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The domestic goat is one of the important livestock species in China.The size of each breed dramatilly and many of them were endangred in recent years because of introduced commercial breeds.Studying on the genetie diversity of Chinese indigenous goat breeds have been carryed out in nowadays.The microsatellite loci were used in this experiment to analysis the genetic diversity of 530 goats from ten indigenous breeds (Shannan White,Hexi cashmere,Zhongwei,Funiu White,Huanghuai,Jining Grey, Yimeng Black,Lubei White,Lvliang Black,Taihang goat) and one introduced breed (Boer Goat).The research results of this study are as the followings;1.Based on the 16 microsatellites loci,we analyze the genetic variation of 11 goat populations.Among loci,the mean number of alleles was 11.31,which proved that the microsatellites recommended by FAO-ISAG are useful for the biodiversity studies in Chinese indigenous goat breeds.2.The observed heterozygosities(Ho),polymorphism information content(PIC), Effective number of alleles(Ne) and inbreeding coefficients(Fis) calculated besed on allele frequency in this 11 breeds is 0.605、0.630、3.348 and 0.126,respectively.The results showed that the genetic variations are abundan in Chinese indigenous goat populations.3.The level of gene flow from Taihang goat into Hexi cashmere goat is very high, followed that between Taihang goat and Huanghuai goat.the gene flow among others is almost in a same higher level(Mean±SD is 8.46±4.81).The mean Fst(0.64) for only Chinese native goat populations suggests that 93.6%of the total genetic variation was from genetic differentiation within each breed and 6.4%of the genetic variation existed among populations,which was also supported by Analysis of Molecular Variance.4.The HWE test showed that all loci gave a deviation when analyzed across population.Deviations from HWE across the loci were present in all of the 11 populations. Deviations from HWE across the population were present in MAF209,SRCRSP15, ILSTS087,MAF65,SRCRSP3,TGLA53,DRBP1,OARFCB20,SPS113 and SRCRSP8 (P＜0.05).Out of 1320 locus pair/population combinations,Exact tests for LE between all marker pairs were carried out within each of the populations and resulted in 638 significant(P＜0.05) outcomes,which were sporadically distributed among the populations,but no specific locus pairshowed a consistent deviation from LE that would have been in each,or even in most,of the populations.5.Three approaches were employed to investigate the genetic relationships among the populations.Firstly,DA and Ds distance matrices were used to build phylogenetic trees with UPGMA and NJ methods.The four Phylogenetic trees are nearly the same. Secondly,in a Principal Component Analysis,the first and second principal component accounted for 45.35%and 17.35%of the variance.The scatterplot revealed that the introduced population is distant from the indigenous population,genetic differentiation among the indigenous breeds is in low level,and the 10 indigenous breeds were clustered into two distinct groups.Thirdly,Population structure analysis based on a Bayesian clustering method showed that a splitting solution was found for K=2 runs in which Boer Goat were identified as distinctive.At K=3,additional structure was detected and the new splitting appeared in Chinese indigeous goat populations.At K=4 or K=5, Inferred membership coefficients of population or individual is very small and could not be applied to clustering well.In a word,the results from Ds/NJ genetic distance cluster, Principal Component Analysis and population genetic structure analysis indicated that the 10 indigenous populations can be clustered into two distinct groups:one group includes Shannan White,Jining Grey,Lubei White,Huanghuai Goat;the other group includes Yimeng Black,Taihang Goat,Funiu White,Hexi cashmere,Lvliang Black,Zhongwei Goat.
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