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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

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

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

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

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.

Genetic diversity of coding sequence (CDS) region of HSP70 gene in Bali cattle Bonawati, Y. G. M.; Suhendro, I.; Jakaria, J.; Noor, R. R.
Journal of the Indonesian Tropical Animal Agriculture Vol 50, No 2 (2025): June
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.50.2.103-110

This study aimed to investigate the genetic diversity of the Heat Shock Protein 70 (HSP70) gene in the coding sequence (CDS) region and its association with physiological responses in Bali cattle. The samples used in this study consisted of 62 Bali cattle from two different locations in Bali and Se-rading. Physiological data, including respiratory rate, heart rate, rectal temperature, and heat tolerance coefficient (HTC), were collected. The HSP70 gene was amplified using two pairs of primers to target the coding region. SNPs of the HSP70 gene were identified through sequencing. The diversity of SNPs in the coding sequence of the HSP70 gene was determined using the FinchTV 1.4.0 application and version X of the Molecular Evolutionary Genetic Analysis (MEGA) program. In contrast, the association of HSP70 gene SNPs with physiological responses in Bali cattle was evaluated using the GLM method in IBM SPSS Statistics 26. The research discovered nine SNPs within the CDS region of the HSP70 gene, comprising eight synonymous SNPs (c.24C>T, c.31C>T, c.117C>A, c.126G>A, c.324G>A, c.333C>T, c.573G>C, c.1074C>T) and one nonsynonymous SNP (c.1265C>T), which caused an amino acid substitution from threonine (T) to methionine (M). The SNP diversity in the coding sequence of the HSP70 gene showed no significant association (P > 0.05) with physiological responses, including respiratory rate, heart rate, rectal temperature, and heat tolerance coefficient (HTC). The SNPs discovered in the coding region of the HSP70 gene exhibited polymorphism in Bali cattle.

Identifikasi Ukuran Tubuh dan Bentuk Tubuh Sapi Bali di Beberapa Pusat Pembibitan Melalui Pendekatan Analisis Komponen Utama Hikmawaty, Hikmawaty; Gunawan, A.; Noor, R. R.; Jakaria, Jakaria
Jurnal Ilmu Produksi dan Teknologi Hasil Peternakan Vol. 2 No. 1 (2014): Jurnal Ilmu Produksi dan Teknologi Hasil Peternakan
Publisher : Department of Animal Production and Technology, Faculty of Animal Science, IPB University in associated with Animal Scientist's Society of Indonesia (HILPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar

Bali cattle is indigenous livestock genetic resources which have distinctive features and ability to grow well in a variety of environments in Indonesia. The aim of this study was to determine the phenotypic profile of Bali cattle in some breeding centers which represented by BPTU Pulukan Bali, VBC Kab. Barru South Sulawesi and BPTHMT Serading NTB. Data were analyzed by using Principal Component Analysis (SAS) to determine the size identifier which was influenced by the environmental factors and genetic factors form the basic information on the characteristics of Bali cattle. The parameters such as dimensions and body weight of Bali cattle due to the possibility of differences in genetic potential, location of origin, implementation of the mating system and environmental management including maintenance were observed. The result showed Bali cattle body size on BPTHMT Serading NTB were smaller (P <0.5) compared to the body size of Bali cattle in BPTU Pulukan Bali and VBC Kab. Barru South Sulawesi while Bali cattle in BPTU Pulukan Bali and VBC Kab. Barru South Sulawesi were relatively similar. Chest girth measured on the body has the highest correlation with body weight in Bali cattle both in males and females in different breeding centers.The size score and the shape between Bali cattle breeding centers in the male and female Bali cattle showed its own characteristics due to their respective locations. Identifier the size of Bali cattle at NTB Serading BPTMHT showed relatively smaller than Bali Cattle in BPTU Pulukan Bali and VBC Kab. Barru SouthSulawesi. Identifier the same shape among all three populations showed the breeding centers have the samecharacteristic genetically.

Profil Hormon Progesteron dan Gen Fekunditas terhadap Sifat Kembar Kambing PE Betina Calon Induk Mulyono, R. H.; Sumantri, C.; Noor, R. R.; Jakaria, Jakaria; Astuti, D. A.
Jurnal Ilmu Produksi dan Teknologi Hasil Peternakan Vol. 6 No. 1 (2018): Jurnal Ilmu Produksi dan Teknologi Hasil Peternakan
Publisher : Department of Animal Production and Technology, Faculty of Animal Science, IPB University in associated with Animal Scientist's Society of Indonesia (HILPI)

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Etawah-grade goat is a graded up line between kacang and etawah goats, which well adapted to Indonesia’s humid tropical climate. The good reproductive trait of Etawah-grade does are inherited from kacang goat (prolific goat). This study used six heads of Etawah-grade does at 1–2 years old (I1 dental condition). IPB University. The body variables were withers height, hip height, body length, chest width, chest depth, thurl width, rump length, chest girth, and cannon circumference, whereas for head variables were acrocranion–prosthion, basion–prosthion, lower jaw length, head height, tuber facial left-right, nasion–rhinion, entorbitale left-right, euryon left-right, supraorbitale left-right. Body score and head score were obtained from Principal Component Analysis (PCA). PCR-RFLP technique was used to determine genotypes of fecundity genes BMP15 (exon 1), BMPR1B (exon 1), KISS1 (exon 1) and KISS1 (intron 1) with restriction enzymes AluI (AG|CT), SduI (GDGCH|C), BsrI (ACTGG|) and MwoI (GCCTAAG|TAGC), respectively. Progesterone leves were measured by EIA (enzyme immuno assay). The results showed that the association between crude fat consumption and progesterone profile was found in this study, but it was not related to twin births with certain genotypes of gene fecundity BMP15 (exon 1), BMPR1B (exon 1), KISS1 (exon 1) and KISS1 (intron 1). The progesterone profile during the pregnancy period did not correlate to their body size and head size.

Investigasi Hubungan Keragaman Gen Leptin Receptor (LEPR) dengan Karakteristik Karkas dan Kualitas Daging Domba Azizah, D.; Noor, R. R.; Gunawan, A.
Jurnal Ilmu Produksi dan Teknologi Hasil Peternakan Vol. 8 No. 3 (2020): Jurnal Ilmu Produksi dan Teknologi Hasil Peternakan
Publisher : Department of Animal Production and Technology, Faculty of Animal Science, IPB University in associated with Animal Scientist's Society of Indonesia (HILPI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/jipthp.8.3.124-130

Improvement of meat quality plays important role for sheep meat producer and costumer market.Leptin Receptor (LEPR) gene is speculated has important role in carcass and meat quality. This studyaims to investigate the relationship between the LEPR gene variation with characteristics of carcassand meat quality in sheep. A total 50 rams consisted 20 of Javanese fat tailed (JFT), 10 of garutcomposite (GCS), 10 of compass agrinak (CAS), and 10 of barbados cross (BCS) were used in this study.Polymorphism of LEPR gene were performed by Polymerase Chain Reaction-Restriction FragmentLength Polymorphism (PCR-RFLP) with Acil as restriction enzyme. The results showed that of theamplification product was 432 bp. The result of polymorphism of LEPR gene were polymorphic withthird genotype including AA, AC, dan CC. The SNP of LEPR gene with genotype AA was associated(P<0.05) with carcass characteristics including empty body weight, cold carcass and with genotype ACon meat quality including tenderness. It could be concluded that the SNP g.40854778 A>C of LEPR genemay contribute to the characterictic carcass and meat quality in sheep

Investigation of polymorphism and expression of the tyrosinase (TYR) gene as a gene controlling coat color in Bali cattle Kholijah, K.; Darwati, S.; Ulum, M. F.; Londra, I. M.; Noor, R. R.; Jakaria, J.
Journal of the Indonesian Tropical Animal Agriculture Vol 49, No 4 (2024): December
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.49.4.297-306

Cattle coat color is governed by numerous genes, notably the tyrosinase gene (TYR). This study analyzed coat color anomalies like albinism and white spotting in Bali cattle. It aims to discern the TYR gene's diversity, expression patterns, and correlation with coat color abnormalities. The research encompassed 189 cattle, including those with standard coat color (n=53), white-spotted (n=11), and albino (n=17) Bali cattle, as well as Simmental (n=37), Limousin (n=14), Madura (n=21), and Peran-akan Ongole (PO) cattle (n=36). Total DNA was extracted and the TYR gene in exon 1 was amplified using forward and reverse primers with a target amplicon length of 994 bp. Direct sequencing unveiled TYR gene diversity, analyzed using BioEdit and MEGA6 software to identify SNPs. PCR-RFLP was used for SNP genotyping, while qPCR analyzed TYR gene expression. Two mutations (SNP g. 939A>G and SNP g. 887C>T) were discovered in Bali cattle TYR exon 1. SNP g. 939A>G exhibited polymorphism, with the highest GG genotype frequency in standard Bali cattle, indicating a high G allele frequency. Conversely, Madura, Simmental, Limousin, and PO cattle had the lowest allele fre-quency. Chi-square (χ² test) results showed non-significance across all cattle types. TYR gene expres-sion differed significantly between standard Bali cattle and albinos (p<0.05).

Comparison of Growth Traits of Male Bali Cattle (Bos javanicus) with Different Adult Coat Colors Suhendro, I.; Jakaria, J.; Priyanto, R.; Manalu, W.; Hartono, S.; Noor, R. R.
Tropical Animal Science Journal Vol. 47 No. 1 (2024): Tropical Animal Science Journal
Publisher : Faculty of Animal Science, IPB University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5398/tasj.2024.47.1.25

Bali cattle have a distinct coloration that indicates the sexual dimorphism of adult cattle. However, coat color deviations are found in bulls due to either genetic impurity or inbreeding. Furthermore, information is needed to determine whether there is a relationship between coat color and cattle performance. This study aimed to evaluate the potential association between coat color deviation and the growth traits of male Bali cattle. A total of 99 adult male Bali cattle from Livestock Breeding and Forage Centre (BPTU) Denpasar, Bali, were used in this study to assess the possible association between coat color and growth capacity. Animals were grouped according to color patterns into full black (FBL), faded black (FDB), black sorel (BSR), and sorel (SRL). Periodically, growth traits of body weight (BW), wither height (WH), body length (BL), and chest circumference (CC) were measured at birth, weaning, and 365 and 730 days of age. The repeated measurement Anova analysis was used to evaluate the relation between coat color and growth traits over time. This study showed no correlation for both traits in calves due to the absence of color deviation in age. However, it turned out to be a significantly positive correlation (p<0.05) when Bali cattle reached puberty at 365 and 730 days. The black adult bulls (FBL & FDB) were significantly larger in growth traits (p<0.05) than their brown (BSR and SRL) counterparts. The coat color of male adult Bali cattle was associated with their growth traits.

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