Advancing genetic improvement in the omics era: status and priorities for United States aquaculture

BMC Genomics, Год журнала: 2025, Номер 26(1)

Опубликована: Фев. 17, 2025

The innovations of the "Omics Era" have ushered in significant advancements genetic improvement agriculturally important animal species through transforming genetics, genomics and breeding strategies. These were often coordinated, part, by support provided over 30 years 1993-2023 National Research Support Project 8 (NRSP8, Animal Genome Program, NAGRP) affiliate projects focused on enabling genomic discoveries livestock, poultry, aquaculture species. parallel advances demand strategic planning future research priorities. This paper, as an output from May 2023 Aquaculture Genomics, Genetics, Breeding Workshop, provides updated status resources for United States species, highlighting major achievements emerging Finfish shellfish genome omics enhance our understanding architecture heritability performance production traits. Workshop identified present aims genomics/omics to build this progress: (1) advancing reference assembly quality; (2) integrating multi-omics data analysis traits; (3) developing collection integration phenomics data; (4) creating pathways applying information across industries; (5) providing training, extension, outreach application phenome. focuses should emphasize collection, artificial intelligence, identifying causative relationships between genotypes phenotypes, establishing apply tools industries, expansion training programs next-generation workforce facilitate sciences into operations productivity, competitiveness, sustainability. collective vision with focus highlighted priorities is intended continued advancement genomics, genetics community industries. Critical challenges ahead include practical analytical frameworks beyond academic communities that require collaborative partnerships academia, government, industry. scope review encompasses use applications study aquatic animals cultivated human consumption settings throughout their life-cycle.

Язык: Английский

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Ensembl 2025

Nucleic Acids Research, Год журнала: 2024, Номер 53(D1), С. D948 - D957

Опубликована: Дек. 4, 2024

Ensembl (www.ensembl.org) is an open platform integrating publicly available genomics data across the tree of life with a focus on eukaryotic species related to human health, agriculture and biodiversity. This year has seen continued expansion in number represented, >4800 >31 300 prokaryotic genomes available. The new site, currently beta, develop, holding >2700 genome assemblies. site provides genome, gene, transcript, homology variation views, will replace current Rapid Release site; this represents key step towards provision single integrated site. Additional activities have included developing improved regulatory annotation for human, mouse agricultural species, expanding Variant Effect Predictor tool. To learn more about Ensembl, help documentation are along extensive training program that can be accessed via our pages.

Язык: Английский

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Empowering bioinformatics communities with Nextflow and nf-core

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 14, 2024

Abstract Standardised analysis pipelines are an important part of FAIR bioinformatics research. Over the last decade, there has been a notable shift from point-and-click pipeline solutions such as Galaxy towards command-line Nextflow and Snakemake. We report on recent developments in nf-core frameworks that have led to widespread adoption across many scientific communities. describe how adopting standards enables faster development, improved interoperability, collaboration with >8,000 members community. The development Domain-Specific Language 2 (DSL2) allows components be shared combined projects. community harnessed this library modules subworkflows can integrated into any pipeline, enabling research communities progressively transition best practices. present case study by six European consortia, grouped under EuroFAANG umbrella dedicated farmed animal genomics. believe process outlined inspire large consortia seek harmonisation their data procedures.

Язык: Английский

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Community assembly of gut microbiomes in yolk sac fry of Atlantic salmon: host genetics, environmental microbiomes, and ecological processes

FEMS Microbiology Ecology, Год журнала: 2025, Номер unknown

Опубликована: Янв. 17, 2025

In this study, we investigated the influence of host genetics and environmental microbiomes on early gut microbiome Atlantic salmon. We aimed at rearing fish in either r- or K-selected environments, where r-selected environment would be expected to dominated by fast-growing opportunistic bacteria thus represent more detrimental microbial than water. Eggs from both wild aquaculture strains salmon were hatched under germ-free conditions. One week after hatching (wph), flasks inoculated with water communities. Three wph, no effect strain observed. r-selection was found take place all flasks, including added Still, differed significantly between that had been (Add-r Add-K respectively). Lower alpha diversity higher abundances Pseudomonas observed for indicating an unfavorable environment. Selection structured microbiomes, but extensive intraindividual variation explained stochastic processes community assembly. The also Add-r flasks. they similarities assembly communities less influenced processes. lower growth rates probably a result negative host-microbe interactions. These findings highlight importance of, challenges related to, managing when cultivating fish.

Язык: Английский

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Dissecting the genetic basis of response to salmonid alphavirus in Atlantic salmon

Research Square (Research Square), Год журнала: 2025, Номер unknown

Опубликована: Март 7, 2025

Background The development of effective disease management strategies is crucial for the assurance welfare and sustainability aquaculture industries. Pancreas (PD) a major challenge faced by Atlantic salmon with viral outbreaks resulting in substantial production losses raising significant concerns farmed populations. Previous research has identified several quantitative trait loci (QTL) associated PD resistance accounting additive genetic component. However, pinpointing underlying causal variation remains challenging, partly due to location QTL within duplicated regions genome that share high sequence similarity. present study leverages latest advancements genomics order uncover landscape identify genomic putative functional impact on response. Results Association mapping haplotype analysis fish challenged salmonid alphavirus (SAV3), either through peritoneal injection or infectious cohabitation, confirmed presence region chromosome Ssa03. Additionally, another Ssa07 was detected, linked infection-specific Transcriptomics genes overlapping Ssa03 revealed expression differences among three tandemly gig1-like genes, whereas allele-specific detected SNPs particular genes. Use long-read sequencing construction disease-associated haplotypes more complex offering detailed exploration architecture resistance. Finally, integration regulatory during infection response improved resolution, providing novel insight into potential pancreas salmon. Conclusions This provides investigation Using advanced resources, copies gig1-like gene were as likely candidates variations impacts uncovered. These findings hold promise application developing aquaculture.

Язык: Английский

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High performance imputation of structural and single nucleotide variants using low-coverage whole genome sequencing

Genetics Selection Evolution, Год журнала: 2025, Номер 57(1)

Опубликована: Март 28, 2025

Whole genome sequencing (WGS), despite its advantages, is yet to replace methods for genotyping single nucleotide variants (SNVs) such as SNP arrays and targeted assays. Structural (SVs) have larger effects on traits than SNVs, but are more challenging accurately genotype. Using low-coverage WGS with genotype imputation offers a cost-effective strategy achieve genome-wide variant coverage, be tested SVs. Here, we investigate combined SNV SV data in Atlantic salmon (Salmo salar). As the reference panel, used genotypes high-confidence SVs SNVs n = 365 wild individuals sampled from diverse populations. We also generated 15 × (n 20 samples) commercial population external called gold-standard approaches. An method selected established performance using (GLIMPSE) was at depths of 1 , 2 3 4 samples within panel. were imputed high accuracy recall across all depths, including out-with For SVs, compared based purely linkage disequilibrium (LD) that supplemented likelihoods (GLs) WGS. Including GLs increased accuracy, trade-off recall, requiring 3-4 depth best performance. Combining strategies allowed us capture 84% panel deletions 87% depth. show length affects performance, provision greatly enhancing longest dataset. This study highlights promise WGS, novel opportunities enhance resolution association studies by capturing

Язык: Английский

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The Genomics Revolution in Nonmodel Species: Predictions vs. Reality for Salmonids

Molecular Ecology, Год журнала: 2025, Номер unknown

Опубликована: Апрель 18, 2025

ABSTRACT The increasing feasibility of whole‐genome sequencing has been highly anticipated, promising to transform our understanding the biology nonmodel species. Notably, dramatic cost reductions beginning around 2007 with advent high‐throughput inspired publications heralding ‘genomics revolution’, predictions about its future impacts. Although such served as useful guideposts, value is added when statements are evaluated benefit hindsight. Here, we review 10 key made early in genomics revolution, highlighting those realised while identifying challenges limiting others. We focus on concerning applied aspects and examples involving salmonid species which, due their socioeconomic ecological significance, have frontrunners applications Predicted outcomes included enhanced analytical power, deeper insights into genetic basis phenotype fitness variation, disease management breeding program advancements. many materialised, several expectations remain unmet technological, knowledge barriers. Additionally, largely unforeseen advancements, including identification applicability large‐effect loci, close‐kin mark–recapture, environmental DNA gene editing under‐anticipated value. Finally, emerging innovations artificial intelligence bioinformatics offer new directions. This retrospective evaluation impacts genomic revolution offers for

Язык: Английский

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Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Фев. 15, 2024

Abstract Uncovering the epigenomic regulation of immune responses is essential for a comprehensive understanding host defence mechanisms, though remains poorly investigated in farmed fish. We report first annotation innate regulatory response turbot genome (Scophthalmus maximus), integrating RNA-Seq with ATAC-Seq and ChIP-Seq (H3K4me3, H3K27ac H3K27me3) data from head kidney (in vivo) primary leukocyte cultures vitro) 24 hours post-stimulation viral (poly I:C) bacterial (inactive Vibrio anguillarum ) mimics. Among 8,797 differentially expressed genes (DEGs), we observed enrichment transcriptional activation pathways to - including interferon stimulated poly I:C. identified notable differences chromatin accessibility (20,617 vitro, 59,892 H3K4me3-bound regions (11,454 10,275 between stimulations controls. Overlap DEGs promoters showing differential or histone mark binding revealed significant coupling transcriptome state. marks their were enriched similar functions global DEG set, but not always, suggesting key being poised Active putative enhancers specific transcription factor motifs, many common responses. Finally, an in-depth analysis changes state surrounding encoding factors was performed. This multi-omics investigation provides improved basis novel functional genomic information, leverageable disease resistance selective breeding.

Язык: Английский

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Functional annotation of regulatory elements in rainbow trout uncovers roles of the epigenome in genetic selection and genome evolution

GigaScience, Год журнала: 2024, Номер 13

Опубликована: Янв. 1, 2024

Rainbow trout (RBT) has gained widespread attention as a biological model across various fields and been rapidly adopted for aquaculture recreational purposes on 6 continents. Despite significant efforts to develop genome sequences RBT, the functional genomic basis of RBT's environmental, phenotypic, evolutionary variations still requires epigenome reference annotations. This study produced comprehensive catalog annotation tracks detecting gene regulatory elements, including chromatin histone modifications, accessibility, DNA methylation. By integrating immunoprecipitation sequencing, ATAC Methyl Mini-seq, RNA sequencing data, this new element helped characterize dynamics its correlation with expression. The also identified potential causal variants transcription factors regulating complex domestication phenotypic traits. research provides valuable insights into epigenome's role in evolution mechanism duplicate retention 100 million years after RBT whole-genome duplication during re-diploidization. newly developed maps are among first fish expected enhance accuracy efficiency studies applications, genome-wide association studies, causative variation identification, selection comparative genomics.

Язык: Английский

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INNOVATIVE MONITORING OF WATER ENVIRONMENT IN VANAME SHRIMP FARMING BASED ON LORAWAN

Journal of Southwest Jiaotong University, Год журнала: 2024, Номер 59(1)

Опубликована: Янв. 1, 2024

The sudden vaname shrimp death factors are overfeeding, disease infection, failure to mount, stress, and high rainfall, which cause potential changes in water pH that trigger anxiety shrimp. next factor is turbid or dirty water. Other include insufficient oxygen content the Therefore, overcome these issues, a sensor explicitly handles conditions needed. system built this research still has two stages, namely real-time monitoring automatic actuators, being developed. placed floating condition with specific materials so it impossible sink. Some tested sensors salinity, pH, turbidity, dissolved sensors. Its wireless telecommunication uses LoRa frequencies of 920–923 MHz. It an 8-dBi omnidirectional antenna Dragino RFM96 Module chip. This provides data on entire environment needed for survive. development after focused actuator, how turn Blower automatically needs results shown from experiment all brackish quality measurements running normally; displayed application server real time using Tago.io app been connected LoRaWAN Module, 915 MHz found end devices. installed were calibrated produce accurate data. Keywords: environment, innovative sensor, farming, monitoring, smart aquaculture DOI: https://doi.org/10.35741/issn.0258-2724.59.1.18

Язык: Английский

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