| Chinese alligator (Alligator sinensis) is an endemic species in China, and also has been recognized as the most endangered crocodile species among the 23 species of crocodiles in the world. Despite of the success in the artificial breeding and rising of Chinese alligator, the rare species is still in edge of extinction. Two points are showed clearly in the status quo of conservation for Chinese alligator. On the one hand, with the steadily increasing of the captive-bred population, the appearance of the inbreeding depression indicates the decline of the situation of germplasm resource. On the other hand, the wild population of Chinese alligator is on the verge of extinction. The current wild population is estimated at about 150 individuals. Currently, it is urgent to reintroduce the captive-bred alligators in nature environment, and enhance the gene exchange among the wild populations and thereby, reestablish the wild population ultimately.As a novel DNA molecular marker technique, the AFLP (Amplified Fragment Length Polymorphism) analysis is based on the selective PCR amplification of restriction fragments from a total digest of genomic DNA. The AFLP technique has some advantages, such as a high level of polymorphism detection, the applicability for any organism without any prior knowledge about the genomic makeup, and so on. In this article, by the AFLP analysis, the genetic variation of 43 Chinese alligator individuals from ARCCAR was detected. It is expected that the research can offer the full and accurate information of genetic background for selection of introduced alligators. 117 AFLP markers were obtained with four pairs of primers in the research. Of 6 individuals, the DNA fingerprintings are significantly different from others. When the 6 specific individuals were moved, it was observed that there were 19 monomorphic loci and 89 polymorphic loci with 84% of the proportion of polymorphic loci. Moreover, the genetic distance (GS) for 37 individuals ranged from 0.13 to 0.97, and the value of average GS was 0.7503±0.0064. However, when the 6 individuals were included, all the 117 loci were polymorphic. At the same time, the range of GS for all individuals was obtained from 0.06 to 0.97, and the value of average GS was 0.6523±0.0079. Analysis of clustering also showed that the 6 individuals were not in cluster with other alligators. According to the dendrograms and sexuality of 43 individuals of Chinese alligator, 27 alligators with much difference of genetic background were selected to reintroduce the wild environment Some individuals have been released successfully the wild habitat.Microsatellite DNA is another powerful molecular genetic marker in research ofconservation genetics. In this paper, the structure of microsatellite and the principle of the detection technique of microsatellite polymorphism are illustrated. In the primary study of the application of the microsatellite primers on Chinese alligator, 12 pairs of microsatellite primers for American alligator (Alligator mississippiensis) were tested on Chinese alligators. 7 pairs of primers were amplified successfully, but these loci were lower polymprphic. So the usability of microsatellite loci on related taxa needs a further research. To acquire the specific microsatellite loci of Chinese alligator, it is feasible to clone, sequence and design primers by the classical method of molecular biology.A pair of Allele-Specific PCR primers (Alli-M and Alli-R) was designed. According to the agarose gel electrophoresis of PCR products, Chinese alligator meat can be identified rapidly and accurately with a single PCR-reaction step. Moreover, even cooked meat could be successfully identified with this method. The accuracy and practicability of the specific primers were confirmed by a blind test and a case of identification for the pending claw sample. In the case of identification, the result of sequencing of 12S rRNA gene of the claw sample was further supported for the result from the identification with the primers of Alli-M and Alli...
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