Genomic architecture of selection for adaptation to changing environments in Nile tilapia

Tilapia is a vital protein source for many countries and is cultured in over 120 countries. Global Tilapia production has stably increased in the last decade. However, in many farming systems the production performance of the optimized strains is much lower than what potentially can be achieved. One important factor is adaptation, which means the ability of an individual to adapt to the changing environment. Based on investigating the situation of most productive countries for Tilapia in Southeast Asia, there are two essential environmental characteristics that mainly attribute to the variation in production, namely oxygen availability (aeration) and salinity of the water. Necessary solutions to decrease the production losses in Tilapia require closing the knowledge gap regarding the genetic basis of adaptation to help efficient selective breeding. Genome-wide association studies (GWAS) based on genotype data, will enable identifying regions in the genome involved in oxygen and salinity stress adaptation. Tilapia species show large differences in growth rate in relation to oxygen availability and salinity. This has led to the production of many commercially used hybrid crossbreeds that show acceptable growth rates in combination with a degree of salinity tolerance. Little is known about the genomic composition of these breeds. By estimating Identity-By-Descent using whole genome data, the contributions of the parental species can be estimated. Whole genome sequence (WGS) analyses will be performed to identify variations in genomic architecture between animals that are at the extremes in performance. Comparative genomics will enable the identification of conserved regulatory elements and provide insight into conserved regulatory networks and metabolic pathways related to adaptation. RNA-Seq will be used to explore the expression differences of hybrids related to salinity adaptation. These analyses will be supplemented with a high-low (oxygen; salinity) GWAS experiments. The objective of the current project is to unravel the genomic architecture underlying salinity and hypoxia adaptation in Tilapia and to explain genomic signatures of selection to facilitate the identification of adaptive trait and animal production improvement.