Maternal genetic diversity and population structure of four mandarin fish ( Siniperca chuatsi ) populations inferred from mitochondrial D-loop sequences

Mandarin fish ( Siniperca chuatsi ) is an economically important freshwater aquaculture species in China, yet the maternal genetic composition of cultured stocks from different regions remains insufficiently characterized. To assess maternal genetic diversity and population structure, 120 individuals were sampled from one wild-origin population from Huzhou, Zhejiang Province (ZJHZ), and three cultured populations from Chizhou, Anhui Province (AHCZ), Wuhan, Hubei Province (HBWH), and Jiangmen, Guangdong Province (GDJM). Mitochondrial D-loop sequencing generated 118 high-quality sequences and identified 22 haplotypes. Haplotype diversity ranged from 0.543 to 0.805, and nucleotide diversity from 0.00604 to 0.01095. Three common haplotypes were shared by all four populations and represented 94 of the 118 individuals, whereas most remaining haplotypes were population-specific and occurred at low frequencies. AMOVA attributed 94.17% of the mitochondrial variation to within-population differences and 5.83% to among-population differences, with the among-population component being statistically significant (FST = 0.05831, P = 0.00196). Pairwise FST tests detected significant maternal differentiation between GDJM and each of the other three populations, whereas differentiation among AHCZ, ZJHZ, and HBWH was generally low. Overall, the four populations shared a broad maternal genetic background while retaining low-frequency variation within individual stocks. These findings provide population-specific baseline information for maternal-lineage identification and female broodstock management in S. chuatsi . However, mitochondrial D-loop data do not capture paternal contributions or genome-wide diversity. Broader geographic sampling combined with genome-wide nuclear markers and pedigree information will therefore be required for a comprehensive assessment of broodstock genetic structure.