Applications of Modern Genetics and Genomic Technologies to Enhance Aquaculture Breeding

Aquaculture is a critical component of global food security, in particular meeting increasing demands for animal protein production associated with human population growth. Freshwater and marine fish, shellfish and crustacean farming now provide over half of the world’s seafood supply, with projections for significant expansion in the coming decades. However, significant barriers must be overcome to enable this expansion, in particular the major negative impact of infectious diseases on most production systems. Selective breeding offers substantial opportunities to enhance production efficiency and help tackle barriers such as disease via cumulative and permanent genetic improvement of farmed strains. In contrast to land-based agricultural sectors (crops/plants, farm animals) where almost all production and current human consumption originate from lines and varieties derived from selective breeding programs, only 10% of the global aquaculture production has benefited from genetically improved strains. Aquaculture seed stocks of many species are often collected periodically from the wild, which pose threats to the natural environment, creates biodiversity issues, and can be unsustainable. Although there are successful examples of well-organised breeding programs, most notably in major finfish species such as Atlantic salmon, the conduct and practical implementation of genetic improvement programs for aquaculture species presents several challenges. Key issues include: (i) biological constraints of aquatic animal species; (ii) difficulties in making a routine data concerning traits of commercial importance especially those which are difficult or expensive to measure (e.g. flesh quality, disease resistance) but are essential for broadening the breeding objectives; (iii) management of genetic gain and inbreeding in closed breeding nuclei; and (iv) controlling the effects of genotype by environment interactions. There are also challenges with regard to the incorporation of genomic information in genetic enhancement programs for aquaculture species. For instance, while genomic selection has been adopted by most major livestock and plant sectors world-wide, commercial application in aquaculture is only routinely being applied in very few species. In addition, with the recent development in high throughput genome sequencing technologies, coupled with better computational approaches, a large amount of ‘omic’ data has been generated. However, challenges exist in utilising this information to understand the factors underlying biology and genetic architecture of complex traits in fish, crustaceans and molluscs. Another question is how the multi-omics technologies (e.g. transcriptomics, proteomics, metabolomics, microbiomics) can help to accelerate genetic gain in aquaculture species. Finally, the potential opportunities gene editing technologies offer to enhance aquaculture production are emerging, but scientific applications of gene editing in aquaculture remain at an early stage.

This Research Topic presents and discusses innovative approaches and recent advances in the field of aquaculture genetics and ‘omics’ to provide solutions to the many challenges. The Research Topic will focus on three main themes: (i) successful selective breeding programs for species of economic importance; (ii) advanced methods to optimise genetic programs; and (iii) potential (practical) applications of ‘omics’ technologies in selective breeding programs. We welcome submissions of original research papers and high quality reviews that fall within the ‘Aims and Scope’ of this special issue. Broader topics the Issue will consider can include:

A. Successful breeding programs for aquaculture species of economic importance
1. Marine finfish
2. Freshwater fish species
3. Freshwater prawn (Macrobrachium rosenbergii or other species) and marine shrimp (Litopenaus vannamei, Penaeus monodon or other species)
4. Molluscs (oysters, abalone, clams, scallops)

B. Methods to optimise genetic programs for aquaculture species
1. Genotype by environment interaction effect (G x E)
2. Management of inbreeding
3. Optimal contribution selection
4. Understanding genetic inheritance of novel traits to select for stress response or ‘resilient’ animals
5. Multi-trait selection
6. Design of breeding programs

C. Potential (practical) application of ‘omics’ technologies in genetic programs for aquaculture species
1. Genetic linkage analysis, quantitative trait locus (QTL) mapping, Genome-wide association studies (GWAS) to detect genes for traits of economic importance in commercial selective breeding programs
2. Genomic prediction
3. RNA sequencing to identify biomarkers and to understand genetics of complex traits
4. Integration of multi-omics (proteomics, metabolomics, epigenetics etc.) into selective breeding programs
5. Gene editing approaches
6. Functional genetic studies