Identification of Selection Signatures and Candidate Genes Related to Environmental Adaptation and Economic Traits in Tibetan Pigs

Simple Summary Modern agricultural methods have led to the introduction of normally highland Tibetan pigs to lowland areas because of their high-quality meat. Similar to humans, indigenous Tibetan pigs residing in high-altitude regions may develop high-altitude de-acclimatization syndrome when exposed to low-altitude environments. Thus, it is important to better understand the low-altitude adaptation mechanisms of Tibetan pigs. We performed a comparative analysis between highland and lowland Tibetan pigs using genotyping data to investigate their genetic differences. Our results showed that immune-related genes were selected in highland Tibetan pigs, whereas genes associated with reproduction, growth and development, and blood pressure regulation were selected in lowland Tibetan pigs. These findings will contribute to research into the genetic basis of environmental adaptation and important economic traits in Tibetan pigs and provide genetic targets for breeding programs to improve Tibetan pigs.Abstract Tibetan pigs are indigenous to the Qinghai-Tibet Plateau and have been the subject of extensive genomic research primarily focused on their adaptation to high altitudes. However, genetic modifications associated with their response to low-altitude acclimation have not been thoroughly explored. To investigate the genetic basis underlying the low-altitude acclimation of Tibetan pigs, we generated and analyzed genotyping data of Tibetan pigs that inhabit high-altitude regions (average altitude 4000 m) and Tibetan pigs that have inhabited nearby low-altitude regions (average altitude 500 m) for approximately 20 generations. We found that the highland and lowland Tibetan pigs have distinguishable genotype and phenotype variations. We identified 46 and 126 potentially selected SNPs associated with 29 and 56 candidate genes in highland and lowland Tibetan pigs, respectively. Candidate genes in the highland Tibetan pigs were involved in immune response (NFYC and STAT1) and radiation (NABP1), whereas candidate genes in the lowland Tibetan pigs were related to reproduction (ESR2, DMRTA1, and ZNF366), growth and development (NTRK3, FGF18, and MAP1B), and blood pressure regulation (CARTPT). These findings will help to understand the mechanisms of environmental adaptation in Tibetan pigs and offer valuable information into the genetic improvement of Tibetan pigs pertaining to low-altitude acclimation and economic traits.