Population genetic diversity of mud crab (Scylla paramamosain) from southeast coastal regions of China based on mitochondrial COI gene sequence.

Mud crab (Scylla paramamosain) is a native and economically important species in East Asia. In order to provide a comprehensive genetic background for the resource protection and management in this species, the genetic diversity and population structure of S. paramamosain were analyzed based on mitochondrial cytochrome oxidase subunit I (COI) gene sequence. Totally, 599 individuals were sampled from 20 populations, including 18 wild and two cultured populations from five provinces along southeastern coast of China. After the sequencing of a 638 bp fragment of COI gene, 84 variable sites were found and no insertion or deletion was detected. The H2 (haplotype 2) was the dominant hapolotye shared by 301 individuals (50.3% of all individuals) and existed in all localities. In addition, a high percent of unique haplotypes (53 of 93 haplotyoes) was found. The average nucleotide diversity (π) of all populations was 0.00194, ranging from 0.00010 (NHF1) to 0.00305 (SHCM). The haplotype diversity (h) ranged from 0.067 (NHF1) to 0.876 (CM) with an average 0.738. All of the populations showed high h (>0.5) except NHF1. Genetic distance ranged from 0.00063 to 0.00337 between populations and from 0.00010 to 0.00374 within populations. The molecular variance analysis (AMOVA) showed that the total genetic variation mainly occurred within populations (99.68%) and only 0.32% was contributed by among populations variation. No significant genetic differentiation was observed among all wild populations except that between BA and SHCM (Fst = 0.0.05707, P < 0.05), indicating a low level of genetic differentiation among localities. It is worth to note that two progeny population (HNF1 and NHF1) showed significantly different genetic variation, which suggested that a large quantity of parents could help to improve the genetic diversity of progeny populations.