| Abstract The genetic diversity of five local goat breeds in Guizhou province and Motou goat, Zhaotong goat in the abut area were studied; the heterosis between Boer and the local goats was predicted. The result showed that 86.67%(13/15) microsatellite loci can be amplified successfully; 53.33ï¼…(8/15) loci have several alleles; the loci percentage that can be analyzed verey well reached to 40%(6/15). The result demonstrated that bovine and goat have high genetic conservation. The local goats, such as Guizhou white goat, Guizhou black goat, Qianbei ma goat, Rongjiang small xiang goat, Motou goat and Zhaotong goat are not in Hardy-Weinberg equilibrium. The local goat breeds of Guizhou province have higher genetic diversity than Motou goat, Zhaotong goat and Boer, ranking from Guizhou white goat poll population, Guizhou white goat horned population, Guizhou black goat, Qianbei ma goat, Motou goat, Rongjiang xiaoxiang goat, Zhaotong goat to Boer. The local goat breeds of Guizhou have 1 or 2 specific alleles with a low frequency respectively in INRA063, ILSTS030, INRABERN192 and RM088. Whether these alleles can be used as breed genetic label need the further study. The results of genetic distance showed that Guizhou white goat is closest to Guizhou black goat, next to Rongjiang xiaoxiang goat, furthest to Qianbei ma goat. The Motou goat has the closest genetic distance to Guizhou white goat and Rongjiang xiaoxiang goat, and the same result was also found between Zhaotong goat and Qianbei ma goat.In the phylogenetic tree, Guizhou white goat, Guizhou black goat, Rongjiang xiaoxiang goat and Motou goat formed a branch, Qianbei ma goat and Zhaotong goat composed another. This is according to the geographical distribution and breeding history of the breeds. However, which branch differentiated earlier need the more researches. The study forecast showed that the heterosis between Boer and Guizhou white goat or Motou goat is the largest.
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