From Broodstock to Progeny: Genetic Variation in Captive-Bred F1 Bahaba taipingensis and Its Relevance to Conservation Release Programs

Bahaba taipingensis (Chinese bahaba) is a critically endangered fish endemic to China’s coastal waters, valued for both ecological and economic reasons and known as the “panda of the sea”. Captive breeding and stock enhancement are key conservation strategies, yet the genetic composition of released individuals directly affects program outcomes. This study combined mitochondrial and whole-genome resequencing to compare F1-generation fish with wild populations. At the mitochondrial level, 60 SNPs were detected in F1 individuals and 72 in wild populations, with haplotype analyses revealing retention of most common maternal lineages but reduced diversity. Nuclear genome analysis showed comparable genetic diversity between groups. Nucleotide diversity (π) was 0.000423 in F1 fish and 0.000401 in the wild population. However, the F1 cohort exhibited a higher inbreeding coefficient (FIS = −0.030) than the wild group (FIS = −0.118), suggesting early allele frequency shifts, thereby suggesting early genotype frequency shifts. Runs of homozygosity (ROH) analysis showed that the total number and length of ROH regions in the F1 cohort (686, 283,089.25 kb) were significantly greater than those in the wild population (171, 52,607.30 kb). Genome-wide FST between groups was 0.035, and PCA indicated genetic homogenization in F1 fish. Ne analysis showed that the wild population declined rapidly over generations and stabilized at a low level, indicating genetic diversity loss under environmental stress and highlighting the role of artificial breeding. These findings highlight the need for improved broodstock management and long-term genetic monitoring.