Whole-genome mapping of quantitative trait loci and accuracy of genomic predictions for resistance to columnaris disease in two rainbow trout breeding populations

International audienceAbstractBackgroundColumnaris disease (CD) is an emerging problem for the rainbow trout aquaculture industry in the US. The objectives of this study were to: (1) identify common genomic regions that explain a large proportion of the additive genetic variance for resistance to CD in two rainbow trout (Oncorhynchus mykiss) populations; and (2) estimate the gains in prediction accuracy when genomic information is used to evaluate the genetic potential of survival to columnaris infection in each population.MethodsTwo aquaculture populations were investigated: the National Center for Cool and Cold Water Aquaculture (NCCCWA) odd-year line and the Troutlodge, Inc., May odd-year (TLUM) nucleus breeding population. Fish that survived to 21 days post-immersion challenge were recorded as resistant. Single nucleotide polymorphism (SNP) genotypes were available for 1185 and 1137 fish from NCCCWA and TLUM, respectively. SNP effects and variances were estimated using the weighted single-step genomic best linear unbiased prediction (BLUP) for genome-wide association. Genomic regions that explained more than 1% of the additive genetic variance were considered to be associated with resistance to CD. Predictive ability was calculated in a fivefold cross-validation scheme and using a linear regression method.ResultsValidation on adjusted phenotypes provided a prediction accuracy close to zero, due to the binary nature of the trait. Using breeding values computed from the complete data as benchmark improved prediction accuracy of genomic models by about 40% compared to the pedigree-based BLUP. Fourteen windows located on six chromosomes were associated with resistance to CD in the NCCCWA population, of which two windows on chromosome Omy 17 jointly explained more than 10% of the additive genetic variance. Twenty-six windows located on 13 chromosomes were associated with resistance to CD in the TLUM population. Only four associated genomic regions overlapped with quantitative trait loci (QTL) between both populations.ConclusionsOur results suggest that genome-wide selection for resistance to CD in rainbow trout has greater potential than selection for a few target genomic regions that were found to be associated to resistance to CD due to the polygenic architecture of this trait, and because the QTL associated with resistance to CD are not sufficiently informative for selection decisions across populations

Integrated washland management for flood defence and biodiversity

In the context of growing interest in finding sustainable solutions to flood management in England and Wales, this study set out to determine the extent to which benefits to flood management and biodiversity can be achieved through an integrated approach to the creation and management of ‘washlands’. For the purpose of the study, a washland is defined as “an area of the floodplain that is allowed to flood or is deliberately flooded by a river or stream for flood management purposes, with potential to form a wetland habitat”. Following a questionnaire survey of engineers and conservationists, a review of selected sites, and a workshop of key stakeholders, it was concluded that there is both scope and willingness to exploit potential synergy. It appears, however, that until now most washlands have either been used mainly for flood storage or for wetland habitat, and there has been only a limited attempt to integrate the two objectives. In many respects, the opportunity for integrating biodiversity depends on the ability to maintain wet conditions on the washland beyond the period of the flood event, and this largely depends on the dominant land use. The scope is greatest where the washland is under grass or woodland, and actions can be taken to ‘engineer’ or manage soil wetness regimes which serve biodiversity interests. Such water management plans and related biodiversity targets are best designed into washland management from the outset, rather than as an afterthought, when conflicts of interest are likely to arise. While there is much interest in pursuing an integrated approach, lack of funding for biodiversity on washlands and the relative complexity of preparing the washland case for appraisal appear to constrain washland development. Nevertheless, washlands are perceived by engineers and conservationists alike to offer potentially sustainable solutions to flooding, enabling biodiversity targets to be met within an integrated approach to catchment flood management. Recommendations were made to: • improve, through the use of guidance and training, understanding between engineers and conservationists of how flood management and biodiversity objectives can be simultaneously achieved; • consider the establishment of a biodiversity fund to support the biodiversity components of washland schemes; • develop practical guidance on the formulation of washland management plans that exploit biodiversity potential by managing wetness conditions in washlands beyond the flood-event period; • review how washland creation and management can be integrated and help to deliver the objectives of Biodiversity Action Plans and Catchment Fl

Technical efficiency of European railways: a distance function approach

This study has two principal objectives. The first objective is to measure and compare the performance of European railways. The second objective is to illustrate the usefulness of econometric distance functions in the analysis of production in multioutput industries, where behavioural assumptions such as cost minimization or profit maximization, are unlikely to be applicable. Using annual data on 17 railways companies during 1988–1993, multioutput distance functions are estimated using corrected ordinary least squares (COLS). The resulting technical efficiency estimates range from 0.980 for the Netherlands to 0.784 for Italy, with a mean of 0.863. The distance function results are also compared with those obtained from single-output production functions, where aggregate output measures are formed using either total revenue or a Tornqvist index. The results obtained indicate substantial differences in parameter estimates and technical efficiency rankings, casting significant doubt upon the reliability of these single-output models, particularly when a total revenue measure is used to proxy aggregate output.

Additional file 2 of Total serum N-glycans associate with response to immune checkpoint inhibition therapy and survival in patients with advanced melanoma

Additional file 2: Table 1. Description of total serum N-glycan UHPLC measured peaks. Table 2. Description of total serum derived traits. Table 3. Summary statistics for the associations between N-glycan traits and response to ICI treatment. Table 4. Summary statistics for the associations between N-glycan traits and progression-free survival. Table 5. Summary statistics for the associations between N-glycan traits and overall survival. Table 6. Summary statistics for the N-glycans shift at follow up with respect to the pre-treatment relative abundances