Sichuan taimen (Hucho bleekeri) is critically endangered fish listed in The Red List of Threatened Species compiled by the International Union for Conservation of Nature (IUCN). Specific locus amplified fragment sequencing (SLAF-seq)-based genotyping was performed for Sichuan taimen with 43 yearling individuals from 3 locations in Taibai River (a tributary of Yangtze River) that has been sequestered from its access to the ocean for more than 30 years since late 1980s. Applying the inbreeding level and genetic relatedness estimation using 15,396 genome wide SNP markers, we found that the inbreeding level of this whole isolated population was at a low level (average F=2.6×10-3±0.079), and the means of coancestry coefficients within and between the three sampling locations were all very low (close to 0), too. Genomic differentiation was negatively correlated with the geographical distances between the sampling locations (p < 0.001) and the 43 individuals could be considered as genetically independent two groups. The low levels of genomic inbreeding and relatedness indicated a relatively large number of sexually mature individuals were involved in reproduction in Taibai River. This study suggested a genomic-relatedness-guided breeding and conservation strategy for wild fish species without pedigree information records.

Table S1. Reads output and quality statistics of SLAF sequencing for 43 sequenced individuals.

Table S2 Descriptive statistics for SLAF tags for the 43 sequenced individuals.

Table S3. Descriptive statistics for the SNP datasets for the 43 sequenced individuals.

Table S4. Descriptive statistics for reads mapped to Hucho hucho genome for 43 sequenced individuals.

Table S5. Genomic inbreeding coefficients of 43 sequenced individuals.

Table S6. Significance test for differences in average genomic inbreeding coefficients between three populations.

Table S7. Estimated genomic relatedness and similarity measures of each individual pairs within and between three populations.

Table S8. Significance test for differences in average genomic pairwise relatedness and similarity coefficient within each of three populations.

Table S9. Significance test for differences in average genomic pairwise relatedness and similarity between different populations.

Table S10. Position on the first three dimensions of multidimensional scaling (MDS) analysis for 43 sequenced individuals.