Articles

Genetic Polymorphisms of the Coding Region (Exon 6) of Calpastatin in Indonesian Sheep Dagong, M I.A; Sumantri, C; Noor, R R; Herman, R; Yamin, M
MEDIA PETERNAKAN - Journal of Animal Science and Technology Vol 34, No 3 (2011): Media Peternakan
Publisher : Faculty of Animal Science, Bogor Agricultural University

Show Abstract | Original Source | Check in Google Scholar | Full PDF (409.71 KB)

Abstract

Calpastatin (CAST) is an indigenous inhibitor of calpain that involved in regulation of protein turn over and growth. The objective of this research was to identify genetic polymorphisms in the entire exon 6 of calpastatin gene in Indonesian local sheep. A PCR-SSCP method was carried out to identify genetic variation of CAST gene. In total 258 heads of local sheep from 8 populations were investigated, three groups of samples were Thin Tail Sheep (TTS) from Sukabumi, Jonggol, and Kissar. The rest samples were Priangan sheep (PS) from Margawati (Garut meat type) and Wanaraja (Garut fighting type) and Fat Tail Sheep (FTS) from Donggala, Sumbawa, and Rote islands. SSCP analysis revealed that three different SSCP patterns corresponded to three different alleles in the CAST locus (CAST-1, 2, and 3 allele) with five different genotypes. Genetic variation between local sheep populations were calculated based on genotypic and allelic frequencies.  Most populations studied were polymorphic, with genotype frequencies of CAST-11, CAST-12, CAST-22, CAST-32, and CAST-33 were 0.286, 0.395, 0.263, 0.046, and 0.007 respectively. CAST-1 and 2 alleles were most commonly found in all populations with total frequency was 0.970, while CAST-3 was a rare allele 0.030 and only found in TTS population. Variation in the CAST gene could be used for the next research as genetic diversity study or to find any association between CAST polymorphism with birth weight, growth trait and carcass quality in Indonesian local sheep.   Key words: Indonesian local sheep, calpastatin, PCR-SSCP, exon 6
A Novel Single Nucleotide Polymorphism in Exon 4 of Insulin-Like Growth Factor-1 Associated with Production Traits in Bali Cattle Maskur, .; Arman, C; Sumantri, C; Gurnadi, E; Muladno, .
MEDIA PETERNAKAN - Journal of Animal Science and Technology Vol 35, No 2 (2012): Media Peternakan
Publisher : Faculty of Animal Science, Bogor Agricultural University

Show Abstract | Original Source | Check in Google Scholar | Full PDF (548.748 KB)

Abstract

Insulin-like growth factor-1 (IGF-1) is one of the gene candidates that can be used in selection strategy by using DNA markers (marker assisted selection). Gene candidate strategy is a molecular biology techniques to identify quantitative trait loci directly, with the assumption that genetic variation associated to quantitative trait variation. This study was designed to identify any new mutations in exon 4 that can cause the  IGF-1 gene polymorphism and then affect the production traits on Bali cattle. Single nucleotide polymorphism (SNP) discovery was conducted by using the direct sequencing technique. Genetic variation of the genes candidate was identified by using PCR-RFLP technique. The results of this study indicate the presence of a new SNP in exon 4 of IGF-1 gene caused by the T/C transition, which can be identified using Rsa1 restriction enzyme. Genotypic polymorphism of IGF-1/Rsa1 has a significant influence on birth weight, weaning weight and average daily gain of Bali cattle. CC genotype had a birth weight rate, weaning weight and average daily gain of: 15.64±1.83; 83.15±9.00, and 0.439±0.07 respectively, higher than the TT and CT genotype. IGF-1/Rsa1 can be used as a genetic marker for selection of birth weight, weaning weight, and daily body weight gain.     Key words: gene, transition, restriction, polymorphism, markers, selection  
Polymorphism Identification of Pit1 Gene in Indonesian Buffaloes (Bubalus bubalis) and Holstein-Friesian Cows Misrianti, R; Sumantri, C; Farajallah, A
MEDIA PETERNAKAN - Journal of Animal Science and Technology Vol 33, No 3 (2010): Media Peternakan
Publisher : Faculty of Animal Science, Bogor Agricultural University

Show Abstract | Original Source | Check in Google Scholar | Full PDF (1237.087 KB)

Abstract

Pit-1 gene has been identified as the pituitary specific transcription factor that regulates the expression of the growth hormone (GH) and prolactin (PRL) genes in the anterior pituitary. The use of polymorphic markers in breeding programmes could make selection more accurate and efficient. A total  of 320 Indonesian buffaloes from four populations and 45 FH cows from nine populations were genotyped for polymorphism of Pit1|Hinf1 gene by the polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) methods. The gene polymorphism was detected only in FH cattle. The frequency of AA, AB, and BB genotype was 2%, 44%, and 53% respectively. The frequency of A allel was 25% and B allel was 75%, but no polymorphism was detected in 320 Indonesia buffaloes.   Key words: buffalo, Pit1 gene, PCR RFLP  
Growth Hormone Gene Polymorphism and Its Association with Partial Cumulative Milk Yields of Holstein Friesian Dairy Cattle Misrianti, R; Anggraeni, A; Andreas, E; Sumantri, C
MEDIA PETERNAKAN - Journal of Animal Science and Technology Vol 35, No 3 (2012): Media Peternakan
Publisher : Faculty of Animal Science, Bogor Agricultural University

Show Abstract | Original Source | Check in Google Scholar | Full PDF (503.573 KB)

Abstract

Growth hormone gene (GH gene) plays an important role in regulating body growth and in developing mammary gland, similar with its interaction to specific receptors. The GH gene has been considered as one of candidate gene associated with selection on lactation trait and milk production. This study was aimed to determine genetic polymorphism of the GH-AluI gene and to associate its genotype variants on various 15-d partial cumulative milk yields in Holstein Friesian (HF) dairy cows. A number of 370 blood samples were collected from six HF populations, respectively from small dairy farmer under the supervision of the North Bandung Milk Cooperation (NBMC) in Cilumber (98) and Pasir Kemis village (96), Dairy Cattle Breeding and Improvement Station (Cikole DCBIS) Cikole (88), Lembang Artificial Insemination Center (Lembang AIC) (17), Singosari Artificial Insemination Center (Singosari AIC (32), and Cipelang Livestock Embryo Center (Cipelang LEC) (40). A polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) method was used to identify variant genotypes of the GH gene using AluI restriction enzyme. Genotyping results produced only two genotypes, i.e. LL and LV genotypes, without VV genotype. Frequency of the former was dominant, whilst that was low for the latter (89% vs. 11%); leading to the frequency of L allele was very high (94%) compared to that of V allele (6%). No significant association between variant genotypes (LL and LV) and various 15-d partial cumulative milk yields.   Key words: growth hormone gene, milk yield, Holstein Friesian
The Use of Cytochrome b Gene as a Specific Marker of the Rat Meat (Rattus norvegicus) on Meat and Meat Products Nuraini, H; Primasari, A; Andreas, E; Sumantri, C
MEDIA PETERNAKAN - Journal of Animal Science and Technology Vol 35, No 1 (2012): Media Peternakan
Publisher : Faculty of Animal Science, Bogor Agricultural University

Show Abstract | Original Source | Check in Google Scholar | Full PDF (2047.534 KB)

Abstract

Falsification of the origin of livestock meat and its processed with rat meat is a problem that must be overcome to ensure food safety. One way that is often used to detect forgeries by using cytochrome b gene as a marker. The purpose of this study was to create a specific primer derived from cytochrome b sequences in rat (Rattus norvegicus) as the DNA marker to detect any contamination of rat meat on fresh livestock meat and its processed meat products. Meatballs were made from beef meat with the addition of rat 1%-25%, and the meatballs were obtained from traditional markets. DNA extraction was conducted from seven species (goat, chicken, cattle, sheep, pig, horse, and rat) by using phenol-chloroform. The highest success rate in detecting the presence of rat meat in a mixture of beef meatballs at concentration of 15% was 100%. The specific fragment of cytochrome b gene in R. norvegicus has no similarity with the cytochrome b gene from six other species, so it can be used as molecular markers to detect the presence of rat meat contamination in the processed of meat products. Amplified fragment length for goats, chickens, cattle, sheep, pigs, horses, and rats 157, 227, 274, 331, 398, 439 and 603 bp respectively. The amplification of cytochrome b gene in seven species of animals with different fragment length indicated the specificity of cytochrome b gene sequences among species.   Key words: cytochrome b (cyt b) gene, Rattus norvegicus, meat products
Analisis Hubungan Keragaman Gen SCD1 (Stearoyl CoA Desaturase) dengan Komposisi Asam lemak Daging Sapi Lokal di Ciamis Hilmia, Nena; Noor, R.R; Sumantri, C; Priyanto, R; E, Gurnadi
Jurnal Ilmu Ternak Universitas Padjadjaran Vol 16, No 2 (2016)
Publisher : Fakultas Peternakan, Universitas Padjadjaran

Show Abstract | Original Source | Check in Google Scholar | Full PDF (292.734 KB)

Abstract

SCD1 merupakan kandidat gen yang berperan dalam mengkonversi asam lemak jenuhmenjadi  tidak  jenuh,  dan  rasio  keduanya  menentukan  kualitas  daging.  Single  NucleotidePolymorphism (SNP) V293A pada gen SCD1 yang   mengubah asam amino Valina menjadiAlaninaberpengaruh terhadap komposisi asam lemak daging. Penelitian ini bertujuan mengidentifikasi keragaman gen SCD1 berdasarkan SNP V293A, dan hubungannya dengan kandungan  asam lemak pada sapi lokal  di Ciamis. Penelitian ini menggunakan 14  sampel daging  dan  DNA  dengan  genotipe  yang  berbeda.  Metode  PCR-RFLPdengan  enzim  Aci1digunakan untuk mendeteksi SNP V293A pada exon 5.   Hubungan keragaman gen SCD1 dengan komposisi asam lemak daging dianalisis dengan uji T. Hasil penelitian ini menunjukkan gen SCD1 pada sapi lokal Ciamis polimorfik, terdapat dua alel, yaitu alel T dan C dengan tiga genotipe,   yaitu TT, CT  dan CC.  SNP V293A pada gen SCD1 tidak  berpengaruh terhadap komposisi asam lemak daging sapi lokal di Ciamis Jawa Barat.Kata kunci : asam lemak daging, PCR-RFLP, Sapi lokal Ciamis, SCD1.
Identification of Single Nucleotide Polymorphism on Growth Hormone Gene in Aceh Cattle Sari, E M; Noor, R R; Sumantri, C; Yunus, M; L, Han J; Muladno, .
MEDIA PETERNAKAN - Journal of Animal Science and Technology Vol 36, No 1 (2013): Media Peternakan
Publisher : Faculty of Animal Science, Bogor Agricultural University

Show Abstract | Original Source | Check in Google Scholar | Full PDF (492.152 KB)

Abstract

This research was aimed to identify the changes of nucleotide (Single Nucleotide Polymorphism) growth hormone gene in the population of Aceh cattle. There were 44 samples of DNA sequenced, and a few samples from Gen Bank (M57764). Based on the analysis using MEGA program, it was identified one new mutation on exon five on 2230 bp in which C nucleotide turned into T nucleotide, and this was called Silent Mutation (Leusine-Leusine/ CTC-CTT). The frequency of Single Nucleotide Polymorphism (SNP) genotype on 2230 bp (C/T) was CC (0.36), TT (0.14) and CT (0.50). The genotype TT was not possessed by Aceh cattle from Saree, but possessed by those from Banda Aceh and Indrapuri. Chi-square test showed not significant differences in allele frequencies for three population. The frequency of genotype SNP on 2291 bp (A/C) was AC (0.11) and CC (0.89). The frequency of allele C was higher than allele A and T.   Key words: Aceh cattle, SNPs, GH gene
Histomorphology and Physical Characteristics of Buffalo Meat at Different Sex and Age Nuraini, H; Mahmudah, .; Winarto, A; Sumantri, C
MEDIA PETERNAKAN - Journal of Animal Science and Technology Vol 36, No 1 (2013): Media Peternakan
Publisher : Faculty of Animal Science, Bogor Agricultural University

Show Abstract | Original Source | Check in Google Scholar | Full PDF (673.903 KB)

Abstract

The aim of this experiment was to evaluate histology and physical variables of buffalo meat at different sex and ages. Thirty head of buffaloes were used in this experiment. Muscle fiber diameter, fasciculus diameter, thickness of connective tissue, pH, water holding capacity, Warner-Bratzler shear force and cooking loss were measured in this experiment. Analysis of variance of randomized factorial design was used to analyse the data. The differences were analysed by Tukey test. The result showed that muscle fiber diameter was influenced by ages. The difference muscle fiber diameter among ages indicated that 8-12 mo and 1.5 yr old have smaller diameter compared to three year old (P
Association of Polymorphisms Calpastatin Gene with Body Weight of Local Sheep in Jonggol, Indonesia Sutikno, Sutikno; Yamin, M; Sumantri, C
MEDIA PETERNAKAN - Journal of Animal Science and Technology Vol 34, No 1 (2011): Media Peternakan
Publisher : Faculty of Animal Science, Bogor Agricultural University

Show Abstract | Original Source | Check in Google Scholar | Full PDF (795.408 KB)

Abstract

Calpastatin (CAST) gene is located on the fifth chromosome of sheep and plays important roles in formation of muscles and meat tenderness after slaughtering. Association of genetic polymorphism in the CAST gene locus MspI and NcoI with body weight was examined in local sheep from Jonggol Animal Science Teaching and Research Unit (JASTRU), Faculty of Animal Science, Bogor Agricultural University. The genotypes for CAST were determined by the PCR-RLFP method. Blood samples were collected from 264 local sheep belonging to JASTRU located in Singosari Village, Bogor District, West Java Province. Extraction of genomic DNA was based on the phenol chloroform method. CAST locus MspI had three genotypes including in MM, MN and NN with frequencies of 0.75, 0.23, and 0.02 respectively. CAST locus NcoI had two genotypes including in MM and MN with frequencies of 0.92, 0.08 respectively. Chi-square test confirmed Hardy-Weinberg equilibrium for the CAST locus MspI and NcoI. There was no significant effects (P>0.05) of CAST locus MspI and NcoI genotypes on body weight of local sheep in JASTRU.   Key words: CAST locus MspI, CAST locus NcoI, body weight, local sheep
Morphometric performances of Katingan cattle in Central Kalimantan Utomo, Bambang Ngadji; Noor, R.R; Sumantri, C; Supriatna, I; Gunardi, E.D
Jurnal Ilmu Ternak dan Veteriner Vol 15, No 3 (2010): SEPTEMBER 2010
Publisher : Indonesian Center for Animal Research and Development (ICARD)

Show Abstract | Original Source | Check in Google Scholar | Full PDF (313.3 KB)

Abstract

The information of Katingan cattle as an indigenous cattle in Central Kalimantan is very limited, especially phenotypic characterization. A number of 72 heads, consist of 57 heads female and 15 heads male of Katingan cattle in adults category were used in this study. The samples were obtained from three sub districts in district of Katingan, those were Tewah Sanggalang Garing (Pendahara Village), Pulau Malan (Buntut Bali Village) and Katingan Tengah (Tumbang Lahang Village). The location were used as the variable of groups (subpopulation). This study was conducted to describe morphometric performance, which was analysed by discriminant and canonical to estimate the phylogenic relationship and to determine the discriminant variable among the group (subpopulation). The SAS package program version 6.0 and MEGA 2 program was used to analyze data. The observed parameters were body length, wither height, chest width, chest depth, chest circumference, hip heigth, hip width, head height, head length and head width. The chest depth and hip height of female cattle from group of Buntut Bali were lower (P < 0.05) than that of Pendahara and Tumbang Lahang groups. The parameter of: chest width, hip width and body length of Buntut Bali groups were higher (P < 0.05) than that of Pendahara and Tumbang Lahang groups. The average body weight of male Katingan cattle from Buntut Bali was higher (P < 0.05) than that of Pendahara and Tumbang Lahang groups but there were not different (P > 0.05) on bodyweight of female Katingan cattle among location. The highest similarity value was Katingan cattle from group of Tumbang Lahang (92,86%) followed by group of Pendahara (40.91%) and group of Buntut Bali (38.89%), repectivelly. Katingan cattle from group of Pendahara and Tumbang Lahang had closest genetic distance (1.406), while the longest genetic distance (2.046) was between group of Buntut Bali and group of Tumbang Lahang. Genetic distance between group of Buntut Bali and Pendahara was 1.929. Katingan cattle from Pendahara and Tumbang Lahang within one cluster. Body length in canonical structure 2 can be used as discriminant variable. Key Words: Katingan Cattle, Morphometric, Genetic Distance, Discriminant Analysis, Canonical