The Agouti gene plays an important role in pigment synthesis in domestic animals. A transversion of 423G[T recognized by BanII was found after a fragment (178 bp) of the goat Agouti gene exon 4 was amplified and sequenced. To investigate its genetic effect and diversity, 677 individuals from 12 indigenous Chinese goat breeds and one imported goat breed from South Africa (Boer goat) were analyzed by PCR-RFLP. Two alleles, T and G, and three genotypes, TT, TG, and GG, were detected. Allele T had a higher frequency in most goat breeds and, combined with the coat color phenotype, is believed to be responsible for the black phenotype or to be linked with the causative site in the goat. The results also indicate that the 423G[T transversion showed lower genetic diversity in goat breeds with black coat color in China. Genetic differentiation among the 13 goat populations was 0.2023. The clustering of populations based on the 423G[T site was basically consistent with the variation of coat color.

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