Assessing the Potential for Genetic Rescue in Critically Endangered Saimaa Salmon: Early Viability and Genomic Outcomes via First Backcrossing

Small, threatened populations often suffer from a limited gene pool, which increases inbreeding and reduces their adaptability. We investigated the phenotypic and genomic effects of hybridization (resulting from backcrossing) on the critically endangered Lake Saimaa landlocked salmon, Salmo salar m. sebago , focusing on a particularly sensitive alevin‐fry life stage. The Saimaa salmon has undergone severe genetic bottlenecks and relies exclusively on a hatchery‐based conservation program. Since 2017, crossings with geographically proximate anadromous Baltic Sea salmon populations (Neva and Tornio) have been conducted as a possible means to restore genetic diversity. Here, we used a maternal half‐sib design to compare early viability of purebred Saimaa salmon with their first‐generation Neva and Tornio backcrosses in semi‐natural conditions. The backcrossed fry survived better than purebreds, showing a 9–12 percentage‐point increase in viability, whereas no significant cross differences were found in body mass. Quantitative genetic analysis further showed that hybrid sires conferred higher genetic merit for survival. Genomic analyses using a high‐density SNP array (47,901 loci) confirmed clear differentiation between pure and backcross groups, validating admixture. Pure Saimaa salmon had heterozygosity ( H S ) of 0.13 (over 50% of loci monomorphic), while backcrosses possessed H S of 0.25 and substantially more polymorphism (96%–97% of loci). Analysis of homozygous genomic segments showed that the inbreeding of Saimaa salmon has predominantly accumulated prior to the conservation program. Widespread reductions in autozygosity were found in both cross types, though introgression varied across the genome and also showed substantial donor‐ and family‐specificity. Overall, the results suggest that hybridization improved early survival through additive and potential dominance effects (reduced genetic load, heterozygote advantage), and expanded genomic variation without immediate indication of outbreeding depression. However, sequential backcrossing across multiple generations is necessary to ensure the preservation of Saimaa salmon's unique genetic identity while enhancing its resilience through the life cycle.