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A. Gunawan
Department of Animal Production and Technology, Faculty of Animal Science, IPB University
Agriculture, Biological Sciences & Forestry Energy

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Acetyl-CoA Carboxylase Alpha Gene Polymorphism and Its Association with Milk Fatty Acid of Holstein Friesian Using Real-Time PCR Method R. Azis; Jakaria; A. Anggraeni; A. Gunawan
Tropical Animal Science Journal Vol. 43 No. 4 (2020): 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.2020.43.4.306

Abstract

Milk fatty acids are largely affected by genetic factors. Acetyl-CoA Carboxylase Alpha (ACACA) gene is one of the important genes in regulation and metabolic function of milk fatty acids in dairy cattle. The objective of this study was to find out the relationship of single nucleotide polymorphism (SNP) ACACA gene with milk fatty acid trait in local dairy cattle. A total of 277 samples of Holstein Friesian (HF) were collected from Indonesian Research Institute for Animal Production (IRIAP), Animal Breeding Center and Forage Feed of Baturraden (ABCFFB), Central Java Province, Animal Husbandry Training Center of Cikole (AHTCC), West Java Province, Singosari Artificial Insemination Station (Singosari AIS), East Java Province, and Lembang Artificial Insemination (Lembang AIS), West Java Province, Indonesia. Genotyping of this SNP marker (g.2203G>T) was analyzed using the real-time Polymerase Chain Reaction (PCR) based on the hybridization TaqMan probe as the method for allelic discrimination. Milk samples were analyzed using Gas Chromatography and Mass Spectrometry (GCMS). The results of this study revealed the GG and GT genotypes. The proportion of the GG genotype frequency (0.88) was higher than the GT genotype (0.11) and the G Allele frequency was shown higher than the T allele in all locations, i.e., 0.942 and 0.08, respectively. The ACACA gene g.2203G>T SNP was significant (p<0.05) for lauric (C12:0) and dodecanoic (C17:1) acids. It was concluded that the ACACA gene g.2203G>T SNP could be useful as a marker selection for milk fatty acid such as lauric and dodecanoic fatty acids.
Characteristics and Potential Production of Frozen Semen of Pasundan Bull Santoso Santoso; Herdis Herdis; R. I. Arifiantini; A. Gunawan; C. Sumantri
Tropical Animal Science Journal Vol. 44 No. 1 (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.2021.44.1.24

Abstract

Pasundan cattle are one of the Indonesian domestic resources of animal-genetic materials that need to be developed and conserved. The aims of this study were to evaluate the characteristics of sperm and the potential production of frozen semen of Pasundan bulls. Ten Pasundan bulls were divided into two groups based on their fresh sperm motilities. Pasundan bulls were grouped based on their sperm motilities into group A (70-79%) and group B (80-89%). Secondary data were collected and confirmed with the primary data. The semen volume, pH, color, consistency, mass movement, sperm concentration, motility, viability, membrane integrity, abnormality, and DNA integrity of fresh semen were evaluated. The semen was then diluted, frozen, and stored at -196°C. The results showed that the pH of the fresh semen in group B was lower (p<0.05) than group A. Sperm concentration per ejaculate showed no difference with a range of 4312.36x106 to 6303.52x106. The viability and DNA integrity of fresh semen were not different between group A (84.41±0.99%; 91.19±0.79%) and group B (86.35±2.16%; 92.58±0.35%). DNA integrity of frozen semen of group B (89.81±1.18%) was higher (p<0.05) than that of group A (86.83±0.60%). The sperm motility of frozen semen of group A (<40%) was lower compared to SNI number 4869-1:2017. The frozen semen production of Pasundan bulls was between 144.18 to 191.29 straws/ejaculate. In conclusion, only bulls from fresh-semen sperm motility 80%-89% (group B) are eligible to be used as a semen source for artificial insemination.
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

Abstract

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.
Variation and Association of Avian β-Defensin 2 Gene with the Concentration of Immunoglobulin Y and the Titer of Newcastle-Disease Antibody in IPB-D1 Chicken D. Lestari; Masruroh; I. Khaerunnisa; S. Murtini; N. Ulupi; A. Gunawan; C. Sumantri
Tropical Animal Science Journal Vol. 45 No. 2 (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.2022.45.2.121

Abstract

Defensins play roles in innate immunity by exhibiting antimicrobial activity against microbes such as gram-negative and -positive bacteria, viruses, and fungi. This study aimed to identify variants of the Avian β-Defensin 2 (AvBD2) and determine their associations with the concentration of immunoglobulin Y and the titer of Newcastle disease (ND) antibody in IPB-1 chicken. The chicken population used in this study was 21-week-old IPB-D1 chickens (n=90). Variations in AvBD2 were analyzed by direct DNA sequencing. IgY concentration was measured by indirect ELISA, and the titer of ND antibody was measured by the hemagglutination-inhibition test. The AvBD2 association was analyzed by the general linear model procedure and Duncan’s multiple range test. The results revealed 10 SNPs located in intron 1 (3 SNPs), exon 2 (3 SNPs), and intron 2 (4 SNPs). Six of these SNPs were associated with IgY concentration. The CC genotype of g.5002 C>T was associated with IgY concentration and produced the highest mean IgY concentration. This g.5002 C>T mutation results in alanine-to-valine substitutions. The CC genotype of g.5002 C>T could be considered as a criterion for selecting chickens with high IgY concentrations.
Genetic Association and Expression of JHDM1A Gene Related to Meat pH in Commercial Pigs A. Kayan; S. Theerawatanasirikul; P. Lekcharoensuk; C. Boonkaewwan; A. Kaewkot; M. Chanaksorn; C. Tantikositruj; A. Gunawan
Tropical Animal Science Journal Vol. 45 No. 2 (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.2022.45.2.128

Abstract

An experiment was conducted to study the association and expression of JHDM1A gene as a candidate gene for meat quality. The polymorphism was genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using restriction enzyme on a total of 300 muscle samples of [Duroc × (Large White × Landrace)] pigs. Results showed that JHDM1A gene was significantly associated with meat pH 45 min post-mortem (p.m.) (p<0.05). Allele frequencies for G and C were 0.53 and 0.47. The genotype frequencies for GG, GC, and CC were 0.24, 0.58, and 0.18, respectively. The Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR) study were analyzed between low and high pH 45 min p.m. groups (n=10 per group) according to the association result. JHDM1A expression was higher in animals with a low post-mortem meat pH 45 min (p<0.05). Therefore, polymorphism and expression in the porcine JHDM1A gene might be the important candidate genes to improve meat quality traits in terms of meat pH.
Differential Expressions of Protamine 1 (PRM1) and Protamine 2 (PRM2) Genes as Markers of Semen Quality in Pasundan Bulls Santoso; A. Gunawan; C. Sumantri; R. I. Arifiantini; Herdis
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.2022.45.4.423

Abstract

Several gene expressions are related to the success of spermatogenesis. Protamine plays an important role in sperm DNA packaging, spermatogenesis, and sperm quality. This study aimed to isolate RNA from spermatozoa and determine the gene expression profiles of protamine 1 (PRM1) and protamine 2 (PRM2). Six Pasundan bulls aged 5-8 years with a body weight of 380 kg-430 kg were used for this study. The Pasundan bulls were classified into group A (70%-79%) and group B (80%-89%) based on their sperm motility in fresh semen. In this study, correlation analysis was performed between fresh semen characteristics (volume, motility, concentration, abnormality, viability, intact plasma membrane (IPM), DNA integrity) and frozen semen characteristics after thawing (motility, viability, IPM, and DNA integrity). Total RNA was isolated from the frozen sperm pellet, and cDNA was synthesized. Specific PCR primers were used for the transcription of PRM1 and PRM2 from sperm. PRM1 and PRM2 gene expressions were evaluated by qRT-PCR, and ACTB was used as a control. The results showed that progressive sperm motility in the fresh sperm positively correlated with sperm viability and IPM. PRM1 and PRM2 were higher (p<0.05) in group B than in group A. This condition indicates the existence and influence of protamine on the parameters of progressive sperm motility. The expression of PRM1 and PRM2 genes could use as markers of semen quality in Pasundan bulls.
Association and Expression of Cluster of Differentiation 4 (CD4) Gene in IPB-D2 Chicken Related to Immunocompetence Index D. Lestari; S. Murtini; N. Ulupi; A. Gunawan; C. Sumantri
Tropical Animal Science Journal Vol. 46 No. 3 (2023): 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.2023.46.3.287

Abstract

The CD4 gene plays an important role in the immune process by producing CD4 molecules that aid in producing antibodies. IPB-D2 chickens are selected from IPB-D2 chickens based on IgY concentration and ND antibody titer. This study aimed to analyze the polymorphism of the CD4 gene, unravel the mRNA expression of CD4 gene in IPB-D2 chicken related to the immunocompetence index, and detect the CD4 gene pathway. The total samples used were 100 IPB-D2 G2 chickens aged 21 weeks. Blood samples were collected for ELISA test, HI test, sequencing test, and seca tonsil tissue for relative mRNA expression. Polymorphism and association data were analyzed using MEGAX, FinchTV, SNPstat, and DNAsp. The relative mRNA expression analysis was conducted using qRT-PCR. The pathway analysis of the CD4 gene was performed using the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis. The result showed there were 4 SNPs of the CD4 gene in IPB-D2 chicken, i.e., g.7526 C>T, g.7825 C>T, g.8100 C>A, and g.8157 T>A. All CD4 SNPSs showed no association with IgY concentration and ND antibody titers. Relative mRNA expression shows that IPB-D2 chickens with high ND antibody titers have a higher level of expression when compared to IPB-D2 chickens with low ND antibody titers. Furthermore, pathway analysis showed the CD4 gene involved in the T cell receptor (TcR) signaling process. This study concludes that the CD4 gene is polymorphic and involved in the T cell receptor signaling process. This study demonstrated that polymorphisms of the CD4 gene in IPB-D2 chicken might not contribute to the IgY concentration and ND antibody titer but can serve as a reference in the study of CD4 genes in the other chicken breeds related to the other immunocompetence index.
Co-Authors A. Anggraeni A. Kaewkot A. Kayan Azis, Rosidi C. Boonkaewwan C. Sumantri C. Tantikositruj D. Lestari Herdis Herdis Herdis I. Khaerunnisa Jakaria Jakaria M. Chanaksorn Masruroh N. Ulupi P. Lekcharoensuk R. I. Arifiantini R. I. Arifiantini R. R. Noor R. S. Harahap S. Murtini S. Murtini S. Theerawatanasirikul Santoso Santoso Santoso