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...

No abstract

This study evaluated the suitability of commercially produced fermented soybean meal (FSBM) known as PepSoyGen™, in a plant-based diet for Florida pompano, Trachinotus carolinus fingerlings. An 8-week growth trial was conducted to evaluate the effect of four isonitrogenous and isolipidic diets containing 0, 206, 309 and 410 g/ kg FSBM, replacing approximately 0%, 50%, 75% and 100% SBM (designated as Basal, FSBM 50, FSBM 75 and FSBM 100, respectively) on growth performance, body composition, serum biochemistry and morphological condition of liver and distal intestine of Florida pompano. There were no significant differences in final mean weight, percentage weight gain, thermal unit growth coefficient and feed conversion ratio in all treatments. For serum biochemistry analysis, there were no significant differences in total protein, albumin, glucose, cholesterol, bile acids, plasma alkaline phosphatase, alanine aminotransferase and aspartate aminotransferase activities in all treatments. Cellular infiltration, presence of goblet cells and the width of lamina propria in the distal intestine were partly improved in fish fed FSBM 75 and 100 compared to the fish fed FSBM 50 and basal diet. Glycogen granulation, inflammation and nuclear change condition in the liver of pompano were better as the inclusion of fermented product increased. Results of this study indicate that FSBM can be utilized as an alternative protein source and microbial fermentation process could improve the functional properties of SBM. K E Y W O R D S fermented soybean meal, growth performance, histology, serum biochemistry, Trachinotus carolinus

The prevalence of infections by trematodes Bolbophorus sp. in populations of pond‐raised channel catfish Ictalurus punctatus was determined by sampling 64 ponds on a farm in northwestern Mississippi. Of the 40 food fish ponds sampled, 23 (58%) contained trematode‐infected fish; 7 pond populations were categorized as having light infections (1–33% infection rates), 5 as having moderate infections (34–66% infection rates), and 11 as having severe infections (≥67% infection rates). Only 3 of the 24 fingerling ponds contained fish infected with Bolbophorus trematodes, and the infection rates were light. Feed consumption and estimated fish production in food fish ponds differed significantly among the four categories of within‐population infection rate, and feed consumption and fish production decreased as infection rates increased. Relative to the production in uninfected populations, estimated fish production was reduced by 14, 35, and 40% in populations with light, moderate, and severe infections, respectively. Estimated catfish receipts and actual feed costs were used in a generalized enterprise budget format to calculate income above variable costs and net returns for each infection‐rate category. The estimated net return to land for uninfected food fish populations was US$1,526/ha. Lower fish production in infected populations resulted in decreased incomes. The net return to land was $592/ha for the light‐infection‐rate category, a 61% reduction from that achieved in uninfected populations. Production receipts from food fish ponds in the moderate‐ and severe‐infection‐rate categories did not cover the costs of production, and the net returns to land were −$781/ha for moderately infected populations and −$1,123/ha for severely infected populations. This study shows that trematode infections reduce fish production and farm economic returns and that the impacts increase as infection rates increase. However, even light and moderate infections—which may go unnoticed by farmers—can seriously affect farm profitability.

No abstract