J. Jakaria
Faculty of Animal Science, Bogor Agricultural University, Jl. Agatis, Darmaga Campus, Bogor 16680

Published : 12 Documents
Articles

Found 12 Documents
Search

THE USE OF MICROSATELLITE MARKERS TO STUDY GENETIC DIVERSITY IN INDONESIAN SHEEP Jakaria, J.; Zein, M.S.A.; Sulandari, S.; Subandriyo, S.; Muladno, M.
Journal of the Indonesian Tropical Animal Agriculture Vol 37, No 1 (2012): (March)
Publisher : Diponegoro University

Show Abstract | Original Source | Check in Google Scholar | Full PDF (191.996 KB)

Abstract

The purpose of this research was to study genetic diversity in Indonesian sheep population usingmicrosatellite markers. A total of 18 microsatellite loci have been used for genotyping Indonesian sheep.Total sheep blood 200 samples were extracted from garut sheep of fighting and meat types, purbalinggasheep, batur sheep and jember sheep populations by using a salting out method. Microsatellite loci datawere analyzed using POPGENE 3.2 software. Based on this study obtained 180 alleles from 17microsatellite loci, while average number of alleles was 6.10 alleles (6 to 18 alleles) from fiveIndonesian sheep populations (garut sheep of fighting type, garut sheep of meat type, purbalingga sheep,batur sheep and jember sheep population). The average of observed heterozygosity (Ho) and expectedheterozygosity (He) values were 0.5749 and 0.6896, respectively, while the genetic differentiation forinbreeding among population (FIS), within population (FIT) and average genetic differentiation (FST)were 0.1006, 0.1647 and 0.0712, respectively. Genetic distance and genetic tree showed that Indonesiansheep population was distinct from garut sheep of fighting and meat types, purbalingga sheep, batursheep and jember sheep population. Based on this results were needed a strategy for conservation andbreeding programs in each Indonesian sheep population.
The expression of heat shock protein 70 gene with organic selenium supplementation and its effetc on productivity of broilers in tropical environment Amizar, R.; Suharti, S.; Jakaria, J.; Mutia, R.
Journal of the Indonesian Tropical Animal Agriculture Vol 42, No 4 (2017): December
Publisher : Diponegoro University

Show Abstract | Original Source | Check in Google Scholar | Full PDF (198.329 KB)

Abstract

The purpose of this experiment is to study the effect of organic selenium (Se) supplementation on the expression of heat shock protein 70 gene (HSP70), glutathione peroxidase (GSH-Px) enzyme activity, malondialdehyde (MDA) and productivity of broilers in tropical environment. Three kinds of environmental pens were designed in this experiment: comfortable environment pens with temperature of air conditioner adjusted at 22oC (R0), tropical environment pens (±30oC ) without organic Se (R1), and tropical environment pens supplemented with 0.30 ppm organic Se (R2). One hundred and twenty broiler chickens (unisex) were used in this study. There were 40 chicks per pen for each treatment. The experimental design was completely randomized with four replications for each treatment. The data were statistically analyzed using the general linear model of SAS program. Results showed that R0 and R2 groups had significantly increased (P<0.05) feed intake, body weight, body weight gain, and decreased feed conversion ratio compared to R1 groups. Meanwhile, the expression of HSP70, GSH-Px enzyme activity and MDA of R2 groups and R0 groups were significantly lower (P<0.05) than that of R1 groups. It was concluded that the broilers given 0.30 ppm organic Se in tropical environment had similar productivity and expression of HSP 70 with broilers kept in comfortable environment.
IDENTIFICATION OF MYOSTATIN GENE c.960delG LOCUS POLYMORPHISM IN INDONESIAN LOCAL SHEEP BY USING PCR-SSCP METHOD Sumantri, C.; Jakaria, J.; Yamin, M.; Nuraini, H.; Andreas, E.
Journal of the Indonesian Tropical Animal Agriculture Vol 36, No 3 (2011): (September)
Publisher : Diponegoro University

Show Abstract | Original Source | Check in Google Scholar | Full PDF (232.068 KB)

Abstract

Myostatin (MSTN) is a protein inhibit muscle growth. This protein is a member of a superfamily ofmolecules called transforming growth factors beta (TGF-b). Deletion in c.960delG (1-bp deletion atposition 960) disrupts the reading frame from amino acid (aa) position 320 to ending in a premature stopcodon in aa position 359 have been found in Norwegian White Sheep. This deletion in the myostatingene is responsible to increase muscle mass, also known as 'double muscling', in sheep. The purpose ofthis study was to identify the polymorphism of myostatin gene in c.960delG locus of local sheep inIndonesia. The 832 DNA sampels from sheep were collected from 13 populations belonging to thePriangan (86), Javanese Thin Tail (389 i.e. Jonggol, Banjar, Ciomas), Javanese Fat Tail (94), West NusaTenggara (136), Rote Island/East Nusa Tenggara (35), Kisar Island/Southwest Maluku (22),Donggala/South East Celebes (45) and Batur cross breed/Wonosobo, Central Java (25). A gene fragmentof MSTN c.960delG length 299 bp was successfully amplified by using the technique of PCR(polymerase chain reaction) and genotyped by SSCP (single strand conformation polymorphism). Theresult showed no polymorphism in this gene. All sheep tested had G/G genotype for c.960delG locus.
ANALYSIS ON Alu-I GROWTH HORMONE (GHAlu-I) GENE IN BALI CATTLE Jakaria, J.; Noor, R.R.
Journal of the Indonesian Tropical Animal Agriculture Vol 36, No 2 (2011): (June)
Publisher : Diponegoro University

Show Abstract | Original Source | Check in Google Scholar | Full PDF (291.33 KB)

Abstract

The research was conducted to identify Alu-I locus of growth hormone (GH) gene in Bali cattle byusing 232 blood samples collected from Bali and Lombok islands. PCR-RFLP and sequencing methodswere used to detect the polymorphism and nucleotide sequence at Alu-I locus of GH gene. The resultshowed that Bali cattle from Bali island has one genotype (LL genotype), whereas Bali cattle originatingfrom Lombok island has two genotypes, namely LL and VV genotypes, respectively. The L and V allelefrequencies from Bali and Lombok islands were 1.00 and 0.00; 0.99 and 0.01, respectively. Thesequencing result of Bali cattle LL genotype showed an AGCT sequence of enzyme Alu-I restriction site.Based on polymorphic informative content (PIC) value, it can be concluded that Alu-I locus of Balicattle from Bali and Lombok islands were monomorphic and polymorphic, respectively.
Prediction of meat quality in Bali cattle using ultrasound imaging Jakaria, J.; Khasanah, H.; Priyanto, R.; Baihaqi, M.; Ulum, M. F.
Journal of the Indonesian Tropical Animal Agriculture Vol 42, No 2 (2017): June
Publisher : Diponegoro University

Show Abstract | Original Source | Check in Google Scholar | Full PDF (214.666 KB)

Abstract

The objective of this study were to predict carcass quality characteristics in Bali cattle using ultrasound imagery. The Number of samples were 81 heads of Bali cattle consist of bulls (62 heads) and cows (19 heads) with various age ranging from 1 to 6 years were collected their body weight and carcass qualities including backfat thickness (BF), longissmus dorsi thickness (LD), rump fat thickness (RF), rump thickness (RT), marbling score (MS) and the percentage of intramuscular fat (PIF). Those were estimated using ultrasound performed on 4.5-6,5 MHz frequency with depth of 8.8-13 cm. The BF, LD, MS and PIF measurement were applied on 12th-13th ribs, while the RT and RF measurement were conducted between ischium and illium. MS determination was calculated using Aus-Meat standard, while PIF was analysis based on Deaton and Rouse (2000). Body weight and carcass quality among traits were analyzed using descriptive and correlation procedures. The results showed that performance of body weight and carcass quality differs between Bali bulls and Bali cows, as well as among the age variations. Correlation analyses among traits (body weight and carcass quality) showed strong positive correlation (P<0.05) ranging from 0.291 to 0.938. In conclusion, ultrasound imaging method could be used to estimate carcass quality characteristics in Bali cattle.
Preliminary study of solute carrier family 23 member 3 (SLC23A3) gene as candidate marker for fatty acid traits in Kampung-Broiler crossbred chickens Gunawan, A.; Basril, S. Y.; Listyarini, K.; Furqon, A.; Bilyaro, W.; Jakaria, J.; Uddin, M. J.; Sumantri, C.
Journal of the Indonesian Tropical Animal Agriculture Vol 43, No 3 (2018): September
Publisher : Diponegoro University

Show Abstract | Original Source | Check in Google Scholar | Full PDF (203.873 KB)

Abstract

SLC23A3 is one of the key genes which control the properties of the of fatty acids content in the meat. The aim of this study was to identify the association of SNP and mRNA expression of SLC23A3 as a candidate marker for fatty acid traits (FAs). Sixty two F2 Kampung × Broilers crossbred chickens population were used in this study. FA composition was measured at 12 weeks of age from thigh meat of crossbred chicken. The PCR-RFLP and qRT-PCR were used for association study and expression analysis of SLC23A3 gene with divergent fatty acid composition. A SNP in coding region c.22385690 A>C of the SLC23A3 gene was associated (P<0.05) with fatty acid composition including stearic acid (C18:0), elaidic acid (C18:1n9t), and linoleic acid (C18:2n6c). The SLC23A3 was detected in liver from high fatty acids (HFA) and low fatty acid (LFA) composition. However, gene expression of SLC23A3 were not differentially expressed between HFA and LFA. These results will explain better understanding of the key important role of the SLC23A3 in fatty acid traits within the liver and will propose SLC23A3 as a potential genomic selection for selection of chickens with fatty acid composition.
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 | Original Source | Check in Google Scholar | Full PDF (68.799 KB)

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.
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 | Original Source | Check in Google Scholar | Full PDF (270.477 KB)

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.
NOVEL SNP OF CALPAIN-1 (CAPN1) GENE AND ITS ASSOCIATION WITH CARCASS AND MEAT CHARACTERISTICS TRAITS IN BALI CATTLE Pratiwi, N.; Maskur, M.; Priyanto, R.; Jakaria, J.
Journal of the Indonesian Tropical Animal Agriculture Vol 41, No 3 (2016): September
Publisher : Diponegoro University

Show Abstract | Original Source | Check in Google Scholar | Full PDF (239.855 KB)

Abstract

Calpain-1 gene (CAPN1) produces an calpain enzyme controlling structure of meat protein and tenderness. The aims of this study were to identify Single Nucleotide Polymorphism (SNP) in exon 5 and 6 of CAPN1 gene and its associate with carcass and meat characteristic traits in bali cattle. A total of 48 bali cattles from BPTU-HMT Bali Cattle, Bali Province were used in the research. SNP in exon 5 and 6 of CAPN1 gene were identify with direct sequencing using MEGA 5 program. Analysis of polymorphism was conducted by PopGen 1.32 software to identify frequencies of genotype, allele and Hardy-Weinberg equilibrium. The association of CAPN1 gene genotype with carcass and meat characteristic traits was analyzed using Generalized Linear Model (GLM) procedure of SAS. Sequencing analysis at exon 5-6 of CAPN1 gene in Bali cattle resulted in eight polymorphic SNPs. They are c.3669T>C, c.3854G>A, c.3881T>C, c.3899C>T, c.3908C>G, c.4002C>A, c.4021G>T and c.4037A>C. The SNPs c.3669T>C, c.3854G>A and c.3899C>T were significantly (P<0.05) associated with rump thickness (RT), rump fat thickness (RFT) and marbling score (MS), while SNP c.4037A>C was not significantly associated with carcass and meat characteristic traits. The SNPs were significantly associated with carcass and meat characteristic traits namely c.3669T>C, c.3854G>A and c.3899C>T. Those SNPs may be used as candidate marker for Marker Assisted Selection (MAS) in bali cattle.  
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 | Original Source | Check in Google Scholar | Full PDF (219.96 KB)

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.