Abstract Two microsatellite markers OarHH35 and BMS2508 which were closely associated to the high reproduction in sheep (Ovis aries) were analyzed for polymorphisms in Xiangdong black goat, Nanjiang brown goat, Guizhou black goat and Boer goat. The number of alleles for OarHH35 was 11, 8, 7 and 10 respectively in four goat(capra hircus ) breeds. The number of alleles for BMS2508 was 9, 5, 6 and 7 respectively in four goat breeds. The polymorphic information contents for OarHH35/BMS2508 in Xiangdong black goat, Nanjiang brown goat, Guizhou black goat and Boer goat were 0.8294/0.8047,0.8399/0.6894, 0.7985/0.6910 and 0.8582/0.7688, respectively. It indicated that there were a significant influence (P < 0.05) of microsatellite markers BMS2508 and OarHH35 for litter size of goat of Xiangdong black goat. In the OarHH35 locus, the least squares means of genotype 135/135 bp was the highest (3.67 number born /litter ), thereinto the least squares means of genotype 123/135 bp and 125/125 bp also reached 3.00 number born /litter. It indicated that allele 135 and 125 bp for the litter size in Xiangdong black goat had significant positive effect. In the BMS2508 locus, the least squares means of genotype 132/145 and 93/132 bp for the litter size was 4.00 and 3.23 number born / litter respectively, but the least squares means of genotype 122/122 bp for the litter size only had 1.00 number born / litter. It indicated that allele 145 and 93 bp loci had significant positive effect on the litter size of Xiangdong black goat, and had significant negative effect between allele 122 bp and the litter size of Xiangdong black goat.
