Important operational changes that have gradually been assimilated and new approaches that are developing as part of the movement toward sustainable intensive aquaculture production systems are presented via historical, current, and future perspectives. Improved environmental and economic sustainability based on increased efficiency of production continues to be realized. As a result, aquaculture continues to reduce its carbon footprint through reduced greenhouse gas emissions. Reduced use of freshwater and land resources per unit of production, improved feed management practices as well as increased knowledge of nutrient requirements, effective feed ingredients and additives, domestication of species, and new farming practices are now being applied or evaluated. Successful expansion into culture of marine species, both off and on shore, offers the potential of substantial increases in sustainable intensive aquaculture production combined with integrative efforts to increase efficiency will principally contribute to satisfying the increasing global demand for protein and food security needs.

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Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries.Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop fo...

Stress and mortality associated with truck transport of largemouth bass Micropterus salmoides were characterized during and after simulated hauling periods of up to 30 hours at a density of 180 g fish/liter of water. Generally, "transported" fish had significantly elevated concentrations of plasma glucose and corticosteroids and decreased plasma chloride concentrations and oso molality. Significant mortality was associated with hauls of 24 and 30 hours (38% and 83-92%, respectively). Plasma characteristics returned to near-normal values 3-28 days after being hauled; recovery time generally was related to length of haul and associated mortality. Stress was reduced significantly and mortality was eliminated when fish were treated for diseases, held 72 hours without food before they were loaded, anesthetized before they were loaded, hauled at a cool temperature in physiological concentrations of salts with an antibiotic and a mild anesthetic, and allowed to recover in the same medium less the anesthetic.

The influence of dissolved natural organic matter (NOM) source on copper toxicity was investigated with larval fathead minnows (Pimephales promelas) in reconstituted moderately hard water. Ninety-six-hour static renewal toxicity tests were conducted to investigate an assumption of the biotic ligand model (BLM) that NOM source does not need to be considered to adequately predict copper toxicity. The nine different NOM isolates used in these toxicity tests were chemically well-characterized substances that were obtained by reverse osmosis as part of an NOM typing project based in southern Norway. Three median lethal concentration (LC50) values were estimated for toxicity tests conducted with each NOM, at nominal dissolved organic carbon (DOC) concentrations of 2, 5, and 10 mg/L. Tests also were conducted in dilution waters in which no NOM was added. Regression analyses were conducted to compare NOM-specific (specific NOM source) LC50s versus DOC concentration relationships to each other, as well as to the overall LC50 versus DOC concentration relationship. Statistical differences were found regarding the effects of NOM source on copper toxicity. Similar analyses were conducted with humic acid (HA) concentrations and spectral absorbance, and differences in the effect of NOM source on copper toxicity were similarly concluded. These results do not support the assumption that copper toxicity can be adequately predicted by utilizing DOC concentration, regardless of NOM source. Evaluation of relationships between LC50 values and other NOM characteristics revealed that despite significant differences due to NOM source on copper toxicity, DOC and HA concentrations were the most effective parameters in explaining variability in LC50 values. When BLM-predicted LC50 values were compared to observed LC50 values, predicted values showed reasonable agreement with observed values, but some deviations occurred due to NOM source and DOC concentration.