Analysis Of Genetic Diversity Of Chinese Indigenous Domestic Ducks Based On Microsatellite DNA Markers

China, as one of the largest duck producers in the world, is rich in duck genetic resources,and there are many indigenous breeds scattered throughout the country. These breeds vary in size, plumage color and other characteristics. In order to roundly find out the status of genetic resources, genetic diversity and genetic relationship of Chinese indigenous ducks, we had surveyed their numbers, conservation situation, utilization, performance, and collected 24 indigenous ducks from different original regions, examined the genotype of 1440 individuals based on 28 microsatellite loci. The genetic diversity was disclosed by calculating the allele frequency, heterozygosity(H),effective number of alleles, polymorphism information content (PIC), Nei's standard genetic distance and DA genetic distance. Phylogenetic Relationship was analyzed by the neighbor-joining method (NJ), principal components analysis (PCA), genetic structure analysis, and so on. Our main results were summarized as follows:(1) The survey of Chinese indigenous ducks from original regions showed that Wendeng black duck and Zhongshan duck breeds were at the verge of extinction.Among the existing 24 indigenous duck breeds, Jianchang duck and Sichuan duck breeds were at risk, and 22 others were in normal state.(2) This research had studied the effect of saving poultry'blood with ethanol and explored the method of extracting DNA from these blood samples. Dealing with the blood sample with 75% ethanol at 4:1 on volume, it was simple and rapid to operate and the samples could be saved for a long time at the normal temperature. Others, by the Method of Phenol-Chloroform, we could extract higher quality of DNA which could be used to further molecule biology research from blood.(3) The allele number and polymorphism information content of the 24 indigenous ducks were examined with 28 microsatellite DNA markers. The results showed that 236 alleles were identified, the allele number was abundant, which was from 5 to 13, and the mean allele number was 8.428 per locus.134.4 effective allele numbers was identified, which was less than the observed value actually, the mean effective allele number was 4.800. Except that the PIC of locus of APL23 and APL79 were of medium level genetic diversity, those of other loci were high. The overall average expected heterozygosity was 0.7613, which showed great genetic diversity and high select potentiality. The effective allele numbers, average polymorphism information content and expected heterozygosity per locus were positive correlation. From the breeds, Xingyi ducks and Sansui ducks in 28 microsatellite markers were of the highest average number of alleles,which were 4.25.And the average minimum number of alleles in the Liancheng white ducks, which were only 3.36.(4) The allele frequency differences of the 24 indigenous duck breeds in the same micro-satellite loci were examined. The results showed that,there were 27 private alleles and a large number of dominate alleles at the 28 microsatellite loci of 24 indigenous ducks. The expected heterozygosity of Sansui duck was the highest, which was 0.6166; the second was Weishan duck, and the least was Jingding Duck, which was 0.5137. The overall average heterozygosity of the 24 indigenous ducks was 0.569, which relatively reflected the lower genetic diversity and narrow potentiality of selection.(5) Genetic differences was analyzed by the F statistic analysis, the number of the populations deviated from HWE per locus ranged from 0 to 8. The genetic differentiation among populations had reached to 0.264 (P <0.001), which was very significant for the whole population, all loci were contributed significantly (P <0.001) to this differentiation. And the deficit of heterozygote was observed at a low level. The concrete values of two genetic distances of DA and DS among the 24 indigenous ducks were consistent. The Nm value ranged from 0.4620 (Sichuan duck-Hanzhong duck) to 1.3692 (Jingding duck-Shanma duck). The genetic distance between Jingding duck and Shanma duck was the nearest, and that of Sichuan duck and Hanzhong duck was the most distant.(6) The geographical elements may own to the close relationship for particular population pairs, however, the equation FST/ (1-FST) = 0.1976736 +0.0000578ln (d) and the result from Mantel's test (P= 0.19192) did not provide enough support for a significant correlation between the genetic and geographical pair wise distances. It was no significant correlation between the genetic diversity of genetic distance and the distributing of these populations. The results concluded that the geographical distributing maybe not the determinant influence on the genetic structure of Chinese chicken populations during the course of their developed history.(7) Combining with the origin of indigenous duck breeds, geography, entironment, special traits, morphologic characteristic, and so on, the phylogenetic relationship based on DA among Chinese indigenous ducks were analyzed, an un-rooted consensus tree was constructed, and the 24 indigenous ducks and divided them into 5 groups. The first group, Ehshi sheldrake, Jingjiang sheldrake and Mianyang sheldrake clustered first, the three populations were all sampled in Hubei province, then clustered with Jianchang duck and Sichuang sheldrake, both in Sichuan province. At last, we clustered a larger colony with Jingxi big sheldrake and Guangxi small sheldrake both from Guangxi province. The second group, Sansui duck and Xingyi duck in Guizhou province, Yunnan sheldrake in Yunnan province and four excellence ducks Liancheng white duck, Putian black duck, Jinding duck and Shan sheldrake in Fujian province clustered a larger colony. The third group, Shaoxing duck in Zhejiang province and Gaoyou duck in Jiangsu province clustered despite a long genetic distance between them. The fourth group, Chaohu duck in Anhui province and Hanzhong sheldrake in Shangxi province clustered first, then clustered with Dayu duck in Jiangxi province. The fifth group, Youxian sheldrake in Hunan province and Linwu duck clustered first, then a larger colony with Beijing duck, Weishan sheldrake in Shandong province and Huainan sheldrake in Henan province clustered at last.(8) For the analysis of population structure from STRUCTURE, the average gene score of the 1440 individuals of the 24 local ducks was more than 0.800 in their concluded sorts respectively. And this reflected the 24 populations all held their own special characteristics respectively.(9) Based on the experiment data and the actuality of Chinese indigenous duck breeds, it is suggested that we should collect the sample of tissue and blood to reserve DNA, which can be used to analyze dynamic change of the genetic structure. During the conservation in vivo, it is necessary to take the measures of combinations of conservation farm with conservation area.