Genetic Diversity of Indonesian Cattle Breeds Based on Microsatellite Markers.

Objective: This research was conducted to study the genetic diversity in the several Indonesian cattle breeds using microsatellite markers as scientific evidence to classify the Indonesian cattle breeds.

Methods: A total of 229 DNA samples consists of 10 cattle breeds were used in this study. The PCR process was conducted using 12 labeled primers. The size of allele was generated using the multiplex DNA fragment analysis. The POPGEN and CERVUS programs were used to obtain nA, ne, Ho, He, allele frequency, FIS, FIT, FST, Nm, HW, and PIC values. The MEGA program was used to generate a dendrogram that illustrate the relationship among cattle population. Bayesian clustering assignments were analyzed using STRUCTURE program. The GENETIX program was used to perform the correspondence factorial analysis (CFA). The GENALEX program was used to perform the principal coordinates analysis (PCoA) and AMOVA. The principal component analysis (PCA) was performed using adegenet package of R program.

Results: A total of 862 alleles were detected in this study. The INRA23 allele 205 is a specific allele candidate for the Sumba Ongole cattle, while the allele 219 is a specific allele candidate for Ongole Grade. This study revealed a very close genetic relationship between the Ongole Grade and Sumba Ongole cattle and also between the Madura and Pasundan cattle. The results from the CFA, PCoA and PCA analysis in this study provide scientific evidence regarding the genetic relationship between Banteng and Bali cattle. According to the genetic relationship, the Pesisir cattle were classified as Bos indicus cattle.

Conclusion: All identified alleles in this study were able to classify the cattle population into three clusters i.e. Bos taurus cluster (Simmental Purebred, Simmental Crossbreed, and Friesian Holstein cattle); Bos indicus cluster (Sumba Ongole, Ongole Grade, Madura, Pasundan, and Pesisir cattle); and Bos javanicus cluster (Banteng and Bali cattle).