An effective method for parentage determination of the clam (Meretrix meretrix) based on SSR and COI markers

Because of the high frequencies of null alleles at microsatellite loci in mollusks, it is difficult to enhance the accuracy of parentage assignment in closely related families by increasing the number of loci. To develop an effective approach, microsatellite markers combined with mitochondrion COI marker were used for parentage assignment with computer simulations and experimental verification in the clam, Meretrix meretrix. In the present study, simulations based on allele frequency data from the candidate parents (sample II) demonstrated that combined exclusion probability of the five microsatellite loci (0.991 for Excl 1 and 0.995 for Excl 2) were not much lower than that of the seven loci (0.993 and 0.999). After discarding the two loci that deviated from Hardy–Weinberg equilibrium in experimental verification, accurate probability of progeny assigned to their fathers and mothers with both parents unknown was 68% and 59% in CF (closely related families), and 76% and 68% in DF (distant related families), respectively, which were much lower than those predicted by the simulations. When the COI marker was used in combination with microsatellite markers, 32 out of 39 offspring that were not previously assigned to their correct parents were assigned to their correct mothers, and 29 doubtful offspring could be assigned to their correct fathers. Consequently, with the combination of the two kinds of markers, the accurate probability of progeny that can be correctly assigned to their true fathers and mothers was increased to 89% and 92% respectively. We suggest that the use of microsatellite markers and COI marker will greatly improve the efficiency of parentage determination in closely related families in the clam.