| The giant panda (Ailuropoda melanoleuca) is an endemic species to China and listed as a Class 1 National Key Protected Species. To save this rare species, a captive breeding program was initiated in the 1950s, and now there are 242 captive giant pandas. The China Research and Conservation Center for the Giant Pandas (hereinafter referred to as WL) holds the largest captive population, from which we sampled 22 wild-born and 79 captive-born individuals. In order to evaluate the influence of founder effect on genetic diversity of the WL population, we first performed paternity determination by microsatellite markers of 24 giant pandas. Then, we identified the WL founders based on the nearly integrated pedigree. Finally, we examined the difference of genetic variation between founders and decendants using seven microsatellite loci and four major histocompatibility complex (MHC) genes. The results are as follows:1) We employed seven microsatellite loci published, including Aime-3,Aime-5,Aime-10,Aime-11,Aime-13,Aime-14,Aime-16. For the WL population, this suites of markers indicated that (a) the average number of alleles was 8.3 (4-12); (b) the average polymorphic information content was 0.746 (0.614-0.879); (c) the exclusion probabilities of identity and paternity reached 100% and 99.99%, respectively. As a result, these seven microsatellites are powerful to perform individual identification and paternity determination.2) We adopted these seven microsatellite loci to conduct paternity testing for 24 captive WL giant panda and identified their respective fathers from potential males all with a confidence level of 95%.3) Combined the results of paternity identification and the 2007 International Studbook for the Giant Panda, we analyzed the genealogical relationship of the WL captive population and identified a total of 24 founders with sharply different contribution rates to the population development. The main founder (studbook No. 308) gave birth to 58 offspring, nearly accounting for 50% of the WL giant pandas. On the contrary, other three founders had only one descendant. Therefore, the uneven distribution of offspring emphasizes the importance of enhancing the breeding of founders with minor contributions.4) A total of 58 alleles for the seven microsatellite loci were identified from both wild (n = 22) and captive (n = 79) populations. The mean number of alleles per locus was 8.3 for both wild and captive populations and thus there was no allelic loss revealed. Nonetheless, we identified obvious bias in the distribution of allelic frequencies relative to the original allelic frequencies in the wild population. Inbreeding coefficient indicated that three F2-generation individuals are inbred, parents of which are offsprings of the main founder (studbook No. 308). This phenomenon reflects that both small effective number of founders and their imbalanced contributions together resulted in the change of genetic structure in the captive population. Therefore, it is urgent to improve the reproduction management of the captive giant pandas in the WL population.5) Twenty-three alleles were identified for the four polymorphic MHC class II genes loci (DQA1, DQA2, DQB1, DRB3) in the wild population (n = 22). Neverthless, just nineteen and eighteen ones were found in the founder (n = 24) and captive (n = 79) populations, indicative of allelic loss resulted from both founder effect and uneven reproduction of founders.6) MHC genotyping results showed that the wild individuals from the Xiangling Mountains carried private alleles but they nearly had no offspring in the WL captive population. On the contrary, the founders of the current WL population were mainly all from the Qionglai and Minshan Mountains. Therefore, it is recommended that some wild individuals (especially from the Xiangling and Liangshan Mountains) should be added in the breeding plan in order to elevate the level of genetic diversity of the giant pandas in the WL population.
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