Pig production contributes importantly to environmental pollution through the emission of nitrogen waste. Since many countries do not meet the plant-protein demand of livestock with current feed cultivation practices, an important part of high-quality protein feed, most importantly soybean meal, is imported from South America. Consequently, the high global demand for protein results in an increased competition of agricultural land for human food and animal feed, ultimately leading to the large-scale loss of ecological habitats. It is therefore desirable to improve protein efficiency, i.e. the proportion of dietary protein that is fixed in the body, of pigs, an important livestock species, through selective breeding. However, little knowledge is available about the inheritance pattern and genetic architecture of protein efficiency. Similarly, the genes underlying protein efficiency and their functions, essential for assessing the potential to breed pigs with higher protein efficiency, has not yet been assessed.