Abstract:

Objective To screen a set of short tandem repeat (STR) markers covering rat chromosomes 1-20 and the X chromosome, with 2-4 markers on each chromosome, and establish a dedicated marker panel for genetic contamination detection and strain identification of 5 commonly used inbred rat strains. Methods Six 6-8 week-old rats (half male and half female) were selected from F344, BN, DA, Lewis, and PVG strain, respectively. Genomic DNA was extracted from rat tail tissues. A total of 61 STR markers were selected, including 27 from the national standard GB 14923—2022 and 34 from the literature. Singleplex STR PCR amplification combined with capillary electrophoresis was used for genotyping of the 5 inbred rat strains, and genotype data were analyzed using GeneMapper ID v3.2 software. Based on the STR genotyping results, genetic distances between strains were calculated with GenAlEx 6.51b2 software, and a phylogenetic tree of the inbred rat strains was constructed using MEGA7 software. Results Among the 61 STR markers, non-specific amplification was observed for D15mit3, while no specific amplification product was obtained for D3wox7. LCA, AGT, and D5Hmgc2 exhibited no inter-strain polymorphism across the 5 inbred strains, while the remaining 56 markers exhibited inter-strain polymorphism. These 56 markers covered rat chromosomes 1-20 and the X chromosome (2-4 markers per chromosome). Among them, 42 markers could be used for genetic contamination detection in inbred rat strains. The amplified product lengths of D7wox14, D15rat123, and D20wox3 differed among the 5 strains, which could be applied for strain identification. The phylogenetic tree showed that the number of STR allelic differences between BN and F344 strains was 49, with a genetic distance of 1.775, both of which were the highest among all strain pairs. This indicated that the two strains exhibited the highest level of genetic differentiation and were the most distantly related. Among the 5 strains, F344, DA, and PVG clustered together, indicating their relatively close genetic distance, while BN and Lewis formed another cluster, indicating a relatively close genetic distance between them. The genetic relationships among the 5 strains were consistent with previous reports. Conclusion This study successfully screened a set of STR markers for molecular genetic detection of 5 commonly used inbred rat strains, including F344, BN, DA, Lewis, and PVG, and established specific marker combinations for genetic contamination detection and strain identification, respectively.