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| 2. |
- Rafati, Nima, et al.
(författare)
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Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies
- 2016
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Ingår i: G3. - : Oxford University Press (OUP). - 2160-1836. ; 6:7, s. 2213-2223
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Tidskriftsartikel (refereegranskat)abstract
- Skeletal atavism in Shetland ponies is a heritable disorder characterized by abnormal growth of the ulna and fibula that extend the carpal and tarsal joints, respectively. This causes abnormal skeletal structure and impaired movements, and affected foals are usually killed. In order to identify the causal mutation we subjected six confirmed Swedish cases and a DNA pool consisting of 21 control individuals to whole genome resequencing. We screened for polymorphisms where the cases and the control pool were fixed for opposite alleles and observed this signature for only 25 SNPs, most of which were scattered on genome assembly unassigned scaffolds. Read depth analysis at these loci revealed homozygosity or compound heterozygosity for two partially overlapping large deletions in the pseudoautosomal region (PAR) of chromosome X/Y in cases but not in the control pool. One of these deletions removes the entire coding region of the SHOX gene and both deletions remove parts of the CRLF2 gene located downstream of SHOX. The horse reference assembly of the PAR is highly fragmented, and in order to characterize this region we sequenced bacterial artificial chromosome (BAC) clones by single-molecule real-time (SMRT) sequencing technology. This considerably improved the assembly and enabled size estimations of the two deletions to 1602180 kb and 60280 kb, respectively. Complete association between the presence of these deletions and disease status was verified in eight other affected horses. The result of the present study is consistent with previous studies in humans showing crucial importance of SHOX for normal skeletal development.
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| 4. |
- Bertholdsson, Nils-Ove, et al.
(författare)
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Allelopathic potential of Triticum spp., Secale spp. and Triticosecale spp. and use of chromosome substitutions and translocations to improve weed suppression ability in winter wheat
- 2012
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Ingår i: Plant Breeding. - : Wiley. - 0179-9541 .- 1439-0523. ; 131, s. 75-80
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Tidskriftsartikel (refereegranskat)abstract
- A search was carried out for allelopathic sources among accessions of Triticum, Secale, Triticosecale and wheat-rye substitution and translocation lines to be used in breeding programmes to improve weed suppression ability of wheat. A bioassay with mustard as target plants was used for the screening. Mustard was chosen among seven tested target plants because it showed a particular high root growth inhibition when grown together with rye compared with wheat. None of the Triticum accessions studied showed potential allelopathic activity of interest for breeding, but most Triticosecale did. Several of the wheat-rye substitution and translocation lines also showed high allelopathic activity. The highest activity was found in lines with a substitution of 1R or 2R. Some multiple substitution lines and lines with only rye chromatin also showed high allelopathic activity. It is suggested that in vitro selection of wheat-rye substitution lines with high allelopathic potential with a bioassay with mustard as target plants could be used to improve weed suppression ability of wheat.
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| 5. |
- Bubolz, Jéssica, et al.
(författare)
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Genetically modified (GM) late blight-resistant potato and consumer attitudes before and after a field visit
- 2022
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Ingår i: GM Crops and Food Biotechnology in Agriculture and the Food Chain. - : Informa UK Limited. - 2164-5698 .- 2164-5701. ; 13, s. 290-298
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Tidskriftsartikel (refereegranskat)abstract
- Late blight, caused by Phytophthora infestans, is the most devastating disease in potato production. Here, we show full late blight resistance in a location with a genetically diverse pathogen population with the use of GM potato stacked with three resistance (R) genes over three seasons. In addition, using this field trials, we demonstrate that in-the-field intervention among consumers led to change for more favorable attitude generally toward GM crops.
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| 6. |
- Jonsson, Ove, et al.
(författare)
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TIMFIE-provtagning för tidsintegrerad haltbestämning av växtskyddsmedel, PFAS, läkemedel och metaller i ytvatten : En pilotstudie
- 2022
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- TIMFIE (Time Integrating, Micro Flow, In situ Extraction) är en enkel och billig tidsintegrerad provtagningsmetod som här användes för bestämning av ett stort antal organiska ämnen från vitt skilda substansgrupper. Tekniken bygger på kontinuerlig fastfasextraktion i fält under en till två veckor och den efterföljande bestämningen av organiska ämnen är kvantitativ och baseras på helvatten, dvs. med partikelbunden fraktion inkluderad.Förutom organiska ämnen som växtskyddsmedel, PFAS och läkemedel mättes i detta projekt även metallhalter och löst organiskt kol (DOC) i det uppsamlade, filtrerade vattnet. Merparten av de studerade metallerna och DOC påverkades dock negativt av fastfaskolonnerna som används för extraktion av de organiska ämnena. En separat TIMFIE utan kolonner ska därför användas vid bestämning av metaller. En fältstudie med veckovisa TIMFIE-provtagningar i tolv provpunkter fördelade på fem regioner utfördes i samarbete med länsstyrelserna i Gotland, Östergötland och Dalarna samt med en avfallsanläggning i Mälardalen. Totalt analyserades 47 TIMFIE-prover för drygt 200 organiska ämnen och 21 metaller, samt ytterligare 8 TIMFIE-prover endast för metaller.I framtiden kommer två olika TIMFIE-provtagare att användas i studier där både organiska och oorganiska ämnen bestäms. Fortsatt arbete med att även inkludera näringsämnen i det oorganiska analyspaketet pågår och möjligheten att göra dessa bestämningar på ett återskapat helvatten undersöks.
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| 7. |
- Lefebure, Robert, et al.
(författare)
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Impacts of elevated terrestrial nutrient loads and temperature on pelagic food-web efficiency and fish production
- 2013
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Ingår i: Global Change Biology. - : John Wiley & Sons. - 1354-1013 .- 1365-2486. ; 19:5, s. 1358-1372
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Both temperature and terrestrial organic matter have strong impacts on aquatic food-web dynamics and production. Temperature affects vital rates of all organisms, and terrestrial organic matter can act both as an energy source for lower trophic levels, while simultaneously reducing light availability for autotrophic production. As climate change predictions for the Baltic Sea and elsewhere suggest increases in both terrestrial matter runoff and increases in temperature, we studied the effects on pelagic food-web dynamics and food-web efficiency in a plausible future scenario with respect to these abiotic variables in a large-scale mesocosm experiment. Total basal (phytoplankton plus bacterial) production was slightly reduced when only increasing temperatures, but was otherwise similar across all other treatments. Separate increases in nutrient loads and temperature decreased the ratio of autotrophic:heterotrophic production, but the combined treatment of elevated temperature and terrestrial nutrient loads increased both fish production and food-web efficiency. CDOM: Chl a ratios strongly indicated that terrestrial and not autotrophic carbon was the main energy source in these food webs and our results also showed that zooplankton biomass was positively correlated with increased bacterial production. Concomitantly, biomass of the dominant calanoid copepod Acartia sp. increased as an effect of increased temperature. As the combined effects of increased temperature and terrestrial organic nutrient loads were required to increase zooplankton abundance and fish production, conclusions about effects of climate change on food-web dynamics and fish production must be based on realistic combinations of several abiotic factors. Moreover, our results question established notions on the net inefficiency of heterotrophic carbon transfer to the top of the food web.
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| 8. |
- Nicholson, Charlie C., et al.
(författare)
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Landscapes of risk : A comparative analysis of landscape metrics for the ecotoxicological assessment of pesticide risk to bees
- 2024
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Ingår i: Journal of Applied Ecology. - 0021-8901 .- 1365-2664.
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Tidskriftsartikel (refereegranskat)abstract
- Pesticide use in agricultural landscapes creates environmental contamination that is heterogenous in space and time. Mobile organisms, such as bees, are exposed to multiple contamination sources when visiting patches that vary in the amount, timing and toxicity of pesticides used. Yet, environmental risk assessments (ERA) typically fail to consider this heterogeneity, in part because of the complexities of estimating exposure to different pesticides, and subsequent risk at organism-relevant scales. We use pesticide assays of 269 bee-collected pollen samples to understand the spatiotemporal variability of risk across a network of 41 field sites in southern Sweden. Observed bee pesticide risk is calculated based on compound-specific residue quantifications in pollen and standardized toxicity data. We then compare the ability of three classes of landscape-scale variables to predict this risk: (1) landscape composition and configuration metrics, (2) landscape load based on national pesticide use data and (3) predictions from a newly developed bee pesticide exposure model. Based on use data, 10 crops account for 81% of the total risk. We detected 49 pesticide compounds in bee-collected pollen. Although herbicides and fungicides constitute the bulk of detected pesticides, both in frequency and amount quantified, unsurprisingly, insecticides contribute the most to risk. Landscape composition and configuration metrics did not predict observed pesticide risk, and interactions with bee species indicate taxa-dependency in predictions. Landscape load predicted observed risk consistently between taxa. Risk estimates from our exposure model were strongly predictive but only when considering realized risk (i.e., risk estimates based on prior pesticide use information). Synthesis and applications. Predicting pesticide risk based on landscape patterns could enable landscape-scale ERA. However, simple metrics of landscape pattern, such as proportion of agricultural land, are not sufficient. We found that risk observed in bee-collected pollen was best predicted when integrating spatialized pesticide use in the pesticide exposure model, underscoring the importance of such data for research, monitoring and mitigation. Further, we propose a guidance framework for future landscape ecotoxicological risk analyses that clarifies data needs relative to risk prediction goals.
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| 9. |
- Nystedt, Björn, et al.
(författare)
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The Norway spruce genome sequence and conifer genome evolution
- 2013
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 497:7451, s. 579-584
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Tidskriftsartikel (refereegranskat)abstract
- Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.
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| 10. |
- Rundlöf, Maj, et al.
(författare)
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Seed coating with a neonicotinoid insecticide negatively affects wild bees.
- 2015
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 521:7550, s. 77-162
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the effects of neonicotinoid insecticides on bees is vital because of reported declines in bee diversity and distribution and the crucial role bees have as pollinators in ecosystems and agriculture. Neonicotinoids are suspected to pose an unacceptable risk to bees, partly because of their systemic uptake in plants, and the European Union has therefore introduced a moratorium on three neonicotinoids as seed coatings in flowering crops that attract bees. The moratorium has been criticized for being based on weak evidence, particularly because effects have mostly been measured on bees that have been artificially fed neonicotinoids. Thus, the key question is how neonicotinoids influence bees, and wild bees in particular, in real-world agricultural landscapes. Here we show that a commonly used insecticide seed coating in a flowering crop can have serious consequences for wild bees. In a study with replicated and matched landscapes, we found that seed coating with Elado, an insecticide containing a combination of the neonicotinoid clothianidin and the non-systemic pyrethroid β-cyfluthrin, applied to oilseed rape seeds, reduced wild bee density, solitary bee nesting, and bumblebee colony growth and reproduction under field conditions. Hence, such insecticidal use can pose a substantial risk to wild bees in agricultural landscapes, and the contribution of pesticides to the global decline of wild bees may have been underestimated. The lack of a significant response in honeybee colonies suggests that reported pesticide effects on honeybees cannot always be extrapolated to wild bees.
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