Application of machine learning in intelligent fish aquaculture: A review

Aquaculture, Journal Year: 2021, Volume and Issue: 540, P. 736724 - 736724

Published: April 3, 2021

Language: Английский

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Fish pigmentation and coloration: Molecular mechanisms and aquaculture perspectives

Reviews in Aquaculture, Journal Year: 2021, Volume and Issue: 13(4), P. 2395 - 2412

Published: June 2, 2021

Abstract Fish coloration, evolved from selection and adaptation, is a prominent feature of remarkable aquaculture merits. possess more pigment cell types than any other vertebrates are an excellent model for the study mechanisms underlying skin coloration pigmentation at levels molecular genetics to system biology. How effectively improve colour in ornamental fish has long been focus on selective breeding programmes. In this review article, we introduce different chromatophore early development pigmentation, describe cellular related morphological physiological changes body demonstrate applications single‐sex control marker–assisted selection. We also reviewed genes that have found involving neural crest migration development, as well those involved melanin‐based explored how use transgenic technology enhancing colour. The genome editing omics technologies relation illustrated. Finally, present our perspectives about future research practice aquaculture. Taken together, expected provide update which will likely promote colour–based programmes

Language: Английский

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Rethinking fish biology and biotechnologies in the challenge era for burgeoning genome resources and strengthening food security

Water Biology and Security, Journal Year: 2021, Volume and Issue: 1(1), P. 100002 - 100002

Published: Nov. 22, 2021

Fish biology has been developed for more than 100 years, but some important breakthroughs have made in the last decade. Early studies commonly concentrated on morphology, phylogenetics, development, growth, reproduction manipulation, and disease control. Recent mostly focused genetics, molecular biology, genomics, genome biotechnologies, which provided a solid foundation enhancing aquaculture to ensure food security improving aquatic environments sustain ecosystem health. Here, we review research advances five major areas: (1) biological innovations genomic evolution of four significant fish lineages including non-teleost ray-finned fishes, northern hemisphere sticklebacks, East African cichlid Asian cyprinid fishes; (2) evolutionary fates consequences natural polyploid (3) domestication selection; (4) development innovation breeding biotechnologies; (5) applicable approaches potential genetic biotechnologies. Moreover, precision biotechniques are examined discussed detail gene editing introgression or removal beneficial detrimental alleles, use sex-specific markers production mono-sex populations, controllable primordial germ cell on-off strategy producing sterile offspring, surrogate broodstock-based strategies accelerate breeding, incorporation sexual regain-based approach create synthetic polyploids. Based these scientific technological advances, propose blueprint improvement new breed creation species analyze seed industry strengthening security.

Language: Английский

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Current status and potential of genomic selection to improve selective breeding in the main aquaculture species of International Council for the Exploration of the Sea (ICES) member countries

Aquaculture Reports, Journal Year: 2021, Volume and Issue: 20, P. 100700 - 100700

Published: May 7, 2021

Selective breeding has been successfully applied to improve profitability and sustainability in numerous aquatic species. Recent developments of high throughput genotyping technology now enable the implementation genomic selection, a method aiming predict value candidates based on their genotype at genome-wide markers. In this review article, we state arts, challenges prospects for application selection aquaculture The particular focus is status several major species International Council Exploration Sea (ICES) member countries: Atlantic salmon, rainbow trout, cod, American catfish, Pacific oyster, European sea bass gilthead bream. While potential clear, tailored species-specific applications will be needed maximise its benefit sector.

Language: Английский

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Genome‐wide association and genomic selection in aquaculture

Reviews in Aquaculture, Journal Year: 2022, Volume and Issue: 15(2), P. 645 - 675

Published: Nov. 17, 2022

Abstract Recent advancements in genomic technologies have led to the discovery and application of DNA‐markers [e.g. single nucleotide polymorphisms (SNPs)] for genetic improvement several aquaculture species. The identification specific regions associated with economically important traits, using, example, genome‐wide association studies (GWAS), has allowed incorporation markers linked quantitative trait loci (QTL) into breeding programs through marker‐assisted selection (MAS). However, most traits economic relevance are expected be controlled by many QTLs, each one explaining only a small proportion variation. For under polygenic control, prediction merit animals based on sum effects at positions across entire genome (i.e. estimated values, GEBV, which used what become known as selection), been demonstrated speed rate gain breeding. aim this review was provide an overview development uncovering basis complex accelerating progress species, well providing future perspectives about deployment novel molecular selective coming years.

Language: Английский

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The farming and husbandry ofColossoma macropomum: From Amazonian waters to sustainable production

Reviews in Aquaculture, Journal Year: 2021, Volume and Issue: 14(2), P. 993 - 1027

Published: Nov. 25, 2021

Abstract Within the rich diversity of South American freshwater fish, Colossoma macropomum (Characiformes: Serrasalmidae), known as tambaqui, cachama or blackfin pacu, can reach 30 kg, is a traditional product in regional fish markets and has drawn attention farmers since 1930s. Considerable progress achieved different fields aquaculture science contributed to growth tambaqui production. Tambaqui proven suitable for both monoculture polyculture systems, extensive intensive production systems aimed at achieving sustainable, higher productivity with minimal environmental impact. Studies reproductive anatomy physiology species proved fundamental development techniques boost commercial production, contributing protocols hormonally induced spawning artificial propagation 1970s. Newly hatched larvae must be fed live foods until they weaned feeds about 100 mg weight. Despite its importance aquaculture, only few studies have reported components quantitative genetic variance parameters weight age, morphometric traits disease resistance. Genomic tools currently available applied detect variation relevant performance accelerate process improvement. While species’ feeding habit allows use diets containing 75%–85% plant protein, much more work needs done optimize aquafeeds. Refinement methods potential significantly aquaculture. We recommend research on diets, improvement system optimization spur further achieve sustainable culture.

Language: Английский

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Aquaculture species diversification in China

Aquaculture and Fisheries, Journal Year: 2023, Volume and Issue: 9(2), P. 206 - 217

Published: Jan. 21, 2023

China has been the top aquaculture producer in world since 2002. Over 800 species and 240 improved varieties have used China's aquaculture, which is most diverse collection of on this planet. Species diversification, along with other technologies, contributes significantly to increase production, whereas use too many resulted some issues related environment sustainability. We provide an updated overview currently Chinese paper. examine critically main drivers diversification examples. also introduce approaches improve certify new for commercial production. believe that further not a priority while improvement technologies major native essential green, profitable, sustainable (GPS) aquaculture. The implications experiences global are discussed.

Language: Английский

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Genetic improvement of oysters: Current status, challenges, and prospects

Reviews in Aquaculture, Journal Year: 2023, Volume and Issue: 16(2), P. 796 - 817

Published: Oct. 30, 2023

Abstract Oysters are one of the most commercially important shellfish species and have been cultured for thousands years. Oyster aquaculture supports major industries in many countries. Over last few decades, oyster breeding developed rapidly to meet continually growing demand. Many researchers made significant efforts toward genetic improvement traits oysters. Some strains with fast‐growing, disease‐resistant, stable shell‐colours through selective breeding. hybrid varieties by crossing different geographical populations or cultivated strains. Several hybrids exhibit considerable variation improved productive performance. Additionally, polyploid induction technologies applied industry, which provides a useful tool performance containment stocks. At present, development molecular also great opportunity improvement. These advances quality oysters, brought economic benefits, conducive sustainability production. Nonetheless, there still some limitations obstacles breeding, such as infectious diseases, summer mortality, conservation germplasm resources, environmental contamination, climate change. The present review an overview current status, challenges, prospects

Language: Английский

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Twelve quick steps for genome assembly and annotation in the classroom

PLoS Computational Biology, Journal Year: 2020, Volume and Issue: 16(11), P. e1008325 - e1008325

Published: Nov. 12, 2020

Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting budgets individual research groups. Third-generation long-read DNA technologies are used, providing extensive genomic toolkits that were reserved for a few select model organisms. Generating high-quality assemblies annotations many aquatic species still presents significant challenges due to their large sizes, complexity, high chromosome numbers. Indeed, selecting most appropriate software platforms annotation pipelines new project can be daunting because tools often only work in limited contexts. In genomics, generating assembly/annotation has an indispensable tool better understanding biology any species. Herein, we state 12 steps help researchers get started projects by presenting guidelines broadly applicable (to species), sustainable over time, cover all aspects assembly from start finish. We review some commonly used approaches, including practical methods extract choices best library preparations. addition, discuss range potential bioinformatics pipelines, structural functional (e.g., transposable elements repetitive sequences). This paper also includes information on how build wide community project, importance data management, make results Findable, Accessible, Interoperable, Reusable (FAIR) submitting them public repository sharing with community.

Language: Английский

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A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiatiated ZZ/ZW sex determination of turbot (Scophthalmus maximus)

Genomics, Journal Year: 2021, Volume and Issue: 113(4), P. 1705 - 1718

Published: April 8, 2021

Understanding sex determination (SD) across taxa is a major challenge for evolutionary biology. The new genomic tools are paving the way to identify features underlying SD in fish, group frequently showing limited chromosome differentiation and high turnover. Turbot (Scophthalmus maximus) commercially important flatfish with an undifferentiated ZW/ZZ system remarkable sexual dimorphism. Here we describe long-read turbot genome assembly used disentangle genetic architecture of by combining genomics classical genetics approaches. consists 145 contigs (N50 = 22.9 Mb), 27 them representing >95% its estimated size. A wide association study (GWAS) identified ~ 6.8 Mb region on 12 associated 69.4% 36 families analyzed. highest markers flanked sox2, only gene differential expression between sexes before gonad differentiation. single SNP showed consistent differences Z W chromosomes. analysis broad sample suggested presence additional and/or environmental factors SD. chromosome-level assembly, one most contiguous fish assemblies date, facilitated identification sox2 as candidate putatively driving this species. This barely any signs differentiation, other beyond main QTL seem control certain proportion families.

Language: Английский

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