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Polymorphism of L-FABP (SNP g. 1593 C>T) Gene and Its Association with Fatty Acid Composition, Carcass, and Meat Quality in Cihateup Duck A. S. Mentari; A. Gunawan; R. R. Noor
Tropical Animal Science Journal Vol. 43 No. 2 (2020): Tropical Animal Science Journal
Publisher : Faculty of Animal Science, Bogor Agricultural University

Fatty acid composition, carcass, and meat quality are quantitative traits which are controlled by several genes or polygenic. One of the genes that plays important role in the fatty acid in meat quality and fatty acid composition is liver-type fatty acid-binding protein (L-FABP). The aims of this study were to identify single nucleotide polymorphism (SNP) of liver-fatty acid binding protein (L-FABP) gene and its association with fatty acid, carcass, and meat quality traits in cihateup duck. Cihateup ducks were originated from Tasikmalaya, West Java, Indonesia. The study used a total of 98 ducks aged of 12 weeks old with the average body size of 1.4±0.12 kg for PCR-RFLP analyses and 76 ducks for the association analyses. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) was used to identify SNP g. 1593 (C>T) of L-FABP gene. The associations of L-FABP genotypes with fatty acid, carcass, and meat quality traits were performed using T-test procedures. The result showed that the SNP of L-FABP gene was polymorphic with three genotypes (CC, CT, and TT). The Chi-square test revealed that the locus of L-FABP (g. 1593 C>T) was in Hardy - Weinberg equilibrium. L-FABP gene was significantly associated (p<0.01) with the carcass portions, providing neck and percentage of neck as well as significantly associated (p<0.05) with saturated fatty acids, i.e., lauric acid (C 12:0) and palmitic acid (C 16:0); polyunsaturated fatty acid, i.e., eicosadienoic acid (C 20:2); carcass portions, i.e. neck and percentage of neck. The SNP g. 1593 (C>T) of L-FABP gene may be a useful marker for selecting and producing duck meat having desirable fatty acids and carcass and meat quality.

The Polymorphism and Expression of CYP2E1 Gene and Its Relation to Carcass and Meat Quality of Indonesian Lamb R. S. Harahap; R. R. Noor; A. Gunawan
Tropical Animal Science Journal Vol. 44 No. 4 (2021): Tropical Animal Science Journal
Publisher : Faculty of Animal Science, Bogor Agricultural University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5398/tasj.2021.44.4.377

The aim of this study was to conduct the genotyping of the single nucleotide polymorphism (SNP) in g.50657948 T>G of the CYP2E1 gene and its relation to the carcass and meat quality. A total of 200 Indonesian lambs consisted of 20 Javanese fat-tail sheep (JFTS), 37 Javanese thin-tail sheep (JTTS), 20 Garut sheep (GS), 21 Jonggol sheep (JS), 34 Garut composite sheep (GCS), 35 compass agrinac sheep (CAS), and 33 Barbados cross sheep (BCS) aged between 10-12 months old were used in this study. The polymorphism of the CYP2E1 gene was characterized using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) with NlaIII enzyme restriction. The CYP2E1 gene found the three genotypes (GG, GT, and TT) and the allele frequencies were in Hardy Weinberg equilibrium. The CYP2E1 gene was significantly associated with meat quality, i.e., pH value and tenderness, as well as fatty acid composition (p<0.05), i.e., saturated fatty acid (SFA): caprylic acid (C8:0), arachidic acid (C20:0), heneicosylic acid (C21:0), behenic acid (C:22:0), and tricosylic acid (C23:0), monounsaturated fatty acid (MUFA): elaidic acid (C18:1n9t) and paullinic acid (C20:1); polyunsaturated fatty acid (PUFA): linoleic acid (C18:2n6c) and y-linolenic acid (C20:3n6). A gene expression analysis indicated that the GG genotype had the highest expression level. It could be concluded that the SNP g.50657948 T>G of the CYP2E1 gene could be used for candidate marker-assisted selection to improve the carcass and meat quality of Indonesian lamb.

The Association of Single Nucleotide Polymorphism -69T>G HSPA1A Gene with Bali Cattle Heat Tolerance I. Suhendro; J. Jakaria; R. Priyanto; W. Manalu; R. R. Noor
Tropical Animal Science Journal Vol. 45 No. 4 (2022): Tropical Animal Science Journal
Publisher : Faculty of Animal Science, Bogor Agricultural University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5398/tasj.2022.45.4.429

Heat shock protein plays an essential role in thermoregulatory during heat stress responses. This study aims to determine the association of single nucleotide polymorphism (SNP) -69T>G in the promoter region of the heat shock protein 70 member 1A (HSPA1A) gene on heat tolerance in Bali cattle. One hundred and sixteen heads of Bali cattle were collected from different locations such as Pangyangan, Bali Island; Serading, Sumbawa Island; and Sembalun, Lombok Island. The SNP was analyzed by genotyping using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), which used BstUI enzyme restriction. Physiological responses including respiration rate (Rr), rectal temperature (Tr), heart rate (Hr), heat tolerance coefficient (HTC), and blood glucose level (Glu) were measured. Association analysis was conducted using a general linear model by setting genotype, altitude, and sex as factors. The SNP -69T>G variant of HSPA1A gene found in this study were wild type (TT) with 144 bp & 498 bp; GG with 144, 236, & 262 bp; and TG with 144, 236, 262, & 498 bp. Bali cattle with the GG genotype had lower (p<0.001) Rr and HTC compared to the other genotypes. It could be concluded that physiological performances were lower at high altitudes, and the SNP -69T>G HSPA1A was associated with the physiological performances of Bali cattle. SNP -69T>G of HSPA1A could be utilized for candidate marker-assisted selection of Bali cattle to improve the performance of heat tolerance.

Haplotype and phylogenetic diversity using mitochondrial 12S rRNA gene marker in Bali cattle T. Suselowati; R. R. Noor; J. Jakaria
Journal of the Indonesian Tropical Animal Agriculture Vol 48, No 3 (2023): September
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.48.3.169-181

Bali cattle is one of Indonesia's original livestock genetic resources. The 12S rRNA can be used as a marker of genetic diversity, and until now, there has been no report on Bali cattle. The study was aimed to analyze the gene of mtDNA 12S rRNA to determine haplotype diversity and phylogenetics in Bali cattle populations of the eastern region of Indonesia. A total of 95 blood samples used consisted of three different populations which were Bali cattle, Ongole crossbred (PO) and Madura cattle as a comparison. This research was analyzed using PCR and sequencing methods. The data were analyzed using the cluster W method for estimating genetic distances, calculating diversity, and reconstructing phylogenetic trees using the MEGAX, DNAsP and Network. The genetic distance values ranged from 0.00200 to 0.01508, and the Haplotype diversity values ranged from 0.66000 to 0.91111. The nucleo-tide diversity values ranged from 0.00174 to 0.01673. There were 16 haplotypes found. The values of Gst, Nst and Fst were 0.00803, 0.07550, 0.07622; respectively. Based on the analysis, there were dif-ferences between Bali cattle from various populations, there were specific haplotypes. The 12S rRNA gene can be used as a genetic marker for diversity studies in Bali cattle and other cattle breeds although the diversity is low.

Analysis of CSN2 Exon 7 gene diversity and its association with Sapera goat milk composition G. Deviandini; R. R. Noor; E. Taufik; S. A. Asmarasari
Journal of the Indonesian Tropical Animal Agriculture Vol 48, No 3 (2023): September
Publisher : Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jitaa.48.3.161-168

Sapera goats, a crossbreed between Saanen and Etawa Grade goats, are known for their milk pro-duction and adaptability to the Indonesian climate. Genetic selection is necessary to improve the Sa-pera goat's milk quality and quantity. CSN2 gene is one of the genes that can affect the composition of goat milk. Therefore, this study aimed to identify the mutation points (SNPs) at the CSN2 exon 7 gene and its association with Sapera goat's milk composition. This study used sixty-six blood and milk sam-ples of Sapera goats collected from the Livestock Research Center, Ciawi. This study found two muta-tion points (SNPs) at g.8946C>T and g.8956G>A. The association analysis showed that SNP g.8946C>T was significantly associated with the lactose and salt content of Sapera goat's milk. In con-clusion, SNP g.8946C>T can be used as a genetic marker to improve the composition of Sapera goat milk with high lactose and salt content.

Identification of single nucleotide polymorphism c.957A>C of PLAG1 gene and its association with growth traits in Bali cattle I. G. R. Putra; D. A. Sari; S. M. Rachmawati; R. Oktaviani; R. R. Noor; J. Jakaria
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 S. N. Karimah; R. R. Noor; J. Jakaria
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 Y. G. M. Bonawati; I. Suhendro; J. Jakaria; R. R. Noor
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.

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