The goal of aquaculture genetics is to understand inheritance of traits and use such knowledge to improve performance traits. Because a single trait may be controlled by many genes located in various genomic locations, the first step is to understand genomic variations in relation to the trait. Over the years, genome work has been the bottleneck because aquaculture involves hundreds of species, and their genomes are complex, with most fish genomes having whole genome duplications, and most shellfish genomes having exceptionally high levels of heterozygosity and polymorphisms. In the last decade, however, breakthroughs in sequencing technologies have led to rapid generation of whole genome sequences, which allowed efficient identification of genomic variations such as single nucleotide polymorphism (SNPs) and microsatellites. Upon availability of genome-wide SNPs, genomic regions affecting traits can be determined using genome-wide association studies (GWAS). Similarly, genomic expression patterns in relation to traits and the environment can be readily determined using RNA-Seq. Coupling of genomic and transcriptomic datasets allow aquaculturists to properly manage the broodstocks and make decisions on selection and breeding. In spite of such progress, challenges remain for aquaculture genetics and breeding.  The first is the incorporation of the environment effects and genotype-environment interactions. Although the environmental effects are often reflected at the level of genome modifications such as DNA methylation, such effects are far less understood to benefit breeding programs. The second is the incomplete knowledge of genomic variations in relation to performance traits; GWA studies have been conducted with only a limited number of species and traits. The third is the gap between genetic understanding and application of such knowledge for breeding. For example, marker-assisted selection can be implemented as soon as traits-linked markers are identified, yet such markers have been used only for a limited number of situations. Similarly, genome selection can be implemented when genome-wide SNPs and phenotypes are available, but aquaculture species have low individual values, and thus genome selection have not been widely used for aquaculture breeding beyond research. Finally, there are broad phenotypic variations among strains/isolates of the same species. Exploitation of simple strategies, such as cross breeding or hybridization, perhaps offers more immediate benefits. In this presentation, examples will be provided for each stage of genome research in relation to genetic improvements of performance traits using catfish as a model.

Keywords. Aquaculture, genome, variations, genome selection, breeding