Genome assisted gene-flow rescued genetic diversity without hindering growth performance of inbred coho salmon (Oncorhynchus kisutch) population selected for high growth phenotype DOI Creative Commons

Junya Kobayashi,

Ryo Honda, S. Hosoya

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 17, 2024

Abstract Selective breeding is a powerful tool for improving aquaculture production. A well-managed program essential, as populations can otherwise lose genetic diversity, leading to reduced selection response and inbreeding excesses. In such cases, diversity in broodstock must be restored by introducing individuals from external populations. However, this reduce the accumulated gains selective breeding. On other hand, selectively introduction of with superior phenotypes will allow restoration without sacrificing these gains. study, we demonstrated possibility using bred (SB) randomly (RB) population coho salmon (Oncorhynchus kisutch). Forty males growth were selected RB genomic crossed 127 collected females SB produce newly (NB) population. Genetic assessed statistics effective number alleles, allele richness, observed heterozygosity 11 microsatellite markers, was higher NB than RB. Additionally, folk length body weight compared among three after 12-month communal culture fertilization. The least-squares means similar between (164.9 mm 57.9 g) (161.1 53.7 g), while both significantly larger those (150.4 43.0 g). Our results highlight effectiveness genome-assisted gene flow restoring compromising their gain growth.

Language: Английский

Advancing genetic improvement in the omics era: status and priorities for United States aquaculture DOI Creative Commons
Linnea K. Andersen, Neil F. Thompson, Jason Abernathy

et al.

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Feb. 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.

Language: Английский

Citations

2
Evaluation of low-density SNP panels and imputation for cost-effective genomic selection in four aquaculture species DOI Creative Commons
Christina Kriaridou,

Smaragda Tsairidou,

Clémence Fraslin

et al.

Frontiers in Genetics, Journal Year: 2023, Volume and Issue: 14

Published: May 11, 2023

Genomic selection can accelerate genetic progress in aquaculture breeding programmes, particularly for traits measured on siblings of candidates. However, it is not widely implemented most species, and remains expensive due to high genotyping costs. Genotype imputation a promising strategy that reduce costs facilitate the broader uptake genomic programmes. predict ungenotyped SNPs populations genotyped at low-density (LD), using reference population high-density (HD). In this study, we used datasets four species (Atlantic salmon, turbot, common carp Pacific oyster), phenotyped different traits, investigate efficacy genotype cost-effective selection. The had been HD, eight LD panels (300–6,000 SNPs) were generated silico . selected be: i) evenly distributed according physical position ii) minimise linkage disequilibrium between adjacent or iii) randomly selected. Imputation was performed with three software packages (AlphaImpute2, FImpute v.3 findhap v.4). results revealed faster achieved higher accuracies. accuracy increased increasing panel density both SNP methods, reaching correlations greater than 0.95 fish 0.80 oyster. terms prediction accuracy, imputed similarly, values very close HD panels, except pacific oyster dataset, where better panel. when without imputation, markers based either distance (instead randomly) resulted whereas near maximal independently panel, showing reliability. Our suggests that, well-selected may achieve addition will result These strategies represent effective affordable methods incorporate into settings.

Language: Английский

Citations

15
Sustainable management and improvement of genetic resources for aquaculture DOI Creative Commons
Anna K. Sonesson, Eric M. Hallerman, Fran Humphries

et al.

Journal of the World Aquaculture Society, Journal Year: 2023, Volume and Issue: 54(2), P. 364 - 396

Published: April 1, 2023

Abstract Effective genetic management of the ~700 aquatic species cultured globally should be addressed for aquaculture to make a significant contribution towards meeting UN's Sustainable Development Goals. This article aims identify current status and challenges relating farmed resources (AqGR) recommendations its improvement. The lack information on many is critical constraint there need characterize these develop systems tools monitor types used their wild counterparts. Risk assessment needed when introducing non‐native managing native including developed types; policies improved increased awareness training in risk are required. To increase uptake selective breeding aquaculture, development adoption better more sustainable business models, long‐term financial instruments such as public–private partnerships. Training technology transfer between sectors can have impact, especially lower‐value species. Nationally applicable regulations adapted AqGR become operational effectively implemented by countries.

Language: Английский

Citations

14
Reproduction and juvenile production DOI
David C. Little,

W. A. Turner,

Halina Sobolewska

et al.

CABI eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 61 - 126

Published: Jan. 13, 2025

Citations

0
Genome-Assisted Gene-Flow Rescued Genetic Diversity Without Hindering Growth Performance in an Inbred Coho Salmon (Oncorhynchus kisutch) Population Selected for High Growth Phenotype DOI Creative Commons

Junya Kobayashi,

Ryo Honda, S. Hosoya

et al.

Marine Biotechnology, Journal Year: 2025, Volume and Issue: 27(1)

Published: Feb. 1, 2025

Abstract Selective breeding is a powerful tool for improving aquaculture production. A well-managed program essential, as populations can otherwise lose genetic diversity, leading to reduced selection response and inbreeding excesses. In such cases, diversity in broodstock must be restored by introducing individuals from external populations. However, this reduce the accumulated gains selective breeding. introduction of with superior phenotypes will allow restoration without sacrificing these gains. study, we demonstrated possibility using selectively bred (SB) randomly (RB) population coho salmon ( Oncorhynchus kisutch ). Forty males growth were selected RB genomic crossed 127 collected females SB population, producing newly (NB) population. Genetic assessed statistics effective number alleles, allele richness, observed heterozygosity 11 microsatellite markers, was higher NB than RB. Additionally, fork length body weight compared among three after 12 months post-fertilization common tanks. The least-squares means similar between (164.9 mm 57.9 g) (161.1 53.7 g), while both significantly greater (150.4 43.0 g). Our results highlight effectiveness genome-assisted gene flow restoring compromising gain growth.

Language: Английский

Citations

0
Genomic selection for selective breeding of tiger pufferfish (Takifugu rubripes) for integration with surrogate broodstock technology DOI Creative Commons
S. Hosoya,

Sota Yoshikawa,

Masaomi Hamasaki

et al.

Aquaculture, Journal Year: 2025, Volume and Issue: 600, P. 742266 - 742266

Published: Feb. 6, 2025

Language: Английский

Citations

0
Genetic parameters and genome-wide association studies of image-derived cardiac traits in Tasmanian Atlantic salmon (Salmo salar) DOI
T.D.W. Luke, Richard Taylor, Wagdy Mekkawy

et al.

Aquaculture, Journal Year: 2025, Volume and Issue: unknown, P. 742436 - 742436

Published: March 1, 2025

Language: Английский

Citations

0
Consequences of domestication in eastern oyster: Insights from whole genomic analyses DOI Creative Commons
Honggang Zhao, Ximing Guo, Wenlu Wang

et al.

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(6)

Published: May 29, 2024

Selective breeding for production traits has yielded relatively rapid successes with high-fecundity aquaculture species. Discovering the genetic changes associated selection is an important goal understanding adaptation and can also facilitate better predictions about likely fitness of selected strains if they escape farms. Here, we hypothesize domestication as a change induced by inadvertent in culture. Our premise that standardized culture protocols generate parallel effects across independent strains. Using eastern oyster model newly developed 600K SNP array, this study tested multiple lines compared their progenitor wild populations. A single contrast was made between pooled (1-17 generations culture) all samples combined. Population structure analysis indicated rank order levels differentiation [wild - wild] < cultured] [cultured cultured]. genome scan to captive environment applied two methodologically distinct outlier tests versus strain identified total 1174 candidate SNPs. Contrasting revealed early evolutionary consequences terms genomic differentiation, standing diversity, effective population size, relatedness, runs homozygosity profiles, genome-wide linkage disequilibrium patterns. Random Forest used identify 37 SNPs had greatest discriminatory power bulked oysters. The were genes enriched cytoskeletal functions, hinting at possible under during larval or pediveliger setting high density. This documents stemming from hatchery-based cultivation oysters, identifies loci responding among strains, provides potentially useful resources monitoring interbreeding farm

Language: Английский

Citations

2
Liver fibrosis in fish research: From an immunological perspective DOI
Quanquan Cao, Hongying Shan,

Zhao Ju

et al.

Fish & Shellfish Immunology, Journal Year: 2023, Volume and Issue: 139, P. 108885 - 108885

Published: June 6, 2023

Language: Английский

Citations

6
Evaluating survival after heat challenges and investigating their correlations with field summer survival for the juvenile Pacific oyster (Crassostrea gigas) DOI
Yong Chi,

Chengxun Xu,

Qi Li

et al.

Aquaculture, Journal Year: 2024, Volume and Issue: 584, P. 740643 - 740643

Published: Feb. 2, 2024

Language: Английский

Citations

1