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Polymorphisms and Associations of the NRAMP-1 and iNOS Genes on Newcastle Disease and Salmonella enteritidis Resistances in SenSi-1 Agrinak Chickens M. Ardiyana; A. Gunawan; S. Murtini; T. Sartika; C. Sumantri
Tropical Animal Science Journal Vol. 43 No. 2 (2020): Tropical Animal Science Journal
Publisher : Faculty of Animal Science, Bogor Agricultural University

NRAMP-1 and iNOS genes were reported to be associated with a defense mechanism against bacteria and virus infections. This study aimed to identify NRAMP-1 and iNOS genes polymorphisms and their associations with the defense mechanisms against Salmonella enteritidis and Newcastle Disease (ND) in SenSi-1 Agrinak chicken. The present study used a total number of 172 SenSi-1 Agrinak chicken. Identifications of NRAMP-1 and iNOS genes polymorphisms were performed by PCR-RFLP method. NRAMP-1 and iNOS genotypes were associated with immunoglobulin Y (IgY) concentration, specific antibodies against S. enteritidis and ND using General Linear Model (GLM). Immunity characteristics were further grouped into high, medium, and low categories. NRAMP-1|SacI exon 11 and iNOS|AluI intron 24 in SenSi-1 Agrinak chickens were polymorphic. TC genotype has a higher immune response to infectious agents compared to TT and CC genotypes. The frequency of C allele was higher than the T allele in the concentration of immunoglobulin Y (IgY), antibodies titers against S enteritidis and ND. The TC genotype of NRAMP-1 gene was significantly associated with ND antibody titers, and the TT genotype of iNOS was significantly associated with S. enteritidis specific antibody. NRAMP-1 and iNOS genes can be used as potential candidate genes for immune traits in SenSi-1 Agrinak chickens.

Genetic Variation of Eight Indonesian Swamp-Buffalo Populations Based on Cytochrome b Gene Marker M. Rusdin; D. D. Solihin; A. Gunawan; C. Talib; C. Sumantri
Tropical Animal Science Journal Vol. 43 No. 1 (2020): Tropical Animal Science Journal
Publisher : Faculty of Animal Science, Bogor Agricultural University

Genetic variation is a major concern in animal genetic resources conservation program. This study aimed to analyze genetic variation and phylogeography of eight Indonesian swamp-buffalo populations based on cytochrome b gene marker. A total of 78 DNA fragment samples originating from eight Indonesian swamp-buffalo populations were used in this study, namely Bombana Island, Bombana mainland, Kolaka, Konawe, North Toraja, West Nusa Tenggara, Banten, and Aceh with 11, 10, 13, 14, 10, 10, 5, and 5 samples, respectively. The cytochrome b gene sequence and genetic variation parameters were analyzed in MEGA software (ver 6), and DnaSP software (ver 5.10.01). The results of this study showed that all DNA-fragment samples were successfully amplified by PCR technique with the size target (906 bp). Based on the distribution of all samples, it was found 9 polymorphic sites, and 10 haplotypes with the haplotype diversities were 0.6590. The average of genetic distances between populations ranged from 0.0000-0.002. They were grouped into two main clusters. The first cluster consisted of Aceh, North Toraja, West Nusa Tenggara, Banten, Kolaka, and Konawe populations, meanwhile, the second cluster consisted of Bombana Island, Bombana mainland, Kolaka, and Konawe populations. The results of the study were concluded that eight Indonesian local swamp-buffalo populations were grouped into two main clusters where Bombana Island and Bombana mainland populations were specific breeds because they were only found in the second cluster and also had specific nucleotides sites on the 57 nucleotides which C base changed to T. The results of this study were useful in formulating the program of conservation and utilization of Indonesian buffalo genetic resources, especially in the buffalo population with specific breeds.

Genetic Diversity of Indonesian Swamp Buffalo Based on Microsatellite Markers F. Saputra; Jakaria Jakaria; A. Anggraeni; C. Sumantri
Tropical Animal Science Journal Vol. 43 No. 3 (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.2020.43.3.191

Indonesia has high genetic resources of local swamp buffalo with good adaptation across regions. However, these animals decline in both population and genetic quality. This research was conducted to study the genetic diversity of Indonesian swamp buffalo. A total of 199 DNA samples (swamp buffalo) from seven provincial populations were used in this study. Genetics identification used three microsatellite markers (CSSM66, ILSTS61, and ILSTS17). Microsatellites were visualized by Polyacrylamide Gel Electrophoresis (PAGE) 10% with silver staining method. Microsatellite data were analyzed using GenAlEx 6.41, Cervus 3.0, and POPTREE2 software. The results showed that a total of 9 alleles were found from the three loci. ILSTS61 had a high PIC (Polymorphism Information Content) compared to the other loci. The high observed heterozygosity of ILSTS61 was found in swamp buffalo from Riau Province, while the Ho value of ILSTS17 ranged from 0.000 to 0.170. This study identified two clusters for Indonesian swamp buffalo, i.e., cluster I (Aceh, North Sumatra, and Riau) and cluster II (Banten, Central Java, West Nusa Tenggara, and South Sulawesi). The two major divergent directions are considered in Indonesia swamp buffaloes across the observed provinces.

Polymorphism of CD1B Gene and Its Association with Yolk Immunoglobulin (IgY) Concentration and Newcastle Disease Antibody Titer in IPB-D1 Chicken M. F. Al-Habib; S. Murtini; A. Gunawan; N. Ulupi; C. Sumantri
Tropical Animal Science Journal Vol. 43 No. 3 (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.2020.43.3.197

The CD1B gene has an important role in the immune system of poultry by mediating antibody induction. The study aimed to identify the CD1B gene polymorphism and its association with the concentration of IgY and ND antibody titers in IPB-D1 chicken. As many as 111 of IPB-D1 chickens at 21 weeks old were used in this study. Polymorphism identification of the CD1B gene was made using the PCR Sequencing method, while the IgY and ND antibody titers were done using the ELISA and HI test, respectively. The associations of gene polymorphism with IgY and ND antibody titers were analyzed using the General Linear Model (GLM) procedure and Duncan`s Multiple Range test. The results show that there are 4 SNPs in exon 3, i.e., c.550 G>A, c.562 T>A, c.588 A>G, and c.612 C>G. All the SNPs are missense, silent mutations, and polymorphic. The c.550 G>A and c.562 T>A SNPs were in Hardy Weinberg’s equilibrium and heterozygosity (0.054-0.252) condition, while the c.588 A>G and c.612 C>G SNPs were not in equilibrium and their heterozygosity was low (0.072-0.252). The combination of 4 SNPs generated 8 haplotypes, i.e., haplotypes 1, 2, 3, 4, 5, 6, 7, and 8. Haplotypes 1, 2, and 8 had high frequencies (17.6%-23.5%). The c.588 A>G and c.612 C>G mutations were significantly associated (p<0.05) with IgY concentration and c.562 T>A were significantly associated (p<0.05) with ND antibody titers. The haplotypes 2 and 8 with a combination of c.588 A>G and c.612 C>G mutations had higher IgY concentration and ND antibody titers (p<0.05) compared to the other haplotypes. In conclusion, this study has identified the CD1B gene as a polymorphic and is associated with IgY concentration and ND antibody titers in IPB-D1 chicken.

Association between GH (g.1456_1457insT), GHRH (g.4474 C>A), and Pit-1 (g.244G>A) Polymorphisms and Lactation Traits in Holstein Friesian Cattle A. Anggraeni; C. Sumantri; F. Saputra; L. Praharani
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.2020.43.4.291

Lactation traits are controlled by many genes, among others, potentially by growth genes. This research was conducted to study genetic polymorphisms of GH, GHRH, and Pit-1 genes and associations of GH (g.1456_1457 InsT), GHRH (g.4474 C>A), and Pit-1 (g.244 G>A) genotypes with milk yield and quality in Holstein Friesian (HF) cattle. Genotyping was conducted for HF dairy cows raised by small farmers from North Lembang (SF-NL) (98 heads) and South Lembang (SF-SL) (95 heads), and also from Cikole Dairy Cattle Station (CDCS) (82 heads) in Lembang, West Java, Indonesia. Progeny tested of HF bulls (17 heads) from LAIC (Lembang Artificial Insemination Center) in West Java and from SAIC (Singosari AIC) (32 heads) in East Java were also genotyped. Effects of genotypes on test day milk yield, fat content, and SNF content were analyzed by General Linear Models. The GHRH g.4474 C>A SNP and Pit-1 g.244 G>A SNP generated high frequencies of C allele to A allele, while the two allelic frequencies of the GH g.1456_1457 InsT varied. Compared to the AA and AC genotypes, the CC genotype of the GH gene resulted higher test day milk yield (p<0.01), fat content (p<0.05), and SNF content (p<0.05). Further the CC genotype of the GHRH gene yielded higher milk yield (p<0.05), while the GG genotype of the Pit-1 gene resulted higher fat content (p<0.05). Therefore the GH g.1456_1457 InsT, GHRH g.4474 C>A SNP, and Pit-1 g.244 G>A SNP are potential to be used as molecular markers for selection on milk yield and quality in domestic HF cattle.

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

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.

Haplotype Diversity of Swamp Buffalo and River Buffalo Based on Cytochrome B Gene: A Study of Meta-Analysis F. Saputra; A. Anggraeni; A. B. L. Ishak; A. Hafid; M. Rusdin; C. Sumantri
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.2021.44.4.399

Buffalo (Bubalus bubalis) is well known as a domesticated buffalo in Asia. The genetic diversity of buffaloes in Asia needs to be studied to ensure a proper breeding program. A meta-analysis study on the cytochrome b gene of the mitochondrial genome from various published data was conducted to evaluate genetic variation and haplo-geography of Asian buffaloes. A meta-analysis is used to provide a comprehensive view of the data. A total of 1369 swamp buffaloes Cytochrome B sequences (from Indonesia (79), Bangladesh (98), China (909), India (4), Laos (96), Taiwan (29), Thailand (54), and Vietnam (100)) and 91 river buffaloes (from China (42), Nepal (42), and Pakistan (7)) were used in this study. Cytochrome B sequences (678 bp) of Syncerus caffer, Bubalus arnee, Bubalus depressicornis, Bubalus quarlesi, Bubalus mindorensis, swamp buffalo, and river buffalo were determined for their haplotypes using DnaSP v6 program. Haplotypes were analyzed by Principal Coordinate Analysis (PCoA) using Adegenet Package and Hierarchical Clustering on Principal Components (HCPC) methods using Factoextra and FactoMineR Package in R-4.0.0 program. Bayesian analysis of genetic differentiation was implemented in BAPS 6.0. Furthermore, we found 56 haplotypes for swamp buffaloes in eight Asian countries and 5 haplotypes for river buffaloes in Pakistan. We also found 5 haplotypes for outgroup (B. arnee, S. caffer, B. depressicornis, B. quarlesi, B. mindorensis). Therefore, we found 66 haplotypes in total with outgroup sequences. Based on the PCoA results, three clusters were found. However, the HCPC found eight clusters. Based on HCPC, countries in East and South Asia have four maternal lineages. This is evidence that buffalo domestication has first occurred in East-South Asia. In conclusion, we found four maternal lineages of swamp buffalo and two maternal lineages of river buffalo from ten countries. We also found one maternal lineage for Syncerus caffer and one maternal lineage for B. depressicornis, B. quarlesi, and B. mindorensis.

Synthetic Gene-Based Heterologous Expression, Proteolytic, and Structural Characterization of Caseinolytic Protease of Lactobacillus plantarum IIA-1A5 M. Yusuf; C. Budiman; I. I. Arief; C. Sumantri
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.2021.44.4.520

Genome sequence of Indonesian probiotic of Lactobacillus plantarum II1A5 contains a gene encoding a proteolytic subunit of caseinolytic protease, designated as ClpP_LP. This study aims to express the Clp gene heterological and apply its proteolytic activity to some livestock products. To address this, the gene encoding ClpP_LP was optimized in silico by improving its Codon Adaptation Index and GC content to 0.94 and 53.62%, respectively. The optimized gene was then inserted into pET28a, transformed into Escherichia coli BL21(DE3), and over-expressed by induction of 1 mM Isopropyl β-D-1-thiogalactopyranoside at 37°C. The result showed that ClpP_LP was successfully over-expressed in a fully soluble form with the specific activity towards milk casein was 7739.89 AU mg-1. This activity was significantly greater than that of chymotrypsin. Further, the three-dimensional model of ClpP_LP was built using SWISS MODEL, which showed that this protein formed a homo-tetradecameric (14-mer) structure with each monomer consisting of 7 α-helix and 10 β-sheets. The identification of the active side showed that the active side of ClpP_LP is Ser-97, His-122, Asp-171, and forms a substrate-binding cavity with a size of about 29.5 Ǻ. Overall, our approach can serve as an appropriate platform for the production of ClpP_LP in a large-scale production for various applications in dairy products and derivatives.

Polymorphism and Association of DMA Gene with Total IgY Concentration and ND Antibody Titer in IPB-D2 Chicken Line D. Lestari; S. Murtini; N. Ulupi; C. Sumantri
Tropical Animal Science Journal Vol. 45 No. 1 (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.2022.45.1.1

The DMA (DM α chain) gene, a member of non-classical MHC class II plays an important role in the process of presenting antigen peptides by producing DM protein. This study aimed to identify the polymorphism of DMA gene and their associations with disease resistance traits such as total IgY concentration and ND antibody titers in IPB-D2 chicken line. The total sample used was 101 chickens consisted of 81 IPB-D2 G0 chickens (53 female and 28 male) and 20 SENSI-1 chickens (15 female and 5 male). Blood samples were collected at 21 weeks old for genotyping, total IgY concentration analysis, and ND antibody titer analysis. SENSI-1 chickens were used as a comparison in the analysis of DMA gene polymorphism. The method for DNA polymorphism of DMA gene was direct-DNA sequencing. The total IgY concentration was analyzed using the indirect ELISA method, while the ND antibody titer used the HI test. Data were analyzed using GLM, genotypic, and haplotype mean values compared with t-test. The results showed that 4 SNPs were found, i.e., g.2328 G>A (exon 3), g.2503 A>G (intron 3), g.2612 G>A, and g.2686 G>A (exon 4). The SNPs of DMA gene were found polymorphic with three genotypes (GG, AG, and GG), and the expected SNP g.2503 A>G only had two genotypes (AA and GG). The g.2328 G>A was associated (p<0.05) with total IgY concentration. A combination of 4 SNPs formed 7 haplotypes. Haplotype 1 was associated with total IgY concentration (p<0.05), and haplotype 5 was associated with ND antibody titer (p<0.05). In conclusion, the g.2328 G>A mutation and haplotype 1 could be potentially recommended as a genetic marker for high total IgY concentration, and haplotype 5 could be potentially recommended as a genetic marker for ND antibody titer in IPB-D2 chicken line.

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

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.

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