| To investigate the status of the genetic resources of Chinese cashmere goats,the genetic diversities of 9 Chinese indigenous cashmere goat populations and one West African goat breed were investigated using 19 microsatellite DNA markers through fluorescence PCR. The markers were recommended by the Food and Agriculture Organization of the United Nations (FAO) and the International Livestock Research Institute (ILRI). At the same time, the correlation between these 19 microsatellite markers and some indexes of the cashmere's properties was analyzed. On the other hand, the part sequences of nine genes influencing production, disease resistance traits were detected, then based on this sequences result, 6 SNPs resulting in the change of amino acid were selected to be analyzed for characterizing the each sample of our study. Finally, we may deduce if these SNPs were selected by nature or mankind.It was shown by the result of microsatellite markers: fourteen of the microsatellite loci were highly polymorphic and effective markers for analysis of genetic diversity and relationship among goat populations. Analysis of polymorphic information content and genetic heterozygosity showed that the Chinese goat populations have rich genetic diversity and most of breeding farms currently conserved these indigenous resources well. Both UPGMA dendrogram and scatter plots of estimates from principal component analyses showed that the Chinese and African goat populations belong to different clades. Among the Chinese goat populations the Hegu and Hexi populations were genetically more distant from the other goat populations. The remaining seven Chinese goat populations were clustered into two clades. The first clade contained Liaoning, Xinjiang, Chaidamu and Shanbei goat populations, while the second clade was made up of goat populations from Inner Mongolia. The result of software STRUCTURE was also consistent with this conclusion.The analysis for the structure of population showed, most of populations were not in Hardy-Weinberg equilibrium; the absence of heterozygote was extremely prominent in most of populations, which suggested the structure of population had changed and inbreeding at the different degree might existed. According to this status, the farmers must take corresponding measures to widen the genetic base of conserved populations, avoiding directional selection; for several segregate populations it is necessary to broaden farm regions and promote the gene communication mutually to improve the status of populations; in addition those goats whose genetic diversities are high should be parents for enlarging propagation and importing again.The relationship between genotypes and cashmere performances was analyzed by least squares variance analysis. The result showed several loci had significant impact on cashmere traits. The effect of MCM527 on cashmere cosiness degree was extremely significant and on cashmere length was significant; the effect of MAF70 on cashmere fiber diameter was significant; the effect of SRCRSP5, BM1818 on cashmere length was significant. We guess that QTLs or genes that control cashmere fiber diameter may exist in goat fourth chromosome; For MAF70, the alleles 140, 154, 156, 158 have positive effect on cashmere fineness , which will be base of Marker Assisted Selection. All the six SNPs lie in the 95% confidence region of the conditional joint distribution of FST and mean heterozygosity, that suggested these SNPs were not selected by nature or mankind. But this method may bring an experience for the similar further study with a large number of genes.These results may provide a scientific basis for the characterization, conservation and utilization of Chinese cashmere goats.
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