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| 2. |
- Meadows, Jennifer, et al.
(författare)
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Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture
- 2023
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Ingår i: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 24
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Tidskriftsartikel (refereegranskat)abstract
- Background: The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 x data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function.Results: We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection.Conclusions: We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.
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| 3. |
- Sonesson, Ulf, et al.
(författare)
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Protein quality as functional unit – A methodological framework for inclusion in life cycle assessment of food
- 2017
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Ingår i: Journal of Cleaner Production. - : Elsevier BV. - 0959-6526 .- 1879-1786. ; 140:Part 2, s. 470-478
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Tidskriftsartikel (refereegranskat)abstract
- In order to develop more sustainable food systems, there is a need to find methods that simultaneously consider environmental impacts and nutritional benefits. The purpose of this study was to develop a functional unit to be used in LCA of foods that builds on the nutritional value of food products. We used the content and quality of proteins as a basis, and included dietary context as part of our method, since the nutritional value of a nutrient depends on the total dietary intake. Our method uses the digestible intake of the nine essential amino acids in the product and relates these values to the equivalent total dietary intake of the same amino acids. We also employed simpler functional units such as “gram (g) protein” and “g digestible protein.” We quantified the functional units for three dietary contexts and applied it on LCA results for bread, chicken fillet, minced pork, minced beef, milk and pea soup. The results showed that the relative differences between products changed when using a protein-based functional unit, with the largest change occurring when going from mass as the functional unit to g protein. By introducing protein digestibility, the systematic under-valuation of the animal products was partly avoided with little additional effort. The most advanced functional unit affected the results compared to the mass-based functional unit most, but required significantly more data. The impact of dietary context was smaller than expected; hence, it might be possible to simplify the inclusion of dietary context by using aggregated descriptions of diets. The method presented is valuable for adding an important aspect of nutrition (protein quality and content) to the LCA results of single products, but there is a large scope for development.
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| 4. |
- de Melo, C. M. R., et al.
(författare)
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Introduction and evaluation on the US West Coast of a new strain (Midori) of Pacific oyster (Crassostrea gigas) collected from the Ariake Sea, southern Japan
- 2021
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Ingår i: Aquaculture. - : Elsevier BV. - 0044-8486. ; 531
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Tidskriftsartikel (refereegranskat)abstract
- We describe the introduction, taxonomic identification and genetic parameters for farm traits of the Midori strain of the Pacific oyster Crassostrea gigas - a possible alternative to the widely farmed Miyagi strain on the US West Coast. Broodstock (G0) oysters collected from the mouth of the Midori river and near Iwajima Island, Ariake Bay, Japan were identified as C. gigas based on the nuclear internal transcribed spacer (ITS) region and 28S gene as well as a mitochondrial (COI) marker. G0 and G1 generations and G2 larvae and spat were maintained in quarantine conditions and subjected to numerous histological exams and PCR tests for detection of pathogens of concern. After the G1 generation and G2 early life stages were found to be free of detectable diseases, G2 spat were planted at farm test sites and adults were used to produce a G3 generation. This G3 generation was cultured under non-quarantine conditions and families were planted at sub-tidal and inter-tidal test sites, in Oregon and California, respectively. Field performance traits were measured to determine the potential for improvement through selection. Overall, Midori oysters showed significantly lower values for harvest yield, survival, individual average weight and dry meat weight compared with oysters from a selected stock of the Miyagi strain of Pacific oyster; however, shell shape index (a measure of shell depth) was significantly greater in Midori oysters. Heritability estimates for group traits at harvest (survival, yield and individual average harvest weight) were high, whereas heritability estimates for individual traits (individual weight, wet meat weight and dry meat weight) and for shell dimension measurements (shell length, shell width and shell depth) were moderate-to-high. Family-by-site (GxE) correlations were low-to-moderate for all measured traits. Genetic correlations were positive and moderate-to-high among group traits and shell dimensions. In contrast, correlations between shell shape and other traits had small-to-moderate negative values but these were not statistically significant. Estimated potential genetic gain for dry meat weight was high (46%) whereas estimated gains for yield, individual average weight, individual weight were high-to-moderate (approximately 10%). In contrast, shell shape showed very little potential for genetic gain through selection. Overall, the Midori strain of the Pacific oyster shows promise as a deep-cupped oyster for the half-shell trade. Statement of relevance: We describe the introduction of a new strain of Pacific oyster (Midori) collected from southern Japan to the US West Coast. Rigorous quarantine protocols and disease tests were applied to ensure that the risks of introducing diseases were minimized. The Midori strain was found to have a deeper cup than the commonly farmed Miyagi strain but the potential estimated gain for improving this trait through selection was small. © 2020 Elsevier B.V.
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| 5. |
- Roberts, N., et al.
(författare)
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Europe's lost forests : a pollen-based synthesis for the last 11,000 years
- 2018
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- 8000 years ago, prior to Neolithic agriculture, Europe was mostly a wooded continent. Since then, its forest cover has been progressively fragmented, so that today it covers less than half of Europe's land area, in many cases having been cleared to make way for fields and pasture-land. Establishing the origin of Europe's current, more open land-cover mosaic requires a long-term perspective, for which pollen analysis offers a key tool. In this study we utilise and compare three numerical approaches to transforming pollen data into past forest cover, drawing on >1000 C-14-dated site records. All reconstructions highlight the different histories of the mixed temperate and the northern boreal forests, with the former declining progressively since similar to 6000 years ago, linked to forest clearance for agriculture in later prehistory (especially in northwest Europe) and early historic times (e.g. in north central Europe). In contrast, extensive human impact on the needle-leaf forests of northern Europe only becomes detectable in the last two millennia and has left a larger area of forest in place. Forest loss has been a dominant feature of Europe's landscape ecology in the second half of the current interglacial, with consequences for carbon cycling, ecosystem functioning and biodiversity.
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