| Chinese alligator is the most endangered and threaten species among the 23 crocodilians. Although captive population of Chinese alligator has developed rapidly in recent years, the genetic quality of some captive population has declined due to loss of genetic diversity, which resulted in its weak immunity and poor adaptability to environment. These problems challenged species administration and became an obstacle for the development of Chinese alligator. How to efficiently manage the captive population and prevent the its quality decline is the essential focus of our study.In the past 30 years, the population of Chinese alligator in Changxing city, Zhejiang Province was administrated half artificially and half naturally. Fortunately, the alligator population has developed steadily without genetic quality decline, which was probably due to the maintenance of its wild breeding. But annual breeding plan is only recorded in Zhejiang population. So we must establish the pedigree in Zhejiang population for the reintroduction of founder population. The Zhejiang population is set up on small groups. So, beside introduction of distantly related individuals, we also need to use effective molecular marker to screen individuals which hold high genetic diversity, disease resistance and strong adaptability to the environment and establish core alligator species. Last we set up scientific breeding for population management.In the present study, we research Zhejiang population with microsatellite DNA markers and MHC markers. The results were as follows.1) The pedigree of Chinese alligator population in Changxing was firstly constructed using 14 microsatellite loci, and the genetic diversity level of its population is low. Meanwhile, after the analysis of pedigree we found a series phenomenon.①The offspring in 46.15% of the total litters is single-fathered.②The offspring in 23.08% of the total litters have two fathers.③The offspring in 30.77% of the total litters have three fathers.④In the cases of multi-fathered litters, each father has different numbers of offspring ranging from 3 to 30.⑤In the cases of only single-fathered litters, each father has different numbers of offspring ranging from 6 to 36.⑥The numbers of offspring in multi-fathered litter is significantly higher(21.75 in average) than those in single-fathered litter(15.83 in average).2) The accumulative individual identification rate in the 14 microsallite loci was 100%, which could be used as a molecular marker of high efficiency for individual identification.3) Using the HURRAH method created by our laboratory for the separation of MHC loci, we obtained 17 MHC I loci and 13 MHCⅡloci with the combination of MHC BAC library analysis and the DNA sequencing. Ultimately, two MHC I loci and one MHC II locus were selected for polymorphonism analysis and population analysis.4) Three MHC polymorphical loci were used for parental population analysis, and 6 alleles were obtained with two alleles found in each MHC loci. The AR in each locus is between 1.055 and 1.713, and the average AR is 1.457. The highest AR was found in the IX17E2 while the lowest found in Beta16. The Ho value in each locus was between 0.037 and 0.504, and He is between 0.036 and 0.475. Ho in all the three loci was higher than expected, with the IX17E2 as the highest. The PIC in the three loci was between 0.036-0.361, and the average PIC was 0.239. The PIC in each locus is less than 0.5. The genetic diversity of MHC loci isn't sufficient.5) MHC loci and microsallite DNA loci showed that genotype distribution and gene frequency of offspring population were more averaged and as expected compared with its parental generation. The results revealed that the introduced alligator species from Xuancheng has breed with Changxing species in the population development.6) This study for the first time constructed the genetic administrative pedigree of Chinese alligator population, and investigated the genetics of this population. With the combination of microsallites loci analysis and morphological parameter, the core alligator species in Zhejiang province was constructed, and the existence of multifathered offspring in the same litter was found.
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