ABSTRAK Pemalsuan daging dan produk olahannya dengan daging tikus merupakan masalah yang harus diatasi untuk menjamin keamanan pangan. Salah satu cara yang sering digunakan untuk mendeteksi pemalsuan adalah dengan menggunakan gen sitokrom b sebagai penanda. Tujuan penelitian ini adalah untuk membuat primer spesifik berasal dari sekuen sitokrom b pada tikus (Rattus norvegicus) sebagai penanda DNA untuk mendeteksi adanya kontaminasi daging tikus pada daging segar dan produk olahannya. Bakso dibuat dari daging sapi dengan penambahan daging tikus 1%-25%, dan bakso yang diperoleh dari pasar tradisional. Ekstraksi DNA dilakukan dari tujuh spesies (kambing, ayam, sapi, domba, babi, kuda, dan tikus) dengan menggunakan metode fenol-kloroform. Amplifikasi gen sitokrom b dari tujuh spesies hewan dengan panjang fragmen yang berbeda menunjukkan kekhususan gen sitokrom b diantara spesies. Hasil amplifikasi panjang fragmen untuk ternak kambing, ayam, sapi, domba, babi, kuda, dan tikus adalah 157, 227, 274, 331, 398, 439 dan 603 pb. Tingkat keberhasilan tertinggi dalam mendeteksi adanya daging tikus dalam campuran bakso daging sapi dengan daging tikus pada konsentrasi 15% adalah 100%. Fragmen spesifik gen sitokrom b dari R. norvegicus tidak memiliki kesamaan dengan gen sitokrom b dari enam spesies lainnya, sehingga dapat digunakan sebagai penanda molekuler untuk mendeteksi adanya kontaminasi daging tikus pada daging segar maupun produk olahannya.

Background and Aim: Heat shock proteins (HSPs) are a group of proteins that play a significant role in protecting cells against cellular stress. HSP70 is a conserved, sensitive, and abundant gene associated with heat stress's physiological adaptability. The objective of this study was to reveal the polymorphisms of the partial sequences of the HSP70 gene (5' untranslated region [UTR]) in seven cattle populations in Indonesia. Materials and Methods: Polymerase chain reaction products (551 bp) of the HSP70 gene amplified from 102 animals representing seven cattle populations (Bali, Belgian Blue × Peranakan Ongole [PO] cross, Galekan, Jabres, Madura, PO, and Rambon) were sequenced by DNA sequencing method. Results: Fourteen single-nucleotide polymorphisms (SNPs), generally found at a low frequency, were detected. Among these SNPs, only 1117G>A, 1125A>C, and 1204T>C were polymorphic in all the analyzed breeds. A Chi-square test showed that the majority of the loci were in Hardy–Weinberg equilibrium (p>0.05). Varying levels of observed (0.050-0.571) and expected heterozygosity (0.049-0.500) were noted. The polymorphism information content values (0.048-0.375) indicated that the SNPs in the HSP70 gene showed low-to-moderate polymorphism in the studied populations. Thirty-six haplotypes were defined according to the identified SNPs, of which haplotype Hap5 (CGACGAGAGTGTCC) and Hap4 (CGACGAGAGTGCCC) were generally dominant in the studied samples. The phylogenetic tree showed a close relationship between Bali and Rambon cattle and between Galekan and Jabres cattle, while the Belgian Blue × PO crossbred cattle were farther apart. Conclusion: The polymorphisms in the 5' UTR of the HSP70 gene identified in this study should be further investigated in a larger population to unravel the association between the SNPs and thermotolerance in Indonesian local cattle populations.

Background and Aim: Myostatin (MSTN), a member of the transforming growth factor-β family, is a negative regulator of muscle mass. This study aimed to detect the genetic variation of the 1160 bp fragment of exon 1 and part of intron 1 of the MSTN gene in several cattle populations raised in Indonesia. Materials and Methods: Polymerase chain reaction products of the MSTN gene amplified from 92 animals representing 10 cattle populations (Peranakan Ongole [PO], Belgian Blue x PO cross, Rambon, PO x Bali cross, Jabres, Galekan, Sragen, Donggala, Madura, and Bali) were sequenced, compared, and aligned with bovine MSTN of Bos taurus (GenBank Acc. No. AF320998.1) and Bos indicus (GenBank Acc. No. AY794986.1). Results: Four nucleotide substitutions (nt 1045 and 1066 in intron 1; nt 262 and 418 in exon 1) and two indels (nt 807 and 869 in intron 1) were synonymous mutations. Among these substitutions, only the nt 262G>C and nt 418A>G loci were polymorphic in all populations, except Bali cattle. The frequencies of the nt 262C (0.82) and nt 418A (0.65) alleles were highest. For the nt 262G>C locus, the CC genotype had the highest frequency (0.66) followed by GC (0.30) and CC (0.03). For the nt 418A>G locus, the AG genotype had the highest frequency (0.52) followed by AA (0.39) and GG (0.09). Conclusion: The results, showing genetic variations in exon 1 and intron 1 of the MSTN gene, might be helpful for future association studies.

Information on the genetic diversity of native and local cattle in Indonesia is vital for the development of breeding and conservation strategies. This study was aimed to assess the genetic diversity and phylogenetic relationship of the Indonesian native (Bali) and local [(Donggala, Madura, Sragen, Galekan, Rambon, dan Peranakan Ongole Grade x Bali (POBA)] cattle populations. Genomic DNA was extracted from blood samples (n= 75). Partial sequences of mtDNA cyt<em> b</em>, 464 bp, were amplified using the polymerase chain reaction technique (forward primer: L14735 and reverse primer: H15149). Thirty-four reference sequences of <em>Bos taurus</em>, <em>Bos indicus</em>, and <em>Bos javanicus</em> were included in the phylogenetic analyses. A total of 55 polymorphic sites and 13 haplotypes were observed in the whole breeds. No variable sites of mtDNA cyt<em> b</em> were observed in Galekan (kept in BCRS) and Rambon cattle. Overall haplotype diversity and nucleotide diversity were 0.515 ± 0.070 and 0.0184 ± 0.0045, respectively. The highest (0.092) and the lowest (0.000) genetic distances were between Bali and Donggala cattle populations and among Galekan (kept in BCRS), Rambon, and POBA cattle populations, respectively. Both mtDNA network and phylogenetic analyses revealed two major maternal lineages (A and B) of the studied population. Most of the sampled individuals (69.33%, present in haplotype H8-H19) were linked to lineage B, which belonged to the same cluster with <em>Bos javanicus</em>. Overall, most of the Indonesian native and local cattle populations had a considerable genetic diversity and shared a common maternal origin with <em>Bos javanicus</em>.

POBA cattle is a crossbred cattle from Peranakan Ongole (PO) and Bali cattle, which is developed by the Beef Cattle Research Institute (BCRI), Ministry of Agriculture of the Republic of Indonesia. This study aimed to identify the genetic and phenotypic characteristics of POBA cattle raised in the BCRI. Genetic diversity of FSH-β gene was also determined in order to identify a possible marker for reproductive status in POBA cattle. Rambon cattle collected from Banyuwangi regency were used as comparison. A 313 bp fragment of the FSH-β gene was amplified using the polymerase chain reaction (PCR). The PCR products were sequenced and aligned to detect polymorphism. As results, a polymorphism (SNP g.2583C/T) in the FSH-β gene, which produced three genotypes (TT, CC, and CT) was detected. The frequency of each allele was 0.13 (allele C) and 0.87 (allele T). However, the FSH-β gene polymorphism did not significantly affect sperm quality, body weight, body size, and cervical condition of POBA cattle.