Genome-wide analysis of mitral valve disease in Cavalier King Charles Spaniels

The Cavalier King Charles Spaniel (CKCS) is prone to severe early onset mitral valve disease. In this study, 36 purebred CKCS dogs were evaluated for mitral valve murmur and divided into early and late onset groups. A genome-wide genetic approach was used to assess whether the condition is determined by a small number of genetic factors. There were no regions of highly discrepant homo/heterozygosity in the two groups. Similarly, there was no evidence for loci associated with mitral valve murmur in a genome-wide association study. This analysis suggests that familial occurrence of mitral valve murmur in the CKCS breed is not due to a single major gene effect, indicating that breeding strategies to eliminate the disease cannot be based on genotype information at this time.     

Comparative and collaborative studies for the validation of a nested PCR for the detection of Xanthomonas axonopodis pv. dieffenbachiae from Anthurium samples

Efficient control of Xanthomonas axonopodis pv. dieffenbachiae, the causal agent of anthurium bacterial blight, requires sensitive and reliable diagnostic tools. The European standard EN ISO 16140:2003 has been followed to compare a nested PCR assay (N‐PCR) to a reference method (isolation and serological identification of bacterial colonies) and to other alternative serological detection methods. The evaluation was performed in two steps: a comparative study and a collaborative study involving 15 European laboratories. Although inclusivity was maximal (100%) for all methods, a maximal exclusivity was obtained only with N‐PCR followed by an enzymatic restriction digestion of the amplicons. Exclusivity indices of 90·6, 88·7 and 47·2% were found for indirect ELISA, immunofluorescence and double antibody sandwich ELISA, respectively. An exclusivity of 92·5% was obtained with the reference method, further increased to 100% if pathogenicity tests were performed as a supplemental assay. The best level of sensitivity (relative detection level) was obtained with the reference method followed by the N‐PCR assay. The N‐PCR performance in terms of relative accuracy, accordance and concordance was very similar to that of the reference method. Moreover, N‐PCR had undeniable advantages compared to the reference method (less labour‐intensive and less time‐consuming). In addition, post‐test probabilities of infection were calculated to select the most appropriate detection scheme related to the prevalence of the pathogen. The N‐PCR assay has since been included in a revised version of the EPPO detection protocol.     

Introgression of antioxidant activity into cassava (Manihot esculenta C.): an effective technique for extending fresh storage roots shelf life

Physiological postharvest deterioration (PPD) of cassava is the main constraint affecting its nutritional and economical values. PPD is induced by wounds when detaching storage roots from mother plant during harvesting. It is accelerated by the reactive oxygen species (ROS) such as oxygen ion (O₂) and peroxide (O₂)^?2. The carotenoid content and its antioxidant property can help in extending shelf life of cassava storage roots. The primary mode of action of carotenoids as antioxidant is to quench singlet oxygen. Cassava breeding was reported to successfully introgress and improve carotenoid content into cassava. The two types of phytoene synthase (PSY) enzymes (PSY1 and PSY2) are key regulators of carotenoids accumulation in cassava. Carotenoids formation and accumulation in cassava storage roots are induced by a single nucleotide polymorphism in PSY2 which causes a non‐conservative amino acid exchange. This single nucleotide polymorphism in PSY gene is co‐segregated with β‐carotene in cassava storage roots, a phenomenon that could help to unravel the mechanism of introgression of carotenoids into cassava. This article investigates breeding feasibility for improving quality of cassava landraces in developing countries.     

Preparation of gluten-free bread using a meso-structured whey protein particle system

This article presents a novel method for making gluten-free bread using mesoscopically structured whey protein. The use of the meso-structured protein is based on the hypothesis that the gluten structure present in a developed wheat dough features a particle structure on a mesoscopic length scale (100 nm–100 μm). Whey protein particles were prepared by cold gelation of soluble whey protein aggregates during phase separation. The addition of a 2.4% whey protein particle suspension to wheat starch resulted in a dough that could be baked into a leavened bread with a specific volume up to 3.7 ml/g and a bubble size comparable with a normal bread. The relevance for structuring the whey protein into mesoscopic particles was confirmed by tests in which only a homogeneous whey protein gel or a whey protein solution was used. The protein particle system gave better results after proving and baking compared with these systems.     

Linking models for assessing agricultural land use change

The ex-ante assessment of the likely impacts of policy changes and technological innovations on agriculture can provide insight into policy effects on land use and other resources and inform discussion on the desirability of such changes. Integrated assessment and modeling (IAM) is an approach that can be used for ex-ante assessment. It may combine several quantitative models representing different processes and scales into a framework for integrated assessment to allow for multi scale analysis of environmental, economic and social issues. IAM is a challenging task as models from different disciplines have a different representation of data, space and time. The aim of this paper is to describe our strategy to conceptually, semantically and technically integrate a chain of models from different domains to assess land use changes. The models that were linked are based on different modeling techniques (e.g. optimization, simulation, estimation) and operate on different time and spatial scales. The conceptual integration to ensure consistent linkage of simulated processes and scales required modelers representing the different models to clarify the data exchanged and interlinking of modeling methodologies across scales. For semantic integration, ontologies provided a way to rigorously define conceptualizations that can be easily shared between various disciplines. Finally, for technical integration, OpenMI was used and supplemented with the information from ontologies. In our case, explicitly tackling the challenge of semantic, conceptual and technical integration of models forced researchers to clarify the assumptions of their model interfaces, which helped to document the model linkage and to efficiently run models together. The linked models can now easily be used for integrated assessments of policy changes, technological innovations and societal and biophysical changes.     

Analysing agricultural users’ patterns of behaviour: The case of OPTIRas™, a decision support system for starch crop selection

Redesigning IT systems for specific user groups encompasses a lot of effort with respect to analysing and understanding user behaviour. The goal of this paper is to provide insights into patterns of behaviour of agricultural users, during the usage of a decision support system called OPTIRas™. This system aids agricultural users in their cultivar selection activities. We analyse logs resulting from OPTIRas™, and we get insights into user’s navigational patterns. We claim that the results of our analysis can be used to support the redesign of decision support systems in order to address specific agricultural users’ characteristics.     

Participatory plant breeding approach for host plant resistance to bean fly in common bean under semi-arid Kenya conditions

Common bean (Phaseolus vulgaris L.) is the most important legume crop in Kenya. It is cultivated across a wide range of agro-ecologies which include high potential and marginal areas. Eastern Kenya alone, largely semi-arid, accounts for 35% of the country’s total bean production. Bean farmers mainly small-scale have limited access to quality seed, chemical pesticides and fertilizer. Therefore, bean yield under on-farm conditions still remains below 500 kg ha⁻¹ while the potential is about 1,200 kg ha⁻¹ under semi-arid conditions. To asses the farmers’ views on bean varieties and a key insect pest and associated constraints contributing to yield loss, research was undertaken. The research included survey to quantify the yield loss and Participatory Rural Appraisal to determine the level of adoption and criteria for variety choice in semi-arid eastern Kenya (SAEK). The results show that farmers consider drought and insect pest problems as main causes for low yields. The adoption rate for improved varieties is high but self sufficiency in beans stands at 23% in the dry transitional (DT) agro-ecology and at 18% in the dry mid-altitude (DM) agro-ecology, respectively. This could be attributed to low adaptability since most of the improved varieties grown were selected for high potential areas but now found in marginal areas. Drought, earliness, yield stability, and insect pest resistance are the main reasons for choice of varieties by farmers. Bean fly (Ophiomyia sp.) was identified as one of the key crop pests of beans limiting yield. Besides, African bollworm (Helicoverpa armigera) and bean aphid (Aphis fabae) were ranked higher. Due to limitations of the conventional breeding approach, a participatory plant breeding approach is suggested so as to provide an opportunity to develop insect pest resistant varieties adapted to the SAEK region.     

Fine‐scale population structure and connectivity of bottlenose dolphins,Tursiops truncatus,in European waters and implications for conservation

1. Protecting species often involves the designation of protected areas, wherein suitable management strategies are applied either at the taxon or ecosystem level. Special Areas of Conservation (SACs) have been created in European waters under the Habitats Directive to protect bottlenose dolphins, Tursiops truncatus, which forms two ecotypes, pelagic and coastal.
2. The SACs have been designated in coastal waters based on photo‐identification studies that have indicated that bottlenose dolphins have relatively high site fidelity. However, individuals can carry out long‐distance movements, which suggests potential for demographic connectivity between the SACs as well as with other areas.
3. Connectivity can be studied using genetic markers. Previous studies on the species in this area used different sets of genetic markers and therefore inference on the fine‐scale population structure and demographic connectivity has not yet been made at a large scale. A common set of microsatellite markers was used in this study to provide the first comprehensive estimate of genetic structure of bottlenose dolphins in European Atlantic waters.
4. As in previous studies, a high level of genetic differentiation was found between coastal and pelagic populations. Genetic structure was defined at an unprecedented fine‐scale level for coastal dolphins, leading to identification of five distinct coastal populations inhabiting the following areas: Shannon estuary, west coast of Ireland, English Channel, coastal Galicia, east coast of Scotland and Wales/west Scotland. Demographic connectivity was very low among most populations with <10% migration rate, suggesting no demographic coupling among them. Each local population should therefore be monitored separately.
5. The results of this study have the potential to be used to identify management units for bottlenose dolphins in this region and thus offer a significant contribution to the conservation of the species in European Atlantic waters. Future studies should prioritize obtaining biopsies from free‐living dolphins from areas where only samples from stranded animals were available, i.e. Wales, west Scotland and Galicia, in order to reduce uncertainty caused by sample origin doubt, as well as from areas not included in this study (e.g. Iroise Sea, France). Furthermore, future management strategies should include monitoring local population dynamics and could also consider other options, such as population viability analysis or the incorporation of genetic data with ecological data (e.g. stable isotope analysis) in the designation of management units.