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GBLUP Outperforms Quantile Mapping and Outlier Detection for Enhanced Genomic Prediction
Get PDFGenomic selection (GS) accelerates plant breeding by predicting complex traits using genomic data. This study compares genomic best linear unbiased prediction (GBLUP), quantile mapping (QM)-an adjustment to GBLUP predictions-and four outlier detection methods. Using 14 real datasets, predictive accuracy was evaluated with Pearson's correlation (COR) and normalized root mean square error (NRMSE). GBLUP consistently outperformed all other methods, achieving an average COR of 0.65 and an NRMSE reduction of up to 10% compared to alternative approaches. The proportion of detected outliers was low (<7%), and their removal had minimal impact on GBLUP's predictive performance. QM provided slight improvements in datasets with skewed distributions but showed no significant advantage in well-distributed data. These findings confirm GBLUP's robustness and reliability, suggesting limited utility for QM when data deviations are minimal
Simulation of long-term impact of dairy cattle mating programmes using genomic information at the herd level
Get PDFGenotyping provides breeders with new information at the single nucleotide polymorphism level that can be used in mating programmes. This study used stochastic simulation to explore the long-term effects of genomic mating allocations combining economic scores and linear programming at the level of commercial herds. The economic scores included genetic level, a favourable monogenic trait (polledness), a recessive genetic defect, and parent relationships. The results showed that compared with only maximising genetic level, including genomic or pedigree relationship in the economic score lowered the rate of pedigree and genomic inbreeding with minimal effect on genetic gain. Including the cost of a recessive genetic defect in the score almost eliminated the risk of expression. We set the start allele frequency of polledness to similar to 12%, and the value of polledness varied in the different scenarios (0, 10, 50, and 100). Including an economic value for polledness of (>= 50) in the economic score increased the frequency of polled animals by up to 0.037 per generation, without negatively impacting other comparison criteria. The use of genomic relationships was favourable for the rate of genomic inbreeding and performed as well as pedigree relationships concerning the rate of pedigree inbreeding. Limiting the number of females per bull and herd to a maximum of 5% instead of 10% also decreased the rate of inbreeding. The 5% females per bull and herd constraint lowered the variation in carrier frequency for genetic defects, which reduced the risk of mating two carriers of an unknown genetic defect in future generations after the widespread use of carriers in previous generations. However, the 10% females per bull constraint accelerated the increase in the polled allele. Therefore, planning matings with genomic information at the herd level involves important risk management decisions, such as balancing the trade-off between using fewer bulls to increase the polled allele frequency more quickly and using more bulls to reduce the rate of inbreeding and the variation in carrier frequency for genetic defects. (c) 2025 The Author(s). Published by Elsevier B.V. on behalf of The animal Consortium. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)
Viktiga livsmiljöer för fisk i svenska kust- och havsområden
Get PDFIntresset för havsbaserad vindkraft har ökat markant med samhällets ökade behov av elektrifiering och förnybar energi. Samtidigt kan etablering av vindkraft påverka det marina ekosystemet där fisk har en central roll. Idag har flera fiskarter dålig status på grund av mänsklig påverkan och det kan uppstå frågetecken kring vilka konsekvenser en storskalig utbyggnad kan ha. Kunskapsläget om hur fisk kan påverkas av havsbaserad vindkraft är fortfarande inte tillräcklig utvecklat för att dra generella slutsatser - hur fiskar kan påverkas av vindparkerna förväntas variera både geografiskt och på en mer lokal skala, på grund av skillnader i artsammansättning, fiskmängder och livsmiljöer. För att få en så god och samlad bild som möjligt är det viktigt både med rumslig information och riskanalyser.Den här rapporten ger en samlad bild av utbredningen av vanligt förekommande fiskarter i svenska kust och hav, kunskapsläget kring den rumsliga utbredningen av viktiga livsmiljöer för fisk och en översiktlig bedömning av hur fisk kan komma att påverkas av havsbaserad vindkraft. Rapporten inleds med en beskrivning av vanliga fiskarter i Sveriges olika havsbassänger, från Bottenviken till Skagerrak, mot bakgrund av geografiska skillnader och framför allt skillnader i salthalt. Därefter ges en sammanfattning de vanligaste metoderna för att ta fram kartor för att ge en mera detaljerad bild av viktiga livsmiljöer för fisk. Möjligheten att ta fram tillförlitliga kartunderlag varierar dock mellan arter, på grund av skillnader både i datatillgång och arternas biologi. I samband med framtagandet av den här rapporten har ett antal befintliga kartunderlag sammanställts till ett enhetligt format anpassat för hantering av vindkraftsärenden. Resultaten presenteras i ett kartverktyg (webbapplikation) för att hjälpa användaren att utforska underlagen och jämföra dem med planerade eller tilltänkta områden för havsbaserad vindkraft.I dagsläget innehåller kartverktyget data för 58 arter, men ytterligare information kan komma att läggas till i takt med att nya kartor kvalitetssäkras eller tas fram. De flesta kartunderlagen representerar uppväxtområden för fisk, framför allt för bottennära eller bottenlevande arter. I verktyget ingår även kartor för lekområden och viktiga livsmiljöer för vuxen fisk. Inga befintliga kartunderlag beskriver viktiga vandringområden på grund av otillräckligt dataunderlag för att ta fram dessa. Endast ungefär hälften av de arter som klassas som hotade finns representerade i kartorna.Områden som identifieras som särskilt viktiga för fisk kan i vissa fall behöva undantas från vindkraftsetablering, medan det i andra fall snarare kan krävas hänsyn genom att anpassa årstid för byggnation, vindparkens design, eller skötsel. Centrala aspekter för de avgöranden som kan behöva göras är vindparkernas planerade utformning, möjligheter att använda skadelindrande åtgärder och fortsatt kunskapsutbyggnad om vindkraftens effekter på fisk. En mer utförlig genomgång av dessa faktorer är utanför målsättningarna för denna rapport, men rapporten ger en sammanfattning och orientering. I takt med att kunskap sammanställs skulle sådan information även kunna inkorporeras i kartverktyget för att underlätta lokalt anpassade riskanalyser. Även om underlagen är anpassade för vindkraftsärenden kan de även stödja andra syften, till exempel inom fiskförvaltning, områdesskydd, eller tillstånds- och dispensärenden gällande byggandet av andra strukturer i vattnet och annan vattenverksamhet
Translocating deadwood in ecological compensation benefits saproxylic beetles, but effects are dependent on substrate density
Get PDFEcological compensation is increasingly used to offset habitat and biodiversity loss resulting from changes in land use, large infrastructure projects (e.g., roads and railroads) or industrial expansions (e.g., mines, harbours), but the effectiveness of specific compensation strategies remain largely untested. When old-growth forest ecosystems are impacted by such projects, designated compensation areas may also require additional restoration or habitat enrichment. For organisms that rely on habitats that require decades to develop, such as advanced decayed wood, restoration will require novel approaches. We tested whether translocation of deadwood of various decay stages and large dimensions enhance saproxylic beetle communities within compensation areas in a large boreal forest landscape in Sweden. Experimental plots (50 m in diameter) within the compensation zone were enriched with 0, 16, or 48 deadwood substrates. We collected beetles using flight intercept traps prior to translocation and again 1 and 4 years after translocation and compared species richness, abundance and assemblage composition across treatment and over time. We showed that translocation of relatively high densities of deadwood (48 substrates per plot) increased species richness of saproxylic beetles. Increased beetle richness could have occurred from direct transport of beetles in experimental substrates and/or through attraction of beetles to the translocated substrates. Our results indicate that translocation of deadwood can serve as an important tool in ecological compensation and restoration if sufficient amounts of deadwood are translocated. While promising, the long-term success of restoring saproxylic biodiversity through translocation of deadwood depends on whether translocated substrates continue to provide suitable habitat for beetles over time and whether benefits for biodiversity can be enhanced through targeted translocation of specific combinations of deadwood
Var har Mälarens vitmärlor tagit vägen?
Get PDFDenna rapport är resultatet av en omfattande undersökning av den bottenlevande vitmärlan, Monoporeia affinis, i östra Mälaren hösten 2024. Den gjordes för att vitmärlor sedan några år försvunnit från de provplatser i Mälaren som ingår i ordinarie provtagningar i nationella miljöövervakningsprogrammet Stora sjöar. Utbredningen av vitmärlor i Mälaren har minskat och de har även minskat i täthet. Fältdelen av studien visade att de nu återfinns på grundare bottnar än tidigare, på cirka 30 meters djup jämfört med tidigare på 40–50 meter, dvs. fjärdarna Görväln, Lambarfjärden, Norra Björkfjärden, Prästfjärden, Gripsholmsviken samt Västra Prästfjärden mellan Stallarholmen och Ridön.Tidigare perioder med populationskrascher i Mälaren sammanfaller med torrperioder, indirekt visat som mindre humusämnen i vattnet och högre konduktivitet vilket kan tyda på att de gynnas av inkommande vattens födotillgång. Vårens kiselalgsmängder som i litteraturen visats vara viktiga för att vitmärlor ska kunna bygga upp biomassan inför reproduktionen har ökat med tiden i Mälaren och anses inte kunna förklara minskningen av vitmärlor. Varmare vatten på bottnarna skulle kunna vara en bidragande orsak till minskningen och litteraturstudien visade att honornas befruktningsandel minskar vid höga hösttemperaturer och att det är tiden innan parning som temperaturen behöver vara under 10 grader för att befruktningsandelen ska ligga över 50 %.Vitmärlor tål syrgashalter ner mot 2 mg/l. På senare år har några fjärdar haft relativt låga syrgashalter i djuphålorna i september, kopplat till lång period med temperaturskiktning av vattnet, vilket skulle kunna förklara varför de undvikit dem under senaste åren. Studien visar hur viktigt det är med bra levnadsförhållanden i de delar av Mälaren som är djupare än 20 meter för att kunna bevara de kallvattensarter som Mälaren har flera av förutom vitmärlan
Pan-Genome Analysis Reveals Local Adaptation to Climate Driven by Introgression in Oak Species
Get PDFThe genetic base of local adaptation has been extensively studied in natural populations. However, a comprehensive genome-wide perspective on the contribution of structural variants (SVs) and adaptive introgression to local adaptation remains limited. In this study, we performed de novo assembly and annotation of 22 representative accessions of Quercus variabilis, identifying a total of 543,372 SVs. These SVs play crucial roles in shaping genomic structure and influencing gene expression. By analyzing range-wide genomic data, we identified both SNPs and SVs associated with local adaptation in Q. variabilis and Quercus acutissima. Notably, SV-outliers exhibit selection signals that did not overlap with SNP-outliers, indicating that SNP-based analyses may not detect the same candidate genes associated with SV-outliers. Remarkably, 29%-37% of candidate SNPs were located in a 250 kb region on chromosome 9, referred to as Chr9-ERF. This region contains 8 duplicated ethylene-responsive factor (ERF) genes, which may have contributed to local adaptation of Q. variabilis and Q. acutissima. We also found that a considerable number of candidate SNPs were shared between Q. variabilis and Q. acutissima in the Chr9-ERF region, suggesting a pattern of repeated selection. We further demonstrated that advantageous variants in this region were introgressed from western populations of Q. acutissima into Q. variabilis, providing compelling evidence that introgression facilitates local adaptation. This study offers a valuable genomic resource for future studies on oak species and highlights the importance of pan-genome analysis in understating mechanism driving adaptation and evolution
Characterization of bacterial communities of ewe's vaginal tract and its potential impact on reproductive efficiency
Get PDFThe success rate of artificial insemination in sheep remains suboptimal, which has led to an emerging interest in the impact of the reproductive tract microbiome on this process. This research aims to identify the ewes' vaginal core bacterial community, examine the factors influencing bacterial composition, and to determine the association between vaginal bacteria and pregnancy success. By using a robust dataset comprising 331 multiparous ewes from three Spanish breeds (Latxa, Manchega, Rasa Aragonesa) across four herds, this study performed the sequencing of the hypervariable regions V3-V4 of the 16S ribosomal RNA gene and the identification of Amplicon Sequence Variants (ASV) to analyze the bacterial community. Our analysis revealed a core bacterial primarily consisting of the genera Streptobacillus, Histophilus, Fusobacterium, Oceanivirga, and Parvimonas. Alpha and beta diversity, as well as Random Forest analysis, identified that herd and breed were the main drivers of bacterial variability. PERMANOVA analysis also showed significant differences in bacterial composition and abundance associated with pregnancy outcomes. Notably, specific ASVs associated with Fusobacterium, Leptotrichia, Histophilus, Escherichia, and Bacteroides were predominantly found in non-pregnant ewes, while genera such as Pseudomonas, Acinetobacter, and Brevundimonas were more abundant in pregnant ewes. This study contributes to the knowledge about the critical roles of specific bacteria in determining reproductive success in sheep and provides novel insights about the importance of different factors involved in the composition of ewes' vaginal bacterial communities
Evaluation of an automatic image classifier for analysis of bacterial growth on a multiple-agar plate developed for bovine mastitis
Get PDFRapid identification of mastitis-causing bacteria is crucial for effective treatment decisions. Several multi-media agar plates have been developed to aid pathogen identification on farms or by veterinarians, but these methods require trained operators. Advances in AI-based automatic image analysis have shown potential for detecting bacterial growth on agar plates in both agriculture and medicine. This study aimed to evaluate the accuracy of an AI-based image bacterial classifier compared to a gold-standard laboratory assessment. A secondary objective was to examine how sample transportation affects diagnoses by comparing results from an on-farm bacterial classifier with those from a laboratory-placed classifier. A total of 1,299 milk samples were collected and analysed at the Swedish Veterinary Agency's Mastitis Laboratory using both accredited laboratory standards and the bacterial classifier. The image classifier is capable of identifying growth of eight different bacteria types on SELMA + multi-agar plates. Out of 1,212 samples that met the analysis criteria, the bacterial classifier provided diagnoses for 70%, while 30% required further evaluation. The classifier demonstrated high specificity for all diagnoses and high sensitivity for common pathogens such as Escherichia coli, Staphylococcus aureus, and non-beta-haemolytic streptococci, though sensitivity was lower for less common pathogens. In a subset of samples analysed by both on-farm and in-lab classifiers and the Mastitis Laboratory, 62% showed consistent diagnoses. The average transportation time was 4.9 days, which influenced bacterial growth. Interestingly, fewer mixed infections were detected post-transport. Automated image classifiers, like Bacticam, hold promise for on-farm mastitis diagnosis, supporting targeted antibiotic treatment and reducing antimicrobial use
A Pilot Field Evaluation of Dietary Ginger Zingiber officinale Effects on Immunity, Blood Metabolic Profile, and Disease Resistance in Labeo rohita Under Semi-Intensive Farming
Get PDFA feeding trial was conducted for 120 days in a pilot field condition to evaluate ginger powder (GP; Zingiber officinale) as a feed supplement for Labeo rohita to improve immunity, blood metabolic profile, and resistance to Aeromonas hydrophila bacterial infection. The study was conducted following a complete randomized design in outdoor cemented tanks (20 m2) with a stocking density of 30 fish (average weight: 20.5 g) per tank. L. rohita fingerlings were divided into five groups and fed a diet with no GP supplementation (control diet; C) or a diet supplemented with 5 g (GP5), 10 g (GP10), 15 g (GP15), or 20 g (GP20) of GP per kg of the control diet. The results showed that fish well-being, determined by measuring the condition factor, remained higher than 1.0 for all the experimental groups. The condition factors of all the groups were not significantly different between the groups, suggesting GP had no negative impact on overall fish health. Immune responses significantly improved in the groups fed with diets supplemented with GP at doses of 10 to 15 g per kg of their diet, as seen in respiratory burst activity, total immunoglobulins, and lysozyme activity at 60 and 120 days. Blood metabolic variables, particularly the albumin level, tended to show some level of improvement in the GP15-fed group. However, the effect was not significant. Total protein and globulin levels and the albumin/globulin ratio were not significantly affected by dietary GP. Importantly, fish fed the GP15 diet showed the highest resistance to the A. hydrophila challenge. In conclusion, ginger powder holds promise as a health-promoting nutraceutical for farmed L. rohita, contributing to their sustainable farming