Fingerprinting of hatchery haplotypes by whole-mitogenome sequencing improves genetic studies of masu salmon Oncorhynchus masou masou

Abstract Stocking hatchery fish can lead to disturbance and extinction of the local indigenous population. Stocking similar lineages to the indigenous population makes it difficult to conduct genetic studies to determine conservation units. We considered that, due to the length of the mitogenome, whole-mitogenome analysis might overcome this problem by enabling identification of hatchery haplotypes. Here, to provide basic information for conservation of indigenous masu salmon Oncorhynchus masou masou , a commonly stocked fish in the Kase River system, Japan, we used whole-mitogenome analysis of fish to identify hatchery haplotypes in the river and in several hatcheries that might be used for stocking. Whole-mitogenome sequencing clearly identified hatchery haplotypes like fingerprints, identifying the tributaries contaminated with hatchery haplotypes. The results suggest that informal stocking of O. m. masou has been performed widely across the Kase River system. Non-hatchery haplotypes mainly belonged to clade I, which was not found in northern Hokkaido Island. Sites without hatchery haplotypes were estimated three, suggesting that these sites are suitable for conservation of the indigenous fish. This study demonstrated that the resolution of the conventional analysis using partial mitogenome is insufficient to distinguish hatchery haplotype from similar lineages. The whole-mitogenome sequences provided accurate information that was not available in the partial sequences, enabling various inferences: e.g., estimation of the origin of stocked fish and circulation of the reared strains. We conclude that whole-mitogenome analysis is useful for the genetic study of this species. The whole-mitogenome data produced will contribute to the conservation, resource management, and further study of O. m. masou .