Genetic and Haplotype Diversity of Manila Clam <i>Ruditapes philippinarum</i> in Different Regions of China Based on Three Molecular Markers

China has the largest production yield of Manila clam <i>Ruditapes philippinarum</i> in the world. Most of the clam seeds for aquaculture are mainly derived from artificial breeding in southern China, likely resulting in the loss of genetic variation and inbreeding depression. To understand the genetic and haplotype diversity of <i>R. philippinarum</i>, 14 clam populations sampled from different regions of China were analyzed by three molecular markers, including <i>COI</i>, <i>16SrRNA</i> and <i>ITS</i>. Based on the results of the <i>COI</i> and <i>ITS</i> genes, the 14 populations showed a moderate to high level of genetic diversity, with an average haplotype diversity of 0.9242 and nucleotide diversity of 0.05248. AMOVA showed that there was significant genetic differentiation among all populations (mean F_ST of the total population was 0.4534). Pairwise F_ST analysis showed that genetic differentiation reached significant levels between Laizhou and other populations. Two Laizhou populations showed great divergence from other populations, forming an independent branch in the phylogenetic tree. The shared haplotypes Hap_2 and Hap_4 of <i>COI</i> appeared most frequently in most clam populations. In contrast, <i>16SrRNA</i> analysis of the clam populations revealed the dominated haplotype Hap_2, accounting for 70% of the total number of individuals. The haplotype diversity of the Laizhou population (Laizhou shell-wide (KK) and Laizhou dock (LZMT)) was relatively higher than other populations, showing multiple unique haplotypes (e.g., Hap_40, Hap_41 and Hap_42). These findings of genetic and haplotype diversity of clam populations provide guiding information for genetic resource conservation and genetic improvement of the commercially important <i>R. philippinarum</i>.