Genome-wide association and genomic prediction of resistance to Flavobacterium columnare in a farmed rainbow trout population

Aquaculture, Journal Year: 2022, Volume and Issue: 557, P. 738332 - 738332

Published: May 10, 2022

Columnaris disease is an emerging affecting farmed rainbow trout (Oncorhynchus mykiss) globally. In aquaculture breeding, genomic selection has been increasingly used to improve traits that are difficult measure on candidate fish (such as resistance traits). Following a natural outbreak of columnaris disease, 3054 exposed and their 81 parents (33 dams 48 sires) were genotyped with the 57 K SNP Axiom™ genotyping array. Genetic parameters host (measured binary survival trait) estimated, genome wide association study was performed, accuracy pedigree-based prediction estimated. After quality controls, 2874 challenged (1403 dead 1471 alive fish) 78 for 27,907 SNPs remained. Pedigree based heritability estimated be 0.18 0.35 observed underlying scale, respectively. Genomic 0.21 0.43 A quantitative trait loci (QTL) detected chromosome Omy3, significant at genome-wide level, along several suggestive QTLs two other chromosomes. The additive effect mortality proportion peak from Omy3 0.11 (0.018; se), implying approximately 22% difference in between alternate homozygous QTL. Pedigree-based 0.59, use evaluation increased by least 13.6%. Using second iteration weighted genomic-based 18.6% compared model. These results confirm suitable target genetic improvement selective farm environment can select more resistant useful approach speed up this process.

Language: Английский

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An overview of the mechanisms underlying hypoxia tolerance differences in aquatic animals and their inspirations for aquaculture

Reviews in Fish Biology and Fisheries, Journal Year: 2023, Volume and Issue: 33(4), P. 1223 - 1236

Published: July 24, 2023

Language: Английский

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Fish Genomics and Its Application in Disease‐Resistance Breeding

Reviews in Aquaculture, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 10, 2024

ABSTRACT Global aquaculture production has been rising for several decades, with up to 76% of the total from fish. However, problem fish diseases is becoming more and prominent in today's context pursuing sustainable aquaculture. Since first genome assembly reported 2002, genomic approaches have successfully implemented breeding enhance disease resistance reduce economic losses caused by diverse diseases. Here, we present a review current progress genomics its application disease‐resistance breeding. First, data all publicly available genomes were curated statistical analysis these performed. Subsequently, genomics‐assisted (including quantitative trait loci mapping, genome‐wide association study, marker‐assisted selection, gene transfer, editing) that applied practical disease–resistance programs are outlined. In addition, candidate genetic markers could possibly be utilized summarized. Finally, remaining challenges further directions discussed. summary, this provides insight into disease‐resistant varieties.

Language: Английский

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Whole-genome resequencing identifies candidate genes and SNPs in genomic regions associated with shell color selection in the Pacific oyster, Crassostrea gigas

Aquaculture, Journal Year: 2024, Volume and Issue: 586, P. 740768 - 740768

Published: March 6, 2024

Language: Английский

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A chromosome-level reference genome of red swamp crayfish Procambarus clarkii provides insights into the gene families regarding growth or development in crustaceans

Genomics, Journal Year: 2021, Volume and Issue: 113(5), P. 3274 - 3284

Published: July 22, 2021

Language: Английский

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Predicting for disease resistance in aquaculture species using machine learning models

Aquaculture Reports, Journal Year: 2021, Volume and Issue: 20, P. 100660 - 100660

Published: March 14, 2021

Predicting disease resistance is one of the most prominent applications aquaculture selective breeding. Reductions in genotyping costs have allowed implementation genomic selection an abundance species and their related diseases showing promising results. Machine learning (ML) models can be value for prediction purposes, as suggested by several studies both plants livestock. The current study aimed to test efficiency various ML predicting using simulated real datasets. More specifically, like decision trees (DT), support vector machines (SVM), random forests (RF), adaptive boosting (Adaboost) extreme gradient (XGB) were benchmarked against best linear unbiased threshold traits backend Markov chain Monte Carlo (GBLUP-MCMC) terms required computational time. Moreover, model ranking was tested datasets where ratio between two observed phenotypes (resistant vs non-resistant) unbalanced. Across all datasets, XGB ranked first with a slight advantage over GBLUP-MCMC, ranging 1–4 %. SVM RF delivered predictions tight proximity ones from GBLUP-MCMC. In addition, 3–4 % lower compared GBLUP-MCMC obtained Adaboost. On other hand, DT consistently low (∼40 GBLUP-MCMC). All had significantly reduced requirements than case XGB, more 20-fold opposed under settings study. competitive highly efficient time (∼3 min). Overall, results suggest that valuable tools breeding resistance.

Language: Английский

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Potential of genomic technologies to improve disease resistance in molluscan aquaculture

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2021, Volume and Issue: 376(1825), P. 20200168 - 20200168

Published: April 4, 2021

Molluscan aquaculture is a major contributor to global seafood production, but hampered by infectious disease outbreaks that can cause serious economic losses. Selective breeding has been widely used improve resistance in agricultural and species, clear potential molluscs, albeit its commercial application remains at formative stage. Advances genomic technologies, especially the development of cost-efficient selection, have accelerate genetic improvement. However, tailored approaches are required owing distinctive reproductive life cycle characteristics molluscan species. Transgenesis genome editing, particular CRISPR/Cas systems, successfully trialled molluscs may further understanding improvement through targeted changes host genome. Whole-organism editing achievable on much greater scale compared other farmed making genome-wide CRISPR screening plausible. This review discusses current state future selective breeding, tools understand molluscs. article part Theo Murphy meeting issue 'Molluscan genomics: broad insights directions for neglected phylum'.

Language: Английский

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The impact of genetic relationship between training and validation populations on genomic prediction accuracy in Atlantic salmon

Aquaculture Reports, Journal Year: 2022, Volume and Issue: 23, P. 101033 - 101033

Published: Feb. 7, 2022

The potential of genomic selection (GS) to improve production traits has been widely demonstrated in many aquaculture species. Atlantic salmon breeding programmes typically consist sibling testing schemes, where that cannot be measured on the candidates are candidates' siblings. While annual close relatives is effective, it expensive due high genotyping and phenotyping costs. Accurate prediction values distant could significantly reduce cost GS. This study aimed evaluate impact decreasing relationship between training validation populations accuracy for two key traits; body weight resistance sea lice; assess interaction genetic with SNP density. Phenotype genotype data from year classes a commercial population were used. predictions zero when was performed across class, albeit this may reflect lack correlation same different classes. Within systematically reducing relatedness resulted prediction; set up contain no relationships > 0.3, accuracies decreased by 44% lice count 53% weight. Less related also tended result highly biased predictions. No clear density found. These results confirm importance programmes, suggests generations using existing approaches would severely compromise efficacy

Language: Английский

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First genome-wide association study and genomic prediction for growth traits in spotted sea bass (Lateolabrax maculatus) using whole-genome resequencing

Aquaculture, Journal Year: 2022, Volume and Issue: 566, P. 739194 - 739194

Published: Dec. 22, 2022

Language: Английский

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Carotenoids modulate stress tolerance and immune responses in aquatic animals

Reviews in Aquaculture, Journal Year: 2022, Volume and Issue: 15(2), P. 872 - 894

Published: Nov. 20, 2022

Abstract Aquaculture continues to expand swiftly and remains the fastest‐growing food industry worldwide amidst ever‐present threats from chronic stressors emerging diseases. Nutrition plays a pivotal role in profitability viability of aquaculture that steered paradigm shift therapeutic nutrition. Carotenoids, also termed tetraterpenoids, have garnered considerable attention owing their attributes immeasurable health benefits, which incited surge global demand. These biological pigments are recognized promote immune systems antioxidant defence mechanisms both aquatic vertebrates invertebrates. This review brings forth existing scientific evidence underscores notable roles carotenoids as biologically active constituents with anti‐stress immunostimulatory potentials farmed animals whilst explicating possible action. Empirical data unequivocally established modulatory functions on endogenous enzymes, innate adaptive arms response, well expression multiple immune‐related genes. The comprehensive information presented is beneficial deepen our understanding utilization potent stress alleviators immunostimulants cultured animals, translated into improved health. Advancements animal welfare could principally contribute reconstructing more sustainable industry. article may be useful for subsequent investigations towards further advances research innovation greener blue revolution solving challenge security.

Language: Английский

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