urolithiasis.MethodsAnalytical cross‐sectional study. Microbial DNA was extracted from previously frozen urine samples and sequenced for the bacterial 16S rRNA V3‐V4 hypervariable regions. Diversity and composition of microbial populations were compared between urolith formers and controls.ResultsAlpha and beta diversity measures were similar between groups. Five individual bacterial taxa differed in abundance (indicator values >0.5 and P < .05): Acinetobacter, 2 Geobacillus variants, and Hydrogenophaga were overrepresented in the urine of urolith formers, and Sphingopyxis was overrepresented in controls. Two distinct subtypes of urine microbial composition were observed based on beta diversity measures, independent of urolith status, and other clinical variables.Conclusions and Clinical ImportanceAlthough we did not detect a difference in the overall urogenital microbial composition between groups, observed differences in individual bacterial taxa might be clinically relevant. For example, Acinetobacter was overrepresented in urolith formers and is associated with CaOx urolithiasis in humans. Two unique clusters of the microbiome were identified, independent of urolith status, which may represent distinct urotypes present in Miniature Schnauzers.     

Exudative epidermitis and porcine circovirus-2 infection in a Swedish SPF-herd

An outbreak of exudative epidermitis (EE) among piglets in a Swedish SPF-herd initiated a survey for indications as to the cause of disease.The herd was established by caesarean section and has been closed to all new animal material, with the exception of semen for artificial insemination (AI). The study comprised serum samples from the SPF-herd over a 10-year period (n=109) and a close monitoring of animals in the herd during the period after the EE outbreak. Serum samples from conventional boars at the AI-station servicing the herd were also included (n=9). All serum samples were tested for antibodies to porcine circovirus-2 (PCV-2). In addition, 3-week-old piglets from three litters (n=24) farrowed close after the initial EE outbreak were closely monitored for clinical signs of skin disease, sampled for Staphylococcus hyicus, tested for antibodies to porcine parvovirus and in sequentially collected serum samples tested for interferon-alpha (IFN-alpha) and interleukin-6.The PVC-2 serology showed that animals in the herd were sero-negative at least until 2 months prior to the EE outbreak. During the period close after the EE outbreak the animals showed varying levels of antibodies to PCV-2 but all the tested animals had sero-converted 4 months later. The AI boars were also sero-positive to PCV-2 at the time of the EE outbreak. Animals in the SPF-herd remained sero-positive to PCV-2 during the following 7 years. In the monitored litters, one piglet had clinical EE and 15 piglets displayed defined erythemas on the abdomen. Fourteen of the piglets also had IFN-alpha in serum on one or more occasions during the study, indicating viral activity among the animals. S. hyicus was isolated from all of the piglets from the earliest sampling point (3 days of age) and onwards, irrespective of clinical signs. PCV-2 was isolated from lymph node tissue collected from one of the EE affected pigs.Further, increases in the number of stillborn piglets, small litters (<6 piglets) and repeat breeders could be correlated to the time of PCV-2 sero-conversion. Coincidence of active viral infection and sero-conversion to PCV-2 points to the virus as the cause of the EE outbreak and reproductive disturbances.