Assessment of genetic diversity in the forest musk deer (Moschus berezovskii) using microsatellite and AFLP markers

Microsatellite genotyping and amplified fragment length polymorphism (AFLP) techniques are often utilized in studies of conservation genetics of endangered animals. To select a more effective marker system for conserving the endangered forest musk deer, we used microsatellite and AFLP markers to estimate levels of genetic diversity of two populations, the pure mother Jinfengshan (JFS) group and the offspring Baisha (BS) group with introduction of new blood. It was expected that JFS would pos- sess significantly higher genetic variability than BS if it is assumed that no new deer were introduced into BS. The results revealed that the 15 microsatellite markers produced 141 alleles and the 22 AFLP primer combinations yielded 908 polymorphic bands, showing that AFLPs had higher resolving power than microsatellites. Nonetheless, compared with other deer, both marker systems indicated that the forest musk deer contains a relatively high level of genetic variation. The 15 microsatellite loci indicated a similar level of genetic diversity was present in the JFS and BS populations, seemingly suggesting that the new blood obviously elevated the level of genetic diversity in BS. However, 22 suites of AFLP markers yielded a significantly higher level of genetic variation in JFS than that in BS, in contrast to the diversity pattern of microsatellites. In view of the difference in resolving power of these two marker systems, we conclude that gene introgression was limited in the BS population, as revealed by the AFLP markers. Furthermore, from the perspective of whole genome variability, we recommend that the AFLP marker system is more suitable for conservation genetics studies on the forest musk deer.