Domestication has played an important role in adapting swine traits, transforming them from wild boars to domestic animals adapted to human needs. This process has marked their DNA, visible in terms of physical appearance, behaviour, reproductive ability and adaptability. However, to fully understand how domestication has influenced their genetics, not only do we have to identify the genes involved, but also determine the tissues and organs in which they are active.

Domestication involves rearing animals in surroundings different from their natural habitat, which ends up modifying their behaviour and physical appearance. A wild animal and a domesticated animal can have genes with the same genetic sequences, but the influence of environmental conditions can cause changes in their DNA which, in turn modify the way in which genes, and hence phenotypes, are expressed.

Outstanding Master of Science Thesis by Diego Vargas

Diego Vargas graduated from the International Master in Animal Breeding and Reproduction Biotechnology, completing his studies with the Master of Science Thesis Integration of selection and transcriptome data to identify the domestication footprint in the swine genome, at the Center for Research in Agricultural Genomics (CRAG) under the supervision of Dr Marcel Amills Eras and Dr Sebastián Ramos-Onsins. His master’s thesis combines genomics and transcriptomics in order to understand the underlying genetic changes that have taken place throughout the domestication process of the Sus scrofa species. Genomic analysis identifies selection signals in the DNA and transcriptomic data reveal how genes are activated in different body tissues.

Diego Vargas took a degree in Genetics and Biotechnology at the National University of San Marcos in his native Peru, where he worked in reproductive biotechnology applied to alpacas, a species of economic importance in South America. Initially focused on animal production, he expanded his interests to animal breeding and reproduction, participating in the International Master in Animal Breeding and Reproduction Biotechnology, organised by CIHEAM Zaragoza, the Autonomous University of Barcelona (UAB) and the Polytechnic University of Valencia (UPV). His master’s studies sparked an interest in quantitative and molecular genetics, turning into a passion that grew under the mentorship of his supervisors at CRAG.

The purpose of the study is to identify the regions of the DNA that show signs of having been selected during domestication. They are used to investigate what genes are active in specific organs and their possible relationship with this process. It will lead to a list of key genes involved in domestication and indicate the target tissues where these changes have taken place, shedding light on the biological processes that facilitated the phenotypic transformation of wild pigs.

Transcriptomic analysis plays a crucial role in this approach. It enables us to distinguish between genes with ubiquitous expression that are activated in many tissues, and genes whose expression is limited to one or a few organs. Focusing on the latter, the work conducted by Diego Vargas has identified tissues associated with physiological processes such as neural development, male fertility, and behaviour, which are critical for understanding the selective effects of domestication.

Impact of and contributions to the study of domestication

The value of this study lies in demonstrating the utility of integrating transcriptomic data into selection analyses, an approach that has not previously been applied to the study of pig domestication. This methodology makes it easier to understand the biological and physiological changes underlying greater docility, reproductive capacity and growth traits of the domestic pig.

It explores domestication genetics in greater depth and opens up new lines of research in animal genetics, such as identifying tissue-specific genes that can be used for more precise breeding programmes that focus on traits linked to specific organs or functions.

This study takes a significant step forward in understanding domestication, combining genomic and transcriptomic tools to unravel the secrets of the domestic pig’s genetic evolution.