ITS sequence variation and phylogenetic analysis on four geographical populations of blood clam Scapharca broughtonii

In order to investigate the genetic structure and variability of Scapharca broughtonii,thus to make proposals for the species culture and breeding,four geographical populations of S.broughtonii were collected from Shandong Penglai(PL),Shandong Huangdao(HD),Jiangsu Qiansandao(QSD)in China,and Tongying in Korea(KTY) respectively,and the genetic variation was analyzed based on ITS nucleotide sequences of rDNA.PCR amplification products were sequenced and aligned subsequently.The 486bp and 541bp necleotide sequences of ITS-1 and ITS-2 respectively were obtained(primers and insertion/deletion sites included).The results showed that though the genetic variation of ITS-1 and ITS-2 was relatively high,the base composition of them was stable.The genetic diversity of the four populations was rich,which indicated that the germplasm resource of the species was in good condition.The genetic diversity of HD population was the richest.Also,the number of variation sites of ITS-1 and ITS-2 were the largest in HD population.There were many neighbor common variation sites in HD and QSD populations.In this study,we calculated the genetic distances between individuals and constructed the molecular phylogenetic tree by using minimum evolution method by MEGA 4.0.The results showed that the nucleotides in one species' genome had different variation frequency,and variation of nucleotides segment couldn't represent the genetic variation of the whole genome.Fifty-five blood clams did not cluster obviously based on the ITS-1 segment base sequences.However,57 blood clams can be clustered into two catigories completely,one as HD and QSD population,the other as KTY and PL populations.The information from nucleotides variation of ITS-2 is similar to the conclusion from multivariate morphomertrics and molecular marker analysis carried out by our research group in the past.The genetic diversity of HD population is very rich,while the KTY population showed relatively low variation.There were certain genetic differences between each population,so that cross-and selective-breeding may be tested according to their biological characteristics.