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...
Aquaculture research verification programs are designed to demonstrate and test research‐based practices recommended by extension services on commercial‐scale operations. From 2010 to 2013, in western Alabama, three management protocols were followed over three crop cycles on a farm producing hybrid catfish (female Channel Catfish Ictalurus punctatus × male Blue Catfish I. furcatus) using high levels of aeration. The protocols were an owner‐defined, multiple‐batch treatment and single‐batch and multiple‐batch treatments defined by the Alabama Cooperative Extension System (ACES). Results from nine production cycles were analyzed to calculate yields, feed conversion ratios (FCRs), cost of production, and net returns. Over three production cycles the owner‐defined, multiple‐batch treatment outperformed the two ACES‐recommended treatments in terms of yield, survival, FCR, and net returns. The owner‐defined treatment could vary, and the producer chose to feed above the recommended daily maximum and observed no low dissolved oxygen levels. High losses owing to disease in the ACES multiple‐batch treatment led to poor results. The owner‐defined multiple‐batch system completed three crops in 2.8 years compared with 3.6–3.7 years for the other two treatments. Thus, this study highlights the importance of research‐based recommendations being verified under commercial catfish production conditions and the value of research verification programs.
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