The aim of this study was to evaluate of genetic diversity of local cattle in Indonesia. We analyzed the polymorphism of mtDNA cytochrome b (cytb) gene using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) method. Seventy-three Indonesian local cattle were used in the study that consisted of Madura cattle from Madura island (n = 15), Madura cattle from Sapudi island (n = 23), Limousin x Madura from Madura island (n = 5), Bali cattle from Kupang (n = 12), Aceh cattle from Aceh (n = 5), Pesisir cattle (n = 4), Bali cattle from West Sumatera (n = 1), and Java cattle from Pacitan (n = 8). The 464-bp fragment of cytochrome b (cyt b) gene was amplified using primers: forward primer of L14735 and reverse primer of H15149. The PCR product was digested using HinfI and TaqI restriction enzyme to identify the polymorphism of mtDNA cytochrome b (cytb) gene. The result showed that there was two haplotypes (A and B). Aceh and Pesisir cattle have 100% haplotype B meanwhile Bali cattle (from Kupang and West Sumatera) and Limura cattle have 100% haplotype A. Whereas, Madura cattle from Madura and Sapudi island and Java cattle have two different haplotypes (A and B). There was mt-DNA cytochrome b polymorphism of local cattle in Indonesia based on PCR-RFLP analysis method. Since the genetic variation in local cattle showed the differences in the specific area, it is necessary to control the cattle populations based on the species.

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ABSTRAKKasein adalah protein susu yang terbagi dalam empat grup yaitu αS1, αS2, β-casein dan kappacasein (CSN3). Gen kappa-kasein berpengaruh terhadap pembentukan komponen dalam susu. Tujuan dari penelitian adalah mengidentifikasi polimorfisme gen kappa-kasein pada sapi perah Friesian Holstein (FH). Sebanyak 59 sampel sapi FH yaitu 32 asal Malang, 10 asal Sukahati Bogor dan 17 asal Pusat Penelitian Bioteknologi-Lembaga Ilmu Pengetahuan Indonesia (LIPI) (ternak koleksi) digunakan dalam penelitian. Sampel DNA diekstraksi dengan metode garam pekat dan dikuantifikasi menggunakan Spektrofotometer. Fragmen DNA spesifik gen kappa-kasein sepanjang 379 pb diamplifikasi menggunakan metode Polymerase Chain Reaction (PCR) dengan suhu annealing 56 o C dan 30 siklus. Teknik PCR-RFLP dengan enzim restriksi HindIII digunakan untuk analisis genotip. Hasil analisis menunjukkan bahwa terdapat tiga varian genotip yaitu AA, AB dan BB pada populasi Malang dan ternak koleksi Puslit Bioteknologi-LIPI sementara dua varian (AA dan BB) ditemukan pada populasi Sukahati. Rata-rata frekuensi genotip AA sebesar 65,28%, AB 31,72% dan BB 3,00% dengan rata-rata frekuensi alel A sebesar 0,81 dan B sebesar 0,19. Populasi sapi FH dalam keseimbangan genetik. Kesimpulan, polimorfisme gen kappa-kasein ditemukan pada ketiga populasi sapi FH dengan frekuensi alel A lebih tinggi dibanding alel B. Alel B diketahui berhubungan dengan produksi susu, komposisi susu dan cheese yield. Peningkatan alel B pada populasi FH berdampak terhadap performans produksi dan komponen susu. Eksplorasi (kuantitatif, kualitatif, dan molekuler) perlu dilakukan untuk aplikasi genetika molekuler pada seleksi sapi perah.Kata Kunci: gen kappa casein, polimorfisme, sapi perah, Friesian Holstein ABSTRACTCaseins are milk protein subdivided into four main groups which are αS1, αS2, β-casein and kappacasein (CSN3). Kappa-casein gene influences the manufacturing of milk properties. The aim of this study was to identify the kappa-casein gene polymorphism in Friesian Holstein (FH) cattle. Fifty nine (59) samples consisted of 32 (Malang), 10 (Sukahati Bogor) and 17 (Research Center for Biotechnology-Indonesian Institute of Sciences's collections) were applied in this study. DNA samples were extracted by high concentrated NaCl and quantified by spectrophotometer. The kappa-casein gene was amplified at 379 bp fragment by PCR method using a pair primer of kappa-casein at 56 o C annealing for 30 cycles. PCR-RFLP technique with HindIII was used for genotyping analysis. The result showed that there were three variants of genotypes (AA, AB and BB) in two populations from Malang and RC for Biotechnology-LIPI's collection while cattle from Sukahati had only AA and AB genotypes. The averages of genotype frequencies were 65.28%; 65.28%; and 3.00% for AA, AB and BB genotypes Polymorphism of Kappa-casein gene in FH cattle (S.D.Volkandari et al.) 213 respectively while frequencies of 0.81 and 0.19 were for A and B alleles, respectively. FH cattle populations were in equilibrium genetics. This finding...

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Aim: This study is aimed at characterizing the genetic and phylogenetic structure of Lakor goats as indigenous livestock from the Southwest Maluku Regency based on mitochondrial COI gene sequences. Materials and Methods: The genomes of 103 follicle samples from Lakor goats, collected from Lakor Island, were analyzed. The polymerase chain reaction was used to amplify 1548 bp of the mitochondrial COI gene using two primer pairs (COIA and COIB). Following sequencing, genetic variation and phylogenetic relationship were established using MEGA version X software. Results: The results of multiple COI gene alignment of the total sequences identified four polymorphic nucleotides that function as genetic markers between individual animals within the Lakor goat population. These correspond to positions 228 (A-G), 519 (G-A), 900 (C-T), and 1266 (T-C). Phylogenetic signals based on the COI gene showed that Lakor goat breed is a monophyletic group or single clade with a bootstrap value of 100% by the neighbor-joining (NJ) and maximum likelihood (ML) evolutionary models. This data indicated that evolutionarily, the Lakor goat breed has a very close kinship with three goat breeds from China: The Meigu goat (KM 244714.1), Chinese Tibet (Capra hircus) (KJ 940969.1), and C. hircus (KP 677510.1). Phylogenetic information based on the cladistics system classified the Lakor goat as a single clade (monophyletic group). The low-genetic diversity within populations indicates that there has been an inbreeding depression occurring at a very high frequency. Conclusion: We conclude that the Lakor goat may be divided into a single clade or monophyletic group based on the COI gene sequence. Four nucleotides were identified that can be used as genetic markers among individual animals within the Lakor goat population, as well as C. hircus and others as derived from GenBank data. The Lakor goat population has a high level of inbreeding depression as a result of geographical isolation, which supports the formation of a monophyletic group with different genetic characteristics, and does not allow the introduction of males from other breeds. Phylogenetic signals indicated that Capra aegagrus (bezoar) is the ancestor of the native goats in Indonesia, including the Lakor goats.

Lakor goat is a domestic animal from Lakor island in South West Maluku Regency. They successfully survive and reproduce with limited water, grass and high temperature. Growth traits is an economic trait which important for breeding strategy (productivity improvement). Pituitary Specific Transcription Factor 1 (POU1F1) is otherwise known as PIT1 gene plays a role of growth and carcass traits. The objective of this study was to identify the POU1F1 gene in Lakor goat from Lakor island in Southwest Maluku Regency. Sixty-three samples of hair tail were collected from three different locations: Ketti Letpey (18), Werwawan Jamluli (26) and Letoda (19). DNA was extracted by DNA isolation kit. POU1FI gene was amplified using PCR technique while genotyping used PCR-RFLP with PstI restriction enzyme. Result showed that only one genotype (TT) was found and monomorphic. It may be caused remote area and limited of ram that indicated inbreeding has occurred. Inbreeding rate or coefficient study and introgression of ram from out of Lakor island by Artificial Insemination (AI) or natural mating is needed.

Background and Aim: Pleomorphic adenoma gene 1 (PLAG1) encodes a multifunctional transcription factor that controls many genes and pathways and is associated with cattle body weight and measurements. This study aimed to evaluate the association between PLAG1 polymorphisms with body weight and measurements in Bali cattle. Materials and Methods: A total of 87 Bali cattle, consisting of 48 bulls and 39 heifers at the Breeding Center for Bali Cattle, were used as the population in this study. Cattle were 2 years old and kept semi-intensively in the pasture. Phenotype data consisting of body weight, withers height, body length, chest girth, waist height, and chest depth were measured. Birth weight data were obtained from birth records, and weight gain, adjusted weaning weight, and yearling weight were calculated using formulas. Blood samples were taken from the jugular vein as much as 5 mL, and genomic DNA was isolated using the salting-out method. Polymerase chain reaction (PCR) was performed to amplify three target polymorphisms, namely, g.48308 C>T, g.32212 (19 bp indel), and g.45233 T>C. The presence of a 19 bp indel was determined by direct observation of the PCR product on a 2% agarose gel. Two other polymorphisms were detected by PCR-restriction fragment length polymorphism using the restriction endonuclease enzymes SacII and BclI. PLAG1 genotype and phenotype associations were analyzed using a general linear model. Results: The results showed that two of the target polymorphisms in PLAG1 did not vary. The DD genotype indicated by 123 bp of PCR product was the only genotype identified for g.32212 19 bp indel, and TT genotype was the only genotype found for g.45233 T>C single-nucleotide polymorphism (SNP). Conversely, g.48308 C>T SNP was found to be polymorphic. In addition, the g.48308 C>T polymorphism of PLAG1 was significantly associated with body length of Bali cattle. Cattle with the CC genotype had a greater body length than the other two genotypes. Conclusion: The g.48308 C>T SNP in PLAG1 was associated with Bali cattle body length characteristics. This finding could be used as a basis for selecting Bali cattle based on body length characteristics.

ABSTRAKGen Growth Hormone (GH) merupakan sebuah gen yang mengontrol sintesis hormon pertumbuhan dan berperan dalam metabolisme tubuh. Identifikasi polimorfisme suatu gen penting dilakukan untuk memperoleh informasi awal dalam mengetahui penanda genetik yang berhubungan dengan sifat-sifat ekonomis yang diinginkan. Pemetaan genetik sangat penting dalam proses seleksi. Sapi Pesisir adalah salah satu sapi lokal Indonesia yang ditemukan di Sumatera Barat dan sangat adatif terhadap lingkungan setempat. Penelitian ini bertujuan untuk mengidentifikasi genotip berdasarkan sebagian gen Growth Hormone (GH891│MspI) pada sapi Pesisir dan sapi Persilangan Simmental-Pesisir (SimPes) dan hubungannya dengan sifat pertumbuhan (ukuran tubuh dan berat badan). Sebanyak 30 sampel darah sapi yang terdiri dari 15 Sapi Pesisir dan 15 Sapi SimPes digunakan dalam penelitian ini. Ukuran tubuh dan berat badan sapi diukur pada umur 12-18 bulan. Metode analisis yang digunakan adalah Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP). Hasil menunjukkan bahwa terdapat tiga (3) variasi genotip (MspI-/-, MspI+/-, MspI+/+) dengan frekuensi alel sebesar 53,3% untuk alel MspI-dan 46,7% untuk MspI+. Tidak ditemukan hubungan yang signifikan antara ukuran tubuh dan bobot badan kedua bangsa sapi tersebut berdasarkan ketiga genotip gen GH (GH891│MspI). Kesimpulan, terdapat tiga genotip gen GH pada populasi sapi Pesisir dan SimPes dan tidak berpengaruh signifikan terhadap performans pertumbuhan sapi.Kata Kunci: genotip, enzim MspI, gen Pertumbuhan, sifat pertumbuhan, sapi Pesisir, sapi SimPes ABSTRACTGrowth hormone gene that controls metabolism and body size of animals and polymorphism of the gene is known related to performance of livestock. Identification of gene polymorphisms was important to get early information to determine genetic markers associated with economically desirable traits. Genetic mapping is one of important characterizations in the selection process. Pesisir cattle is one of local cattle in Indonesia that are reared in West Sumatera and have become adaptive to local environment. The present study aimed to identify the genotype of Growth Hormone gene (GH891│MspI) of the Pesisir cattle and crossbred Simmental-Pesisir cattle (designated as SimPes) and relationship between growth performance (body weight and body size). The present study was Pesisir and Crossed SimPes Cattle (T. Hartatik et al.) 1 conducted to 30 blood samples consisted of 15 Pesisir cattle and 15 SimPes cattle. Body weight and body size were measured at 12-18 months of age. The Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) method was used in this research. The results showed that there exist three variant genotypes (MspI-/-, MspI+/-, MspI+/+) and that allele frequencies of MspI-and MspI+ were 53.3% and 46.7%, respectively. Non-significant effect has found between GH's genotype and growth traits (Body measurement and body weight) in both of breed cattle. In conclusion, three variant genotypes (GH891│MspI) in Pes...