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

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

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Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture

Frontiers in Genetics, Journal Year: 2022, Volume and Issue: 13

Published: Nov. 2, 2022

Major progress has been made with genomic and genetic studies in aquaculture the last decade. However, research on epigenetic regulation of traits is still at an early stage. It apparent that most, if not all, are regulated both levels. This paper reviews recent understanding important such as growth, reproduction, disease resistance, stress responses. Although it challenging to make generalized statements, DNA methylation mostly correlated down-regulation gene expression, especially when promoters enhancers. As such, growth factors their receptors negatively growth; hypomethylation genes for tolerance increased tolerance; male or female sex differentiation leads into males females, respectively. environmental mediated level regulation, environment-induced changes appeared be intergenerationally inherited, but evidences transgenerational inheritance limited.

Language: Английский

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Recent advances in crustacean genomics and their potential application in aquaculture

Reviews in Aquaculture, Journal Year: 2023, Volume and Issue: 15(4), P. 1501 - 1521

Published: Jan. 23, 2023

Abstract Genomic resources are increasingly being used to improve the production efficiency and profitability of aquaculture. Crustaceans a large group invertebrates that encompasses some most important farmed species in aquaculture industry. However, very few crustacean genomes have been published although an genome project was proposed as early 1997. Breakthroughs next‐generation third‐generation sequencing technologies development high‐complexity sequence assembly strategies promoted publication increasing number genomes, thus paving broad way for biological genetic studies applications In this review, we summarize recent advances genomic research June 2022, including assembly, characteristics, mechanisms underlying various phenotypes, such environmental adaptation, lifestyle, development, sex determination. This review also discusses application aquaculture, dissection economic traits genome‐based selective breeding via genome‐wide association selection. High‐quality not only understanding basis biologically economically but improvement species. utilization genomics still lags far behind those other animals. Therefore, additional multi‐omics technological needed accelerate

Language: Английский

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The chromosome-level genome provides insights into the adaptive evolution of the visual system in Oratosquilla oratoria

BMC Biology, Journal Year: 2025, Volume and Issue: 23(1)

Published: Feb. 6, 2025

The marine crustacean Oratosquilla oratoria is economically significant in seafood and aquaculture industries. However, the lack of high-quality genome assembly has hindered our understanding O. oratoria, particularly mechanisms underlying its developed visual system. We generated a chromosome-level for (2.97 Gb, 44 pseudo-chromosomes) using combination sequencing strategies. Our analysis revealed that more than half was covered by repeat sequences, LINE elements showed expansion. Furthermore, phylogenetic close relationship with Dendrobranchiata Pleocyemata. In addition, evolutionary rate slightly faster slower Interestingly, we observed expansion middle-wavelength-sensitive (MWS) opsins tandem duplication, partially contributing to their unique capabilities. Compared other crustaceans, evolved thicker cornea possibly driven adaptations ecological requirements. Employing comparative transcriptome analysis, identified tandemly duplicated cuticle protein (CP) cluster specifically expanded expressed ocular tissues potentially thick oratoria. study established first Stomatopoda species, providing valuable genomic resource studying molecular system

Language: Английский

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The crustacean DNA virus tegument protein VP26 binds to SNAP29 to inhibit SNARE complex assembly and autophagic degradation

Journal of Virology, Journal Year: 2024, Volume and Issue: 98(2)

Published: Jan. 8, 2024

Autophagy generally functions as a cellular surveillance mechanism to combat invading viruses, but viruses have evolved various strategies block autophagic degradation and even subvert it promote viral propagation. White spot syndrome virus (WSSV) is the most highly pathogenic crustacean virus, little currently known about whether such WSSV can for escape. Here, we show that though proliferation triggers accumulation of autophagosomes, blocked in species red claw crayfish. Interestingly, soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex including

Language: Английский

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Transcriptome analysis reveals the effects of dietary protein level on growth performance and metabolism in adult Procambarus clarkii farming in rice field

Aquaculture Reports, Journal Year: 2024, Volume and Issue: 35, P. 101949 - 101949

Published: Feb. 2, 2024

To assess the optimal dietary protein requirement of adult red swamp crayfish (Procambarus clarkii) farming in rice field, six isoenergetic and isolipid diets were formulated to contain graded levels 28%, 31%, 34%, 37%, 40% 43% crude (called Diet 28–43 group). Each diet was assigned a triplicate 20 experimental with average initial body weight (15.17 ± 0.23) g for 42 days. Our results showed that final weight, gain rate specific growth 34, 37, 40 43 groups significantly higher than those other (P < 0.05), but no significant difference found meat yield, hepatosomatic index survival among all groups. The highest content muscle fed containing 37% 0.05). Hemolymph total protein, globulin bilirubin concentration positive correlation level, alanine transaminase activity negatively correlated level Different had effect on aspartate > Activities trypsin lipase intestine affected by while amylase Moreover, increased antioxidant non-specific immunity enzyme activity. Broken-line regression analysis based maximum performance 32.68%. According present study performance, 28 group (SM) 34 (LM) individuals selected transcriptome sequencing. there 444 differential genes SM LM, which 282 up-regulated 162 down-regulated. DEGs LM mainly enriched citrate cycle, pyruvate glycolysis/gluconeogenesis, etc. Beyond that, transcriptomic also hinted glycolysis/gluconeogenesis cycle signaling pathways might be its change mechanisms. In addition, aldo, eno, pk, pdhb, adh, sdha, fh, mdh2, cs identified as key factors involved pathways. conclusion, combining data, we recommended 32.68%− 34.00% rice-shrimp pattern.

Language: Английский

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Transcriptomic and Biochemical analysis of Procambarus clarkii upon exposure to Pesticides: Population-Specific responses as a sign of pollutant resistance?

Environmental Research, Journal Year: 2025, Volume and Issue: unknown, P. 120963 - 120963

Published: Jan. 1, 2025

Language: Английский

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Construction of the Red Swamp Crayfish (Procambarus clarkii) Family Selection Population and Whole Genome Sequencing to Screen WIPFI Candidate Genes Related to Growth

Genes, Journal Year: 2025, Volume and Issue: 16(2), P. 174 - 174

Published: Jan. 31, 2025

Background/Objectives:Procambarus clarkii is an important freshwater aquaculture species in China which has the characteristics of rich nutrition and delicious taste. However, expansion scale, germplasm degradation, other problems that have become increasingly prominent seriously restrict sustainable development crayfish industry. Genetic improvement urgent need for industry, selective breeding way to improve varieties. Methods: We established full-sibling family populations red swamp performed whole-genome resequencing F3 family-selected population wild from four regions Hunan Province (Nanx, Mil, Caish, Wangc). Results: The results showed there was a clear separation between population, decline rate slightly faster than population. There local gene flow populations, as well families. In addition, 52 SNP loci related body weight traits were identified by genome-wide association analysis, candidate WIPF1 growth screened out. Conclusions: line selection obtained more stable lines. this study Wiskott-Aldrich syndrome protein-interacting protein member 1 (WIPF1) first time. provide theoretical basis exploring mechanism P. carrying out in-depth genetic improvement.

Language: Английский

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Genome re-sequencing and PCR amplification based simple and rapid sexing method for Procambarus clarkii

Aquaculture Reports, Journal Year: 2025, Volume and Issue: 42, P. 102728 - 102728

Published: March 11, 2025

Language: Английский

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Genomic adaptive potential to cold environments in the invasive red swamp crayfish

iScience, Journal Year: 2023, Volume and Issue: 26(8), P. 107267 - 107267

Published: July 3, 2023

Biological invasion refers to the introduction, spread, and establishment of non-native species in a novel habitat. The ways which invasive successfully colonize new different environments remain fundamental topic research ecology evolutionary biology. Here, we investigated genomic transcriptomic characteristics red swamp crayfish (Procambarus clarkii), widespread invader freshwater environments. Targeting recently colonized population Sapporo, Japan that appears have acquired high degree cold tolerance, RNA-seq analysis revealed differentially expressed genes response exposure, those involved protease inhibitors cuticle development were considered top candidates. We also found remarkable duplications for these gene families during evolution their concerted expression patterns, suggesting functional amplification against low temperatures. Our study thus provides clues unique genetic P. clarkii, possibly related adaptation.

Language: Английский

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