Polymorphism Analysis Of MHC Class Ⅱ B Gene In Chinese Alligator (Alligator Sinensis) And Molecular Identification Of Several Wildlife Species

We analyzed the polymorphism of MHC class II B gene in 14 Chinese alligators (Alligator sinensis) sampled from three different areas: the wild population of Xuancheng in Anhui, the captive population of Changxing in Zhejiang and the captive population of Anhui Research Center for Chinese Alligator Reproduction. The gene fragment was amplified using a pair of specific primers designed from the MHC gene sequence of the Spectacled caiman (Caiman crocodilus). A total of thirty-four different sequence (15, 10 and 9, respectively) were detected in sampled Chinese alligators. The rates of nonsynonymous substitutions (dN) occurred at a significantly lower frequency than that of synonymous substitutions (dS), which was not consistent with the common rule, this might indicate that the polymorphism of exon 3 does not seem to be maintained by balancing selection. Furthermore, many alleles such as Alsi-29 and Alis-34 were found in all three subpopulations, which may indicate that gene flow had ever taken place before.We also identified Sika deer (Cervus nippon kopschi) and three monkey skeleton samples (BZ01, BZ02 &BZ03; sent by Medical Supervise Bureau of Bozhou City) with different molecular methods. To identify Sika deer, we adopted Sequence Characterised Amplified Region (SCAR) method, using 100 random primers to analyze randomly amplified polymorphic DNA (RAPD) fragments of 12 individual samples from four cervid species: Black muntjac (Muntiacus crinifrons), Reeve's muntjac (Muntiacus reevesi), Sika deer, and Tufted deer (Elaphodus cephalophus). Only one primer among the 100 produced a clear specific band for identifying DNA of sika deer. We cloned and sequenced 449 bp from this fragment of DNA. We then designed a pair of 18 bp primers (MHL-U/MHL-D) according to the sequence, resulting in a 251 bp sequence characterised amplified region (SCAR) for Sika deer. By combining this pair of SCAR primers with a universal set of mammalian DNA primers, the identification of Sika deer tissue samples by a simple common multiplex PCR assay is straightforward, rapid, and reliable. To identify the monkey skeleton samples, we adopted the DNA sequences alignment method based on the mitochondrial 12S rRNA & Cyt b gene partial sequences. The results show that the sample BZ01 is Tibetan macaque (Macaca thibetana) and the samples BZ02 & BZ03 are Rhesus monkey (Macaca mulatta). Besides, it was pointed out when using the DNA sequences alignment method to identify related species, DNA...