Genetic diversity analysis of Indonesian indigenous goat breeds based on microsatellite markers

Goats are important livestock in Indonesia as a source of animal protein and income. Indonesia has several indigenous goat breeds with distinct characteristics. 379 unrelated goats were randomly selected from seven indigenous Indonesian goat breeds and collected from individual farmers in various Indonesian provinces. Microsatellite characterization of indigenous Indonesian goats was carried out using 12 specific microsatellite markers. The total number of alleles obtained from the 12 microsatellite loci was 97, with an average score of 8.08, and the number of effective alleles ranged from 1.413 (ILSTS005) to 4168 (INRA23), with an average value of 2.608. A total of 11 private alleles was found in some goat breeds, but the frequencies were very low, 0.71 – 8.86%. The average of polymorphic information content ranged from 0.239 (ETH10) to 0.726 (INRA23). The mean rate of inbreeding value between populations (Fis) was 0.050, and within the population (Fit) was 0.151. The mean expected heterozygosity was 0.54, and the mean observed heterozygosity was 0.52. Except for the Gembrong goat (GEM), the observed number of alleles, polymorphic information content, and expected heterozygosity were all moderate. This study will support the management of livestock genetic resources and conserving endangered Indonesian goat breeds, such as the Gembrong goat.