Search

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.

Susanti R, Iswari RS, Fibriana F, Indriawati. 2018. The duck cytochrome oxidase I (COI) gene: Sequence and patterns analysis for potential barcoding tool. Biodiversitas 19: 997-1003. The local duck DNA barcoding is still rarely conducted in Indonesia while DNA barcoding is extensively used as a tool of species identification and delineation tool. This study aimed to analyze the sequence and patterns of Central Javanese ducks mitochondrial cytochrome c oxidase subunit 1 (COI) gene. Feather samples of seven breeds of native duck were collected from traditional husbandries in Central Java. The samples were employed for DNA extraction and COI gene amplification. Five haplotypes were obtained from 35 samples, i.e., haplotype A, B, C, D, and E. Also, 9 variable sites with synonym substitution was detected in four nucleotides number 55, 61, 100, and 109; whereas five synonym substitutions were identified in the nucleotides number 36, 48, 51, 66, and 756. In conclusion, this study annotates that COI mtDNA gene is essential for local ducks barcoding system.

Objective: Kebumen Ongole Grade (Kebumen OG) are known as good performance cattle with body weight and body measurement higher than National Standard of Ongole Grade cattle. Productivity is influenced by genetic and environmental factors. Insulin-induced gene-1 (INSIG1) gene is one of many genes that are considered important in influencing carcass characteristics and playing an important role in lipid metabolism (adipogenesis and or lipogenesis). So, the aim of this study was to identify of SNP A4366G in INSIG1 gene and associated with slaughter characteristics of unproductive Kebumen OG cows.Methods: In this study used 44 unproductive Kebumen OG cows from slaughter house in Kebumen. Slaughter characteristics contain of slaughter weight, hot carcass weight and dressing percentage. Three milliliters of blood samples were collected from vena jugularis. DNA were extracted from blood samples using salting out method. Genotyping of INSIG1 gene (A4366G) used PCR-RFLP method with TaqI restriction enzyme. Genetic diversity data in this study were allele and genotype frequencies, heterozygosity, PIC and HWE. Association of genotypes of INSIG1 gene with slaughter characteristics were analyzed using ANOVA univariate model.Results: Polymorphic of INSIG1 (A4366G) gene was found in the unproductive Kebumen OG cows. Three variants of genotypes (AA, AG, GG) with two alleles (A and G) were found with allele frequencies 0.795 for G allele. The population was in equilibrium genetic. Association of slaughter characteristics with genotypes were not significant (p>0.05).Conclusions: Polymorphic of INSIG1 gene (A4366G) was found in unproductive Kebumen OG cows population with dominant of G allele. The population was in genetic equilibrium. The association of slaughter characteristics with genotype of INSIG1 gene (SNP A4366G) was not significant.

Insulin-like growth factor-1 (IGF-1) gene plays an important role in the endocrine system of animals by regulating nutrient metabolism, growth, and milk production. There have been extensive molecular genetics research studies on cattle but less studies have focused on buffalo (Bubalus bubalis). This study aimed to confirm the association of IGF-1 gene in swamp or river buffalo (B. bubalis spp.) with growth and milk production traits. DNA samples were obtained from 12 buffalos (eight swamp buffalo and four river buffalo). One Bali cattle (Bos javanicus) was included as an outgroup (control). The eight swamp buffalo originated from East Nusa Tenggara (n = 1), Baluran, East Java (n = 4), and Banyuwangi, East Java (n = 3) , while the four river buffalo originated from Sei Putih, Medan of North Sumatera. All DNA samples were amplified using an IGF-1 primer for 30 cycles, and amplicons were visualized on 1% agarose gel. Five of the 13 samples were sequenced to determine nucleotide sequence variation between the swamp and river buffalo. The results revealed that the size (225–231 bp) of all the fragments was in in accordance with that of IGF-1. There was not found genetic variation among the buffalo samples. The results indicate that buffalo samples bear growth and milk production traits.

Bali cattle are superior meat producers, but they are susceptible to Jembrana disease. The injection of the crude vaccine was considered ineffective, so the env-su gene was selected to express the Jembrana Surface Unit (JSU) protein as a candidate for the Jembrana vaccine. This study aimed to analyze the potential of the JSU protein as a candidate for the Jembrana vaccine and analyze the increase in the env-su gene expression which codon has been optimized in silico. Vaccine design was carried out through in silico including the selection of the SU protein sequences of the genus Lentivirus and sequence alignment of UniProt. The construction phylogeny tree of SU protein using MEGA-X program, optimization of env-su gene codon with preference codon Esherichia coli str. K-12 substr. MG1655 using Optimizer. The optimized env-su gene was inserted into the plasmid pET-21a (+) using GenScript. The result of sequence alignment showed that there is no SU protein that has a percent identity value of more than 30% with JSU protein. The SU JDV and BIV proteins are monophyletic groups and have a percent identity of 20.57%. Codon optimization showed an increase in CAI by 1,000 and GC 54.5%, and a decrease in ENc to 22 and AT 45.5%. EcoR1 and HindIII can recognize the gene target and MCS cut regions on the plasmid so that the env-su gene can be inserted into the pET-21a (+) plasmid. The JSU protein has the potential to be a candidate for the Jembrana vaccine, but it needs further research in vitro and in vivo.

Objective: Bovine Leukocyte Adhesion Deficiency (BLAD) is a genetic disorder in Holstein-Friesian (HF) cattle that have a significant economic impact on dairy cattle breeding. Mutation c.383A>G in Cluster of Differentiation Molecule 18 (CD18) gene was known as related to BLAD. This study aimed to detect the CD18 gene mutation that causes BLAD of HF cattle in the West Java Province.Methods: The genomic DNA was extracted from 88 blood samples of HF cattle from Cibungbulang-Bogor (n=34), Ciampea-Bogor (n=31), and Sukabumi (n=23) by the GB300 DNA extraction kit, GeneaidTM. The CD18 gene mutation was detected by PCR-RFLP analysis using the TaqI restriction endonuclease.Results: All samples in this study produced two fragments DNA, i.e., 359 bp and 260 bp with the monomorphic homozygote genotype (BB). HF cattle with BB genotype indicated as normal cattle and did not carry BLAD.Conclusions: All samples in the three populations of West Java were free of BLAD genetic disorder. Identification of BLAD on HF cattle in other places, including bulls in the Center of Semen Production in Indonesia was needed to prevent this genetic disorder.

An investigation involving large number of animals is often resulting incomplete or in accurate information such as animal parentage, or misidentify on sex due to unlabeled sex samples. A PCR method by applying Y chromosome markers (UTY and SRY) facilitates in determination of unknown sex problem. This study was intended to determine sex from unlabelled sex of blood samples by applying PCR method using a pooled-DNA template. Twenty five of unknown sex blood samples from Nusa Penida, Bali were used in this study. The samples were plotted into 5 pooled-DNA whith each pool DNA consisted of 5 individuals DNA. Two pairs of sex primers, UTY (58oC) and SRY (60oC) with 35 cycles were applied to amplify the samples. The result showed there was only one pooled-DNA (P4) amplified by UTY (484bp). Whereas re-PCR of the positive pooled-DNA (P4) using SRY primer, only one out of 25 samples determined as male Bali cattle (325bp). This finding suggests that UTY and SRY primers are suitable for sex determination and the pooled-DNA could be used as an efficient PCR method both in consumables and PCR process for sex determination. Keywords: Determination, sex, unknown sample, pooled DNA, Bali cattle.

There are several factors influencing the protein expression. The study was aimed to increase the yield of protein recombinant JSU-pET by applying combination of temperature and medium culture composition. This research was composed in a 2x2 factorial design with two level temperatures of 37oC and 25oC and 2 medium compositions of LB and mLB (modified). Escherichia coli bearing JSU-pET plasmid were grown in two applied media and incubated in two applied temperatures. The cells were harvested by centrifugation the pellets were then lysed. The lysed cells were centrifuged, the supernatant then purified by Ni-NTA Resin Agarose. The purified JSU protein recombinant was characterized and quantified by spectrophotometer. The Result showed that the JSU protein recombinant was successfully expressed on the right size (37kDa) in all treatments even though the JSU-pET showed sharper band in m LB at 37oC. Statistically the protein yield was not significant different (P>0.05), however culture temperature of 25oC showed higher yield (0.618±0.095 vs 0.704±0.094) than cultured at 37oC (0.598±0.137 vs 0.553±0.041), respectively either cultured in LB or mLB. This finding suggests that a lower culture temperature could increase protein yield both either in LB or modified LB.

Calpastatin is one of gene markers affecting meat tenderness. The study aimed to evaluate genetic variation of calpastatin (CAST) gene of Bali cattle (Bos javanicus) in lndonesia. A total of 61 samples consisting of 21 Bali cattle, 22 Ongole cattle (Bos indicus), and 18 Friesian Holstein (FH) cattle (Bos taurus) were applied. The Ongole and FH cattle were involved for breed comparison. DNA was extracted from fresh blood using a High Salt method and measured their quality by a Spectrophotometer. A 523 bp of Calpastatin gene fragment was amplified by Polymerase Chain Reaction and Restriction Fragment Polymorphism (PCR-RFLP) technique with RsaI restriction enzyme for genotyping. Result showed that two variants alleles (C and G) and three genotypes (CC, GC, GG) were found in those Bali, Ongole and FH samples. Allele G was dominant allele with the highest G allele was in Bali cattle population (0.88). The higher percentage of allele C was found in Ongole and Friesian Holstein compared to that in Bali cattle. The Ongole breed tends to have a potential source of lean meat quality. This finding identified that genetic variation of CAST gene was exist in Bali cattle and adapted cattle of Ongole and FH in Indonesian.

Pada era globalisasi akhir-akhir ini, tidak mungkin menghindar dari masuknya bahan makanan olahan atau tanpa diolah dari luar negeri. Tujuan penelitian ini yaitu menguji sensitivitas (kerentanan) teknik PCR untuk deteksi kandungan rendah kontaminan daging babi pada daging sapi mentah. Sebanyak 5 tingkat kontaminan daging babi (0,05; 0,10; 0,15; 0,20 dan 0,25%) dalam 5 gram berat total campuran daging telah diuji. Ke lima campuran daging dan 100% daging sapi serta 100% daging babi, dikoleksi DNA nya menggunakan kit DNA (QIAGEN). Satu pasang primer spesifik untuk porcine Leptin digunakan dalam amplifikasi DNA dengan kit PCR. Suhu annealing ditentukan dengan optimasi PCR terlebih dahulu. Dua siklus PCR (25 dan 35) diaplikasikan dalam amplifikasi. Produk PCR divisualisasi pada 1020% gradient PAGE untuk spesifik porcine Leptin. Hasil menunjukkan bahwa ukuran potongan Leptin (152pb) telah teridentifikasi pada ke lima sampel sampuran maupun pada control positif (pork), namun tidak terindikasi pada kontrol negatif (daging sapi). PCR dengan 35 siklus menghasilkan tampilan pita lebih baik dari 25 siklus. Studi ini menyarankan bahwa PCR dengan 35 siklus dapat digunakan sebagai metode cepat untuk identifikasi pencepamaran daging babi dengan dengan tingkat sensitivitas pencemaran daging babi sampai 0,05%.

Caseins are milk protein subdivided into four main groups which are αS1, αS2, β-casein and kappa-casein (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 Hind III 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 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 concludes that polymorphism was found in three of FH populations with A allele was more common in kappa-casein locus. B allele is known having association with milk production, milk component and cheese yield. Increasing of B allele would influence on milk performance of FH cattle. Explorations of quantitative, qualitative and molecular genetics are important to improve dairy cattle performance.