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...

The myostatin (MSTN) gene is important because of its role in regulation of skeletal muscle growth in all vertebrates. In this study, CRISPR/Cas9 was utilized to successfully target the channel catfish, Ictalurus punctatus, muscle suppressor gene MSTN. CRISPR/Cas9 induced high rates (88–100%) of mutagenesis in the target protein-encoding sites of MSTN. MSTN-edited fry had more muscle cells (p < 0.001) than controls, and the mean body weight of gene-edited fry increased by 29.7%. The nucleic acid alignment of the mutated sequences against the wild-type sequence revealed multiple insertions and deletions. These results demonstrate that CRISPR/Cas9 is a highly efficient tool for editing the channel catfish genome, and opens ways for facilitating channel catfish genetic enhancement and functional genomics. This approach may produce growth-enhanced channel catfish and increase productivity.

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There is considerable interest in the culture of whiteleg shrimp (Litopenaeus vannamei) in inland low-salinity water in Alabama and other states in the Sunbelt region of the US. However, the growing season is truncated as compared with tropical or subtropical areas where this species is typically cultured, and temperature is thought to be a major factor influencing shrimp production in the US. This study, conducted at Greene Prairie Aquafarm located in west-central Alabama, considered water temperature patterns on a shrimp farm in different ponds and different years; and sought possible effects of bottom water temperature in ponds on variation in shrimp survival, growth and production. Water temperature at 1.2 m depth in 22 ponds and air temperature were monitored at 1-hr intervals during the 2012, 2013, 2014 and 2015 growing seasons. Records of stocking rates, survival rates and production were provided by the farm owner. Correlation analysis and linear mixed model analysis of variance were used. Results showed that hourly water temperatures differed among ponds. The range of water temperature in each pond explained 41% of the variance in average final weight of shrimp harvested from each pond. In conclusion, the results suggest that variation in water temperature patterns has considerable influence on shrimp growth and survival in ponds. K E Y W O R D Sinland shrimp culture, Litopenaeus vannamei, low-salinity, shrimp production, water quality, water temperature

The resistance of Channel Catfish Ictalurus punctatus, hybrid catfish (female Channel Catfish × male Blue Catfish I. furcatus [CB hybrids]), and Channel Catfish and hybrid catfish expressing the introduced cecropin B gene to Ichthyophthirius multifiliis infestation was investigated in two experiments. In experiment I, four fingerling groups were challenged, including cecropin‐transgenic Channel Catfish, cecropin‐transgenic CB hybrids, non‐transgenic Channel Catfish, and non‐transgenic CB hybrids. Non‐transgenic Channel Catfish survived for a shorter time than the other three groups. Survival rate was significantly different between non‐transgenic Channel Catfish and the other groups, which had similar survival rates. In experiment II, non‐transgenic CB hybrids had a less severe infestation than non‐transgenic Channel Catfish. Mortality rates were 62.4% and 40.2% for non‐transgenic Channel Catfish and CB hybrids, respectively. The mean survival time for non‐transgenic hybrids was significantly longer (>5 d) than that of non‐transgenic Channel Catfish. The results suggest that genetic enhancement of Ichthyophthirius resistance can be accomplished in Channel Catfish by either cecropin transgenesis or interspecific hybridization. In addition to survival rate, improving survival time is important because the extension of survival time provides greater opportunity to apply treatments to stop the protozoan infestation.

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Fish‐borne zoonotic trematodes (FBZT) are extremely important zoonotically and can infect humans via the consumption of poorly cooked fish containing active metacercariae. In this context, the present study aimed to update the epidemiological information of FBZT among Nile tilapia (Oreochromis niloticus) collected from Giza and Fayoum Governorates. Concerning the molecular characterization and phylogenetic analysis of adult flukes from experimentally infected pigeons and histopathological alterations of both larval and adult trematode flukes. Oreochromis niloticus were found to be infected with different encysted metacercaria (EMC); Prohemistomum, Haplorchis and Pygidiopsis species from wild caught in Giza and farmed fish in Fayoum with the total mean of prevalence that 81.89 ± 6.48, 18.03 ± 2.9 and 34.64 ± 3.42 respectively. Three recovered flukes from experimentally infected domestic pigeons (Columba livia domestica); Prohemistomum vivax, Haplorchis pumilio and Pygidiopsis genata in their small intestine. First molecular characterization and phylogenetic analysis of heterophyid flukes; P. genata and H. pumilio. The sequences obtained in this study were registered in the GenBank with accession numbers (MT672308.1 and MT707975.1) respectively. Moreover, constructing a phylogeny and phylogenetic relationships between two heterophyid species was performed through analytic study of the second internal transcribed spacer nuclear ribosomal genes (rDNA‐ITS2). Phylogenetic analysis of P. genata and H. pumilio showed 99.42% nucleotide similarity with that sequence from Israel (AY245710) and 99.71% from Vietnam (EU826636.1). In addition, histopathological alterations of EMC and adult flukes induced necrosis of fish muscle bundles and a severe inflammatory response with muscular necrosis in intestinal tract of infected pigeons.

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