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All Journal Journal of the Indonesian Tropical Animal Agriculture
P. P. Agung, P. P.
Research Center for Biotechnology - Indonesian Institute of Sciences, Jl. Raya Bogor KM. 46, Cibinong 16911, West Java
Agriculture, Biological Sciences & Forestry Earth & Planetary Sciences

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Journal : Journal of the Indonesian Tropical Animal Agriculture

 1 
The polymorphism in g.1256G>A of bovine pituitary specific transcription factor-1 (bPIT-1) gene and its association with body weight of Pasundan cattle Putra, W. P. B.; Agung, P. P.; Said, S.
Journal of the Indonesian Tropical Animal Agriculture Vol 44, No 1 (2019): March
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.44.1.19-27

Abstract

Bovine Pituitary specific transcription factor 1 (bPit-1) is one of amino acid that controling pituitary gland in mammals. The pituitary gland is important for secretion of growth hormone from growth genes. This study was carried out to detect polymorphism in the exon 6 of bPit-1 (g.1256G>A) in Pasundan cattle using PCR-RFLP method and its association with body weight. Total of 69 heads (15 males and 54 females) of Pasundan cattle from breeding station (BPPIBT-SP Ciamis, West Java) were used in this study. Research showed that two genotypes of bPit-1/HinfI gene were identified in this study i.e GG (0.90) and AG (0.10) with allele frequencies of 0.05 (A) and 0.95 (G). The polymorphic informative content (PIC) and number of effective allele (ne) values were 0.09 (low) and 1.11. respectively. The Chi-square (χ2) value in the population studied was 0.20 and in Hardy-Weinberg equilibrium (χ2<5.99). It was concluded that the polymorphism of bPit-1/HinfI in Pasundan cattle included of low category and was not associated with body weight.
Identification of KLF3 gene polymorphism in Indonesian Friesian Holstein cattle Agung, P. P.; Laoditta, F.
Journal of the Indonesian Tropical Animal Agriculture Vol 43, No 3 (2018): September
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.43.3.195-200

Abstract

The KLF3 gene was a potential genetic marker candidate due to its involvement in many biological processes such as cell proliferation, cell differentiation, and apoptosis. This study was conducted to identify the KLF3 gene polymorphism in the Indonesian FH cattle. A total of 302 individual cattle blood samples from West Java (n=138), Central Java (n=34), and East Java (n=130) provincies were used to obtainDNA samples. The DNA sequencing was performed using 9 samples (each location of sampling represented by 3 samples) for initial identification of the KLF3 gene polymorphismand followed by PCR-RFLP analysis using all DNA samples. There were two SNPs identified in the intron region of the KLF3 gene i.e. SNP g.59607486delC and SNP g.59607554A>G. The SNP g.59607554A>G could be detected using PCR-RFLP method with HpyCH4IV restriction enzyme and resulted three genotypes of the KLF3 gene (AA, AG, and GG) but its heterozygosity value was low in the Indonesian FH cattle. The AA genotype has the highest frequency (0.73), while the AGand GG genotypes frequency were 0.24 and 0.03, respectively. Information about the KLF3 gene polymorphism in this study can be considered for further study to analyse its association with milk and protein yield traits.
Association of growth hormone (GH) gene polymorphism with growth and carcass in Sumba Ongole (SO) cattle Agung, P. P.; Anwar, S.; Putra, W. P. B.; Zein, M. S. A.; Wulandari, A. S.; Said, S.; Sudiro, A.
Journal of the Indonesian Tropical Animal Agriculture Vol 42, No 3 (2017): September
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.42.3.153-159

Abstract

A study was conducted to identify the polymorphism in the intron 3 of the Growth Hormone (GH) gene and also to evaluate the association of the GH gene polymorphism with growth parameters and dressing percentage in the Sumba Ongole (SO) cattle. A total of 267 individual DNA samples were used in the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) analysis. The SO cattle growth parameters data (n=44) including birth weight (BW), weaning weight at 205 days of age (WW205), yearling weight at 365 days of age (YW365) and also dressing percentage (DP) (n=122) were investigated in this study. There were three genotypes (AA, AB, and BB) of the GH gene based on the PCR-RFLP analysis with allele frequency was 0.87 and 0.13 for A allele and B allele respectively. The highest genotype frequency in the SO cattle is AA (0.76) and the lowest is BB (0.02). The Heterozygosity Observed (Ho) value in the SO cattle population is 0.23 and Polymorphism Information Content (PIC) value is 0.20. Therefore, the genetic diversity in the SO cattle based on the GH gene polymorphism is quite low. There is no association (P>0.05) in BW, WW205, YW365, and DP with genotypes of the GH gene. As the result, the GH gene in this study cannot be used as a genetic marker in the SO cattle breeding program.
ESTIMATION OF MOST PROBABLE PRODUCING ABILITY VALUE FOR CALF BIRTH'S PERFORMANCE IN SUMBA ONGOLE COWS Said, S.; Agung, P. P.; Putra, W. P. B.; Anwar, S.; Wulandari, A. S.; Sudiro, A.
Journal of the Indonesian Tropical Animal Agriculture Vol 41, No 2 (2016): June
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.41.2.53-60

Abstract

An estimation of most probable producing ability (MPPA) value based on the calves performance is very important for the cow selection. The birth data record of 48 Sumba Ongole (SO) cows and record data from 52 callf birth’s performance were used to estimate the value of MPPA. High of r value (r > 0.30) was obtained at the body length (BL). Birth weight (BW), withers high (WH) and chest girth (CG) had a moderate value (0.10 < r < 0.30) of repeatability. The MPPA value of the cumulative calf birth’s performance of cows based on the highest birth records was 4.64 (cow number 3770) and the lowest was -4.64 (cow number 2283). Calf number B2076 (cow number 3586) had the highest ratio of WH (115.70); BL (124.26); CG (118.90), while the highest ratio of BW (168.35) was obtained in calf number B2095 (cow number 3731). It was concluded that the BW of birth had a moderate value of r (0.10) and could be used as a selection criteria accurately. 
SELECTION OF SUMBA ONGOLE (SO) CATTLE BASED ON BREEDING VALUE AND PERFORMANCE TEST Said, S.; Agung, P. P.; Putra, W. P. B.; Anwar, S.; Wulandari, A. S.; Sudiro, A.
Journal of the Indonesian Tropical Animal Agriculture Vol 41, No 4 (2016): December
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.41.4.175-187

Abstract

Selection of livestock was purposed to increase productivity. A performance test was conducted using 25 males and 25 females of Sumba Ongole (SO) cattle. The performance test were conducted in three periods (2014, 2015 and 2016) for about 535 days. Descriptive statistics ws used to analyze data of body weight. Cattle with age between 300 to 600 days were used for evaluation. Result showed that heritability value of yearling weight (YW365) was 0.77+0.68 as a high category. The highest breeding value of YW365 were 66.05 kg (male) and 41.89 kg (female). The average of corrected final weight (CFW) weight were 172.55+34.22 kg (male) and 159.80+37.73 kg (female). The performance test in this study obtained six A class (1 bull and 5 cows) based on the standard minimum of body measurements for SO cattle.
IDENTIFICATION OF UTERIN MILK PROTEIN (UTMT) GENE IN BALI CATTLE USING DIRECT SEQUENCING Jakaria, J.; Saputra, F.; Paramitasari, K. A.; Agung, P. P.; Maskur, M.
Journal of the Indonesian Tropical Animal Agriculture Vol 41, No 1 (2016): March
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.41.1.1-6

Abstract

The objective of this research was to identify diversity of exon 5 UTMP gene fragment in Bali cattle using direct sequencing. The total 60 blood samples of Bali Cattle derived from BPTU Bali in Bali siland (20 heads), BPTU Serading in Sumbawa island (20 heads) and Village Breeding Center in Barru District South Sulawesi (20 heads) were used to evaluate their genetic diversity at exon 5 UTMP gene. The forward and reverse data sequences were analyzed using Bioedit program and alignment analysis was carried out using MEGA5 program. Meanwhile haplotype analysis was performed by DnaSPv5 program. The result showed that partial sequences in exon 5 UTMP gene had 16 haplotypes with the highest number of haplotypes ware found in VBC Barru district South Sulawesi (8 haplotypes). Moreover, the highest average of haplotype (h) and nucleotide (p) diversity were found in VBC Barru district South Sulawesi were 0.7949 and 0.0016, respectively. In addition, minisatellite insersion was found in exon 5 UTMP gene fragment on Bali cattle which are consist of 5'-CCA GTC ATG AAG AAG GCA GAG GTC GTC GTG CCG GCG AAA-3'. According to our results, haplotype and minisatellite variation in exon 5 UTMP gene fragment can be used as a candidate genetic marker specific for reproductive trait in the Bali cattle and for its strategy breeding program in the future.
POLYMORPHISM STEAROYL-COA DESATURASE (SCD) GENE AND ASSOCIATON WITH CHARACTERISTICS MEAT IN BALI CATTLE Alwiyah, A.; Naraini, H.; Agung, P. P.; Jakaria, J.
Journal of the Indonesian Tropical Animal Agriculture Vol 41, No 4 (2016): December
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.41.4.188-195

Abstract

Stearoyl-CoA desaturase (SCD) is an enzyme produced by SCD gene which is responsible for a conversion of saturated fatty acids (SFA) to mono-unsaturated fatty acid (MUFA) in adipose tissue. This enzyme affects the fats in intramuscular so having influence on marbling. The purpose of this study was to obtain the polymorphisms of the SCD gene and their associations with meat quality traits in Bali cattle. The number of samples used were 48 heads of cattle consisted of 24 bulls and 24 cows from BPTU-HMT Bali cattle in the province of Bali. The SCD gene has been amplified using forward primer 5’-ACC CCT TGG TGT GTG GTT GTT CTT C-3 ‘and reverses primer 5'-CCT GAC GAT ACT ATG TTT CTA CTT C-3'. The polymorphisms of the SCD gene were identified by direct sequencing method. Meat quality traits such as thick of longissimus dorsi (TLD), thick of back fat (TBF), thick of fat rump (TFR), thick of rump (TR), marbling score (MS), and the percentage of intramuscular fat (PIMF) were analyzed using the Veterinary Ultrasound Scanner. To determine Hardy-Weinberg equilibrium status, both allele and genotype frequencies were analyzed using GENEPOP program (V3.2). Association of the SCD gene SNP and meat quality traits was analyzed by GLM. This result showed that there were 5 monomorphic SNPs (c.10153A>G, c.10318C>A, c.10329C>T, g.10394G>A, g.10486A>C) and 3 polymorphic SNPs (g.10360G>A, g.10428C>T, g. 10487G>A) were in HW equilibrium. Association analysis showed that g.10428C>T SNP significantly affected marbling score (MS) and percentage of intramuscular fat (PIMF) (P<0.05). Based on these results, g.10428C>T SNP of the SCD gene may be used as a candidate marker to select meat quality traits in Bali cattle.
MYOSTATIN GENE ANALYSIS IN THE FIRST GENERATION OF THE BELGIAN BLUE CATTLE IN INDONESIA Agung, P. P.; Said, S.; Sudiro, A.
Journal of the Indonesian Tropical Animal Agriculture Vol 41, No 1 (2016): March
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.41.1.13-20

Abstract

A study was conducted to identify the variations of the myostatin and also to evaluate the existence of genetic marker for “double muscling” (11-bp deletion in the third exon of the myostatin gene) in the first generation of Belgian Blue cattle in Indonesia using the Single Strand Conformation Polymorphism (SSCP) and the sequencing analysis. A total of 8 DNA samples belonged to Karya Anugerah Rumpin (KAR) Farm were used in the Single Strand Conformation Polymorphism (SSCP) and the sequencing analysis. There were 3 allele types of myostatin gene based on the SSCP analysis. The Belgian Blue sire has type A allele. The Simmental, Wagyu, SO x BX, Charolais, and the PO cattle have the type B allele, while the Belgian Blue x FH and the Belgian Blue x SO have the type C allele (heterozygous). There are 11-bp deletion in the third exon myostatin gene for the Belgian Blue sire based on the sequencing analysis. The myostatin gene in the Belgian Blue F1 generation individual was heterozygous. This study provides scientific evidence that the 11-bp deletion in the third exon of myostatin gene in the Belgian Blue sire was inherited to its F1 generation (male and female).
THE POTENCY OF SUMBA ONGOLE (SO) CATTLE: A STUDY OF GENETIC CHARACTERIZATION AND CARCASS PRODUCTIVITY Agung, P. P.; Anwar, S.; Wulandari, A. S.; Sudiro, A.; Said, S.; Tappa, B.
Journal of the Indonesian Tropical Animal Agriculture Vol 40, No 2 (2015): June
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.40.2.71-78

Abstract

A study was conducted to assess the genetic characterization of the Sumba Ongole (SO) cattlebased on DNA microsatellites and also to study the potency of SO cattle based on carcass productivity.Blood samples were collected from 28 individual cattle and 12 microsatellite primers as recommendedby FAO were used to identify the genetic characterization of the SO cattle population. Data of carcassproductivity were collected from 506 individual cattle that slaughtered in Karawaci abattoir, Banten,Indonesia. The heterozygosity values of microsatellite loci ranged from 0.143 to 1.000 (mean 0.536).The highest PIC values was 0.814 (locus TGLA122), while the lowest was 0.280 (locus BM1818).Cattle in range of 351-475 kg slaughter weight was most slaughtered in year 2013 and 2014 with carcasspercentage ranged from 52.89% to 53.43%. The highest carcass percentage (56.34%) was obtained fromcattle in range of 626-650 kg slaughter weight while the lowest (51.42%) was obtained from cattle inrange of 250-275 kg slaughter weight. The results of genetic characterization showed that allmicrosatellite locus were highly polymorphic and highly informative for detecting the level of geneticdiversity in the SO cattle population. The results of carcass productivity showed that the SO cattle hasexcellent potential as beef cattle compare with other local breeds cattle in Indonesia.
Genetic polymorphism analysis of 5' untranslated region of thyroglobulin gene in Bali cattle (Bos javanicus) from three different regions of Indonesia Anwar, S.; Putra, A.C.; Wulandari, A.S.; Agung, P. P.; Putra, W.P.B.; Said, S.
Journal of the Indonesian Tropical Animal Agriculture Vol 42, No 3 (2017): September
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.42.3.175-184

Abstract

The g.422C>T nucleotide variations in the 5’ untranslated region (5’UTR) of TG gene (called as TG5) has been reported to be associated with level in intramuscular fat (IMF) content or marbling in beef cattle. The objective of this study was to confirm genetic polymorphism of TG5 gene in Bali cattle populations from three different regions as the main resources of Bali cattle in Indonesia. A total of 200 head of Bali cattle have been performed genotyping on TG5 gene using polymerase chain reaction-restriction fragment lenght polymorphism (PCR-RFLP) method and sequence analysis. Results of the study confirmed that TG5 was monomorphic in Bali cattle wherever their origin regions. Moreover, nine candidate SNPs were detected within 5’UTR of TG gene in Bali cattle compared to Genbank reference sequences, although no SNP variations among Bali cattle sample studied. The new other genetic markers within an entire TG gene suggested to be explored and verified for their polymorphisms in Bali cattle. The nine candidate SNPs were also required further verification and validation in a larger sample to be regarded as new SNPs between Bali cattle and Genbank reference sequences.
Co-Authors A. Alwiyah, A. A. S. Wulandari, A. S. A. Sudiro, A. B. Tappa F. Saputra, F. H. Naraini, H. Jakaria Jakaria K. A. Paramitasari, K. A. Laoditta, F. M. S. A. Zein, M. S. A. Maskur Maskur Putra, A.C. S. Anwar S. Said W. P. B. Putra W.P.B. Putra Wulandari, A.S.