The Food and Agriculture Organisation of the United Nations (FAO) reports that by the year 2050 the global human population is likely to reach 9.7 billion, rising to 11.2 billion by 2100 (https://population.un.org/wpp/Publications/Files/Key_Findings_WPP_2015.pdf). This population growth poses several challenges to the global food system, which will need to produce more healthy food using fewer natural resources, reducing the environmental impact, conserving biodiversity and flexibly adjusting to changing societal expectations. Meeting this demand requires environmentally sustainable improvements to farmed animal health and welfare, and of efficiency and diversification (e.g. to include a broader range of locally adapted species) [1]. The changes in breeding strategies and management practises required to meet these goals will need to build on an improved ability to accurately use genotype to predict phenotype in the world’s farmed animal species, both terrestrial and aquatic.