Improving aquaculture stocks through selective breeding: Orientating in the labyrinth of genomic technologies and prediction models

Aquaculture is the fastest-growing food-producing sector. Moreover, with the wild fisheries production volume being relatively stable for several decades now, aquaculture will play an even more central role in the years to come in covering the protein needs of the rising world human population. More specifically, as current projections expect the world population to reach 9 billion by 2050, the corresponding demand for protein production is expected to increase by at least 70%. Furthermore, the challenge above needs to be achieved in a sustainable manner that does not deplete our planets finite resources or jeopardize the livelihood of future generations.

Selective breeding can promote the sustainability of the aquaculture sector by reliably identifying the animals with the highest genetic potential for farming purposes. Even though selective breeding schemes in aquaculture are still not applied in the majority of the farmed species, their potential for promoting the sustainability of the aquaculture industry is apparent. Following selective breeding practices that have been proven most successful in both terrestrial animals and plants, the aquaculture producers of farmed species like Atlantic salmon and Nile tilapia have nowadays the opportunity of farming stocks that can grow substantially faster than their wild counterparts and that can be more resilient towards many commonly encountered diseases.

Recent advancements in DNA sequencing and genotyping technologies have allowed the inclusion of genomic information in selection decisions, transforming the discipline of selective breeding. Simultaneously, substantial research efforts over the last two decades resulted in developing powerful machinery of elaborate prediction models for harnessing genomic information most effectively. Since through genomics, the underlying genetic components controlling traits of interest can be detected and relationships amongst the breeding candidates can be estimated more reliably than traditional pedigree records would allow, a boost in the efficiency of selective breeding practices has been repeatedly documented in both animal and plant breeding programs.

Notably, we witnessed several successful research and industry applications of selective breeding practices in several aquaculture species over the last decade. Nevertheless, the plethora of available sequencing technologies and prediction models poses challenges to academic and industry researchers in making the right choice of tools for each specific application. Furthermore, as neither sequencing technology nor a single prediction model is free of shortcomings, it is essential for aquaculture breeding practitioners to be familiar with their inner machinery and inherent limitations to successfully apply them in practice. 

In my docent lecture, I will present the current state-of-the-art status of sequencing and genotyping technologies. Furthermore, prediction models commonly applied in aquaculture breeding will be discussed. Relying on a broad spectrum of my former and current research projects, breeding applications using genomic information will be presented for various aquaculture species highlighting limitations and opportunities for further improvement. Finally, thoughts and research actions for improving the Swedish aquaculture sector will be shared, focusing on the progress of the national breeding programs of Arctic charr and rainbow trout.