Genetic Structure, Selective Signatures, and Single Nucleotide Polymorphism Fingerprints of Blue Tilapia (Oreochromis aureus), Nile Tilapia Oreochromis niloticus), and Red Tilapia (Oreochromis spp.), as Determined by Whole-Genome Resequencing

Tilapia (<i>Oreochromis</i> spp.) is a globally important farmed fish. Analyses of genetic variation across different types of tilapia are essential for the development of superior breeding populations. We investigated the genetic structures of breeding populations of blue tilapia (<i>Oreochromis aureus</i>) (OA), Nile tilapia (<i>Oreochromis niloticus</i>) (ON), and red tilapia (<i>Oreochromis</i> spp.) (OS) by whole-genome resequencing. The results showed that the OS population had maintained high genetic diversity but significant genetic differentiation from the OA population. Principal component analysis, phylogenetic analysis, and genetic clustering analysis revealed a clear pattern of genetic differentiation among the three populations. The genetic structure of the ON population differed from that of the OA population but was similar to that of the OS population. Population kinship analysis revealed a close relationship between the ON and OS populations. Selective scanning analyses of three comparison groups (OA vs. ON, OA vs. OS, and ON vs. OS) revealed population-selected regions related to metabolism, endocrine, and immune systems, harboring key genes (<i>qrsl1</i>, <i>pde4d</i>, <i>hras</i>, <i>ikbkb</i>, <i>prkag1</i>, <i>prkaa2</i>, <i>prkacb</i>, <i>irs2</i>, and <i>eif4e2</i>). These key genes were related to growth, reproduction, and disease resistance, indicating that breeding programs have selected for these traits. Due to the lack of stable morphological characteristics of juvenile fish and the changes in external environmental conditions that lead to changes in individual morphological characteristics, SNP fingerprints were successfully constructed for the identification of the three populations based on the differences in SNPs. Based on the five core SNP markers, two combinations of SNP markers were developed to accurately identify the three populations of tilapia at the genomic level. These results provide new information about tilapia genetic resources and reference data for identification and breeding purposes.