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All Journal Journal of the Indonesian Tropical Animal Agriculture
R. R. Noor, R. R.
Departemen Ilmu Produksi dan Teknologi Peternakan, Fakultas Peternakan IPB Bogor 16680
Agriculture, Biological Sciences & Forestry Earth & Planetary Sciences

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Polymorphism of stearoyl-CoA desaturase (SCD1) gene in Indonesian local cattle Hilmia, N.; Noor, R. R.; Sumantri, C.; Gurnadi, R. E.; Priyanto, R.
Journal of the Indonesian Tropical Animal Agriculture Vol 42, No 1 (2017): March
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.42.1.1-5

Abstract

Stearoyl-Coa desaturase (SCD1) gene is one of genes that involves in converting saturated fatty acids to unsaturated fatty acids. SNP at exon 5 in SCD1 gene that changes amino acid valine to alanine (V293A) has an influence to meat fatty acid composition. The aim of this research was to analyze SCD1 gene polymorphisms based on SNP V293A at exon 5 of three Indonesian local cattle. The identification of SCD1 gene polymorphisms was done by using 98, 20 and 7 DNA sample from Ciamis, Bali/Banteng, and Ongole Grade (PO) cattle, respectively. PCR_RFLP method with AciI enzim was carried out to identify SNP Val293Ala. Allelic frequencies and heterozygosity value were analyzed by using POPGENE32. The result showed that SCD1 gene at Ciamis local cattle and PO cattle were polymorphic. Their frequencies were 74.5% and 71.4% for T and 25.5% and 28.6% for C, respectively. There were three genotypes on Ciamis local cattle i.e TT, CT and CC with their frequencies were 52%, 44.9% and 3.10%, respectively. There were two genotypes on PO cattle i.e TT and CT with their frequencies were 42.9% and 57.1%, respectively. Meanwhile, SCD1 gene in Bali cattle was monomorphic. Heterozygosity value of SCD1 gene in Ciamis and PO cattle were 0.38 and 0.44, respectively. Their heterozigosities were categorized as medium. 
SINGLE NUCLEOTIDE POLYMORPHISMS OF LIPOPROTEIN LIPASE GENE AND ITS ASSOCIATION WITH MARBLING QUALITY IN LOCAL SHEEPS Hidayati, H.; Sumantri, C.; Noor, R. R.; Priyanto, R.; Rahayu, S.
Journal of the Indonesian Tropical Animal Agriculture Vol 40, No 1 (2015): March
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.40.1.1-10

Abstract

Lipoprotein lipase (LPL) is a key enzyme that plays in metabolism and transport lipoprotein andtherefore has an influence on blood triglyceride levels. LPL controls triacylglycerol partitioning betweenadipose tissue and muscle that increases fat storage or provides energy in the form of fatty acids formuscle growth. The research was aimed to explore Single Nucleotide Polymorphisms of LPL gene andto associate SNP with marbling quality. A total of 66 genomic DNAs consisted of sumatera thin-tail edsheep (50 heads) and garut sheep (16 heads) were used in this study. Polymerase Chain Reaction wasused to amplify genomic DNA and direct sequencing method was to identify polymorphism sequences.The sequences were analyzed with Bio Edit and MEGA 5.2. The BLAST sequence was obtained fromgene bank X.68308.1. The association between the genotype and marbling quality was analyze by oneway ANOVA and further between mean differences were tested using least sgnificant difference. Theresults showed that 3 novel SNPs i.e. insertion g.26>C; insertion g.27> G and c.192T>C on garut sheepand a SNP insertion g.26>C/G on sumatera thin-tail ed sheep. The diversity of LPL gene at c.192T>Cwas associated with heneicosanoic acid, whereas TT genotype (0.04%) was higher than CC (0.03%) andCT (0.02%).
Identification of single nucleotide polymorphism c.957A>C of PLAG1 gene and its association with growth traits in Bali cattle Putra, I. G. R.; Sari, D. A.; Rachmawati, S. M.; Oktaviani, R.; Noor, R. R.; Jakaria, J.
Journal of the Indonesian Tropical Animal Agriculture Vol 46, No 3 (2021): September
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.46.3.199-208

Abstract

The PLAG1 gene is one of the genes that affect the growth traits located on chromosome 14 in cattle. This study aims to obtain SNP of the PLAG1 gene in exon 1 and exon 2 and their association with growth traits in Bali cattle. The number of samples used was 52 samples of Bali cattle, 10 samples of Peranakan Ongole (PO), and 8 samples of Limousine cattle. Identification of SNPs PLAG1 gene was analyzed by direct sequencing method and genotyping of selected SNPs was carried out using PCR-RFLP. Association of genotypes of SNP c.957A>C with growth using t-test. There were 7 SNPs in exon 2 of the PLAG1 gene, namely SNP c.339A>G, c.489C>T, c.795A>G, c.957A>C, c.1023C>T, c.1056A>G, and c.1353A>G. SNP c.957A>C was validated by PCR-RFLP using TaqI enzyme and obtained three genotypes, namely genotypes AA, AC, and CC with allele frequency A and C, respec-tively 0.10 and 0.90 in Bali cattle, while in PO and Limousine cattle were monomorphic. Genotype association of SNP c.957A>C PLAG1 gene were not associated with birth weight (BW0), weaning weight at 205 days of age (WW205), yearling weight at 365 days of age (YW365), yearling weight at 730 days of age (YW730), and average daily gain (ADG). SNP c.957A>C as a specific SNP for Bali cattle needs to be investigated in further research as a candidate marker for growth traits in Bali cattle.
Identification of SNP g.10428C>T of Stearoyl-CoA Desaturase gene related to meat quality in Bali cattle using PCR-RFLP method Karimah, S. N.; Noor, R. R.; Jakaria, J.
Journal of the Indonesian Tropical Animal Agriculture Vol 46, No 4 (2021): December
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.46.4.295-303

Abstract

The objectives of this research was to analyze the polymorphisms of SNP g.10428C>T in the SCD gene using PCR-RFLP and its association with meat charactheristics in Bali cattle. The number of 52 Bali cattle from BPTU-HTP Denpasar were used in this study and which were compared to Belgianblue (n=30), Limousine (n=14), Peranakan Ongole (PO) (n=30) and Wagyu (n=7). The polymorphism of the SCD gene was characterized by the use of the PCR-RFLP technique with HinfI enzyme restriction. The characteristics of the meat quality in Bali cattle were estimated using ultrasound imaging method. Genotyphic and allelic frequencies, heterozygosity values, and the Hardy-Weinberg equilibrium have been calculated using PopGen 1.32. The association between genotypes of SNP g.10428C>T SCD gene and meat quality characteristics was calculated using t-test. The results showed that homozygous genotypes (CC and TT) and heterozygous genotypes (CT) of the SCD|HinfI gene with C (0.26) and T (0.74) allele frequencies were and  in Bali cattle. The CC genotype was found in Belgian-blue, Limousine, PO, and Wagyu cattle with the allele C frequency of 1.00. The observed heterozygosity (Ho=0.44) higher than expected heterozygosity (He=0.39) showed high diversity in Bali cattle. Genotypes of SNP g.10428C>T SCD gene were associated with backfat thickness, marbling score, and percentage of intramuscular fat. Thus the SNPs g.10428C>T have potential as marker-assisted selection candidates for Bali cattle.  
Co-Authors C. SUMANTRI Gurnadi, R. E. H. Hidayati, H. Jakaria Jakaria Karimah, S. N. N. Hilmia Putra, I. G. R. R. OKTAVIANI R. Priyanto Rachmawati, S. M. S. Rahayu, S. Sari, D. A.