P. P. Agung

Morphological profile and estimation of genetic distance of Simmental crossbred.

Research was done to study the profile of morphological characteristics of Simmental cross cattle in West Sumatera on several age categories and estimating the genetic distance compared to Simmental pure breed based on morphological parameters. Several morphological parameters of the 82 of Simmental cross cattle in West Sumatera and the 23 of Simmental pure breed has been measured. To analyze morphological data and the genetic distance a discriminant analysis was done. Based on statistical tests (t-test), body length, body height, hip height, hip width, chest circumference, chest width, chest depth, head length, and head height had significant difference (P<0.05) between 24-60 months Simmental pure breed and Simmental cross cattle bulls. Based on the similarity phenotypic analysis, it is known that all subpopulations of cattle in this research had a relatively high value (73.68-78.57%). Chest depth was the highest different morphometric factor (0.910). Morphological distribution map indicated that the Simmental cross cattle (subpopulations Agam and Lima Puluh Kota) evenly distributed across all quadrants (I-IV) while the Simmental pure breed (subpopulations BIB Lembang and BIBD Tuah Sakato) distributed only in the I quadrants and II quadrants. The highest genetic distance was identified between cattle in Agam and BIBD Tuah Sakato while the lowest genetic distance was identified between cattle in Agam and Lima Puluh Kota. Based on phenogram tree structure, the observed Simmental cattle could be classified into 2 clusters, subpopulations of BIBD Tuah Sakato and BIB Lembang that represent Simmental pure breed configured their own cluster as well as a subpopulation of Agam and Lima Puluh Kota that represent Simmental cross cattle configured the others.

Study of Genetic Diversity among Simmental Cross Cattle in West Sumatra Based on Microsatellite Markers

A study was conducted to assess the genetic diversity among Simmental Cross cattle in West Sumatra using microsatellite DNA markers. A total of 176 individual cattle blood samples was used for obtaining DNA samples. Twelve primers of microsatellite loci as recommended by FAO were used to identify the genetic diversity of the Simmental Cross cattle population. Multiplex DNA fragment analysis method was used for allele identification. All the microsatellite loci in this study were highly polymorphic and all of the identified alleles were able to classify the cattle population into several groups based on their genetic distance. The heterozygosity values of microsatellite loci in this study ranged from 0.556 to 0.782. The polymorphism information content (PIC) value of the 12 observed loci is high (PIC>0.5). The highest PIC value in the Simmental cattle population was 0.893 (locus TGLA53), while the lowest value was 0.529 (locus BM1818). Based on the genetic distance value, the subpopulation of the Simmental Cross-Agam and the Simmental Cross-Limapuluh Kota was exceptionally close to the Simmental Purebred thus indicating that a grading-up process has taken place with the Simmental Purebred. In view of the advantages possessed by the Simmental Cross cattle and the evaluation of the genetic diversity results, a number of subpopulations in this study can be considered as the initial (base) population for the Simmental Cross cattle breeding programs in West Sumatra, Indonesia.

Genetic Diversity of Indonesian Cattle Breeds Based on Microsatellite Markers

Objective This research was conducted to study the genetic diversity in several Indonesian cattle breeds using microsatellite markers to classify the Indonesian cattle breeds. Methods A total of 229 DNA samples from of 10 cattle breeds were used in this study. The polymerase chain reaction 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 the observed number of alleles, effective number of alleles, observed heterozygosity value, expected heterozygosity value, allele frequency, genetic differentiation, the global heterozygote deficit among breeds, and the heterozygote deficit within the breed, gene flow, Hardy-Weinberg equilibrium, and polymorphism information content values. The MEGA program was used to generate a dendrogram that illustrates 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 analysis of molecular variance. 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 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 Crossbred, and Holstein Friesian cattle); Bos indicus cluster (Sumba Ongole, Ongole Grade, Madura, Pasundan, and Pesisir cattle); and Bos javanicus cluster (Banteng and Bali cattle).