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All Journal Jurnal Agripet Jurnal Ilmu Ternak dan Veteriner Animal Production : Indonesian Journal of Animal Production
Isyana Khaerunnisa
National Research And Innovation Agency (BRIN)
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Environmental Science Veterinary

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The Ghrelin Receptor (Ghsr) Gene Polymorphism in Indonesian Local Chicken and Crossbreed Is Associated With Carcass Traits Khaerunnisa, Isyana; Jakaria, Jakaria; Arief, Irma Isnafia; Budiman, Cahyo; Sumantri, Cece
ANIMAL PRODUCTION Vol 19, No 2 (2017)
Publisher : Universitas Jenderal Soedirman, Faculty of Animal Science, Purwokerto-Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (943.521 KB) | DOI: 10.20884/1.jap.2017.19.2.596

Abstract

Ghrelin receptor (GHSR) gene is candidate gene for growth performance in chicken by modulating growth hormone release from the pituitary by binding to its ligand of ghrelin. Ghrelin gene, or growth hormone secretagogue (GHS) gene, is well known as feed intake and energy homeostasis regulator in mammals and birds. The objectives of this study were to identify the polymorphism of the T1857C GHSR locus in Indonesian local chicken and to evaluate its effects on carcass traits. The gene polymorphism was identified using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using Hin6I restriction enzyme. Effect of genotype on carcass composition was analyzed using SAS General Linear Model (GLM) procedure. The genotyping was performed on 343 individuals including Merawang, Pelung, Sentul, Kampung, broiler (strain Cobb, parent stock), F1 crossbred of Kampung x broiler (strain Cobb, parent stock), and F2 crossbred of Kampung x broiler (strain Cobb, parent stock). All individuals were successfully amplified and were resulted in a 470 bp PCR product. This locus was polymorphic with two alleles (T and C) and three genotypes (TT, CT, and CC). The T allele and TT genotype were predominant in all populations. Individuals with CT genotype were significantly had higher live weight at 26w, carcass weight, commercial cuts weights, and muscles weights than TT genotype in F2 crossbred of Kampung x broiler population. Association of the T1857C GHSR locus-polymorphism with chicken carcass composition has been described in Indonesian chicken, providing evidence that GHSR might be an important candidate gene for chicken carcass traits.
Indonesian River Buffalo Molecular Phylogeny Compared to Other Mammals Based on STAT1 Sequence Fuad Hasan; Armyn Hakim Daulay; Ferdy Saputra; Isyana Khaerunnisa
Jurnal Agripet Vol 22, No 1 (2022): Volume 22, No. 1, April 2022
Publisher : Agricultural Faculty

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.17969/agripet.v22i1.20889

Abstract

ABSTRACT. Genes differ in sequence, size, and functional domains among species. According to studies, STAT1 provides information on the rate of evolution that correlates with its function in the immune system. STAT1 is also considered a genetic marker for economic traits in mammals. Studying sequence comparison is an important issue in bioinformatic study and can explain phylogenetic. Therefore, this study aimed to identify the molecular phylogeny of river buffalo (Bubalus bubalis) and other mammals based on STAT1 gene sequences. This study used 7 STAT1 sequences from Ensembl (Bos grunniens, Bos indicus, Bos Mutus, Capra hircus, Cervus hanglu yarkandensis, Moschus moschiferus) and previous studies (Bubalus bubalis). The sequences were analyzed using the MEGA X 10.2.6 software to observe the nucleotide composition and the phylogeny (based on UPGMA). The adegenet package in the R 4.0.0 software is used to observe the STAT1 sequence dimensionally among mammals. The STAT1 sequence has almost similar diversity among the livestock of the same genus. Based on the STAT1 sequence, Bubalus bubalis has closer genetic proximity to the genus Bos than to another genus. In conclusion, we found STAT1 is more dynamic in evolution and more conserved and found in the similar related genus.  (Filogeni kerbau Indonesia dibandingkan mamalia lain berdasarkan runutan nukleotida gen STAT1) ABSTRAK. Gen berbeda dalam urutan, ukuran, dan domain fungsional di antara spesies. Menurut penelitian sebelumnya, STAT1 memberikan informasi tentang laju evolusi yang berkorelasi dengan fungsinya dalam sistem kekebalan. STAT1 juga dianggap sebagai penanda genetik untuk sifat bernilai ekonomi pada mamalia. Studi perbandingan urutan merupakan isu penting dalam studi bioinformatika dan dapat menjelaskan filogenetik. Oleh karena itu, penelitian ini bertujuan untuk mengidentifikasi filogeni molekuler kerbau sungai (Bubalus bubalis) dan spesies mamalia lain berdasarkan sekuens gen STAT1. Penelitian ini menggunakan 7 sekuen STAT1 yang diambil dari Ensembl (Bos grunniens, Bos indicus, Bos mutus, Capra hircus, Cervus hanglu yarkandensis, Moschus moschiferus) dan penelitian sebelumnya (Bubalus bubalis). Sekuen dianalisis menggunakan program MEGA X 10.2.6 untuk melihat komposisi nukleotida dan filogeni (berdasarkan UPGMA). Adegenet package dalam program R 4.0.0 digunakan untuk mengamati urutan STAT1 secara dimensional diantara mamalia. Sekuen STAT1 memiliki keragaman yang hampir sama di antara ternak dari genus yang sama. Berdasarkan sekuen STAT1, Bubalus bubalis memiliki jarak genetik yang lebih dekat dengan genus Bos dibandingkan dengan genus lainnya. Sebagai kesimpulan, kami menemukan STAT1 lebih dinamis dalam evolusi dan lebih terkonservasi serta ditemukan dalam genus terkait yang serupa.
Avian Beta Defensin 2 (AvBD2) Gene Polymorphism Identification in IPB-D1 Chicken Masrurah Masrurah; Isyana Khaerunnisa; Sri Murtini; Cece Sumantri
Jurnal Ilmu Ternak dan Veteriner Vol 26, No 2 (2021): June 2021
Publisher : Indonesian Center for Animal Research and Development (ICARD)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14334/jitv.v26i2.2715

Abstract

Avian Beta Defensin 2 (AvBD2) gene, which is located in chromosome 3, plays an important role in the immune system of the chicken by inhibiting the development of microorganisms such as bacteria that infect body tissues. Defensins are produced through epithelial cells immediately after tissue injury or infection, which then processes the maturation of dendritic cells to initiate an immune response in the lymph nodes. The purpose of this study was to discover the polymorphism of the AvBD2 gene in IPB-D1 chickens. PCR and direct-DNA sequencing methods were used to identify the diversity of intron 1, exon 2, and intron 2 AvDB2 genes in 47 chickens. Genotype and allele frequency, and heterozygosity calculations were carried out to obtain information of the AvBD2 gene polymorphism. A total of 10 single nucleotide polymorphisms were found in the AvBD2 gene located in intron 1 (g.4843T>A, g.4853G>A, and g.4859T>C), exon 2 (g.4881A>G, g.4889G>A, and g.5002C>T), and intron 2 (g.5075C>T, g.5111T>G, g.5116G>T, and g.5177G>T). All SNPs are polymorphic. The g.5002C>T mutation causes changes in the amino acid Ala to Val which has the potential to be a candidate for characterizing disease resistance in IPB-D1 chickens.
Novel Mutation of Exon 5 Prolactin Gene in IPB-D1 Chicken Lailatul Rohmah; Sri Darwati; Niken Ulupi; Isyana Khaerunnisa; Cece Sumantri
Jurnal Ilmu Ternak dan Veteriner Vol 25, No 4 (2020): December 2020
Publisher : Indonesian Center for Animal Research and Development (ICARD)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14334/jitv.v25i4.2525

Abstract

The prolactin gene (PRL) is a gene that controls the incubation and egg production in laying chickens. The nature of incubation will reduce egg production and disrupt the reproductive system in local chickens. The purpose of this study was to identify the polymorphism of prolactin genes in IPB-D1 chickens using the direct sequencing method. The polymorphism of the exon 5 prolactin gene was carried out on 46 samples of IPB-D1 chicken DNA which was a collection of the Division of Animal Genetics and Breeding, Faculty of Animal Science IPB. DNA sequences as a reference for designing exon 5 primers were obtained from the National Center for Biotechnology Information (NCBI) with the GenBank access code: AF288765.2. DNA extraction was carried out using the phenol-chloroform technique. DNA amplification resulted in a PCR product with a size of 557 bp. In this study, the genotype frequency, allele frequency, heterozygosity value and Hardy-Weinberg equilibrium were calculated. The results of the study found 5 SNPs in exon 5, namely g.7823A>G, g.7835A>G, g.7886T>A, g.8052T>C, and g.8069T>C. All SNPs are polymorphic and in Hardy-Weinberg equilibrium except g.8052T>C. The g.7823A>G, g.7835A>G, g.8052T>C SNPs are synonymous mutations that do not change amino acids, while the g.7886T>A and g.8069T>C SNPs are non-synonymous that change amino acids. Both g.7886T>A and g.8069T>C SNPs are potential as a marker assisted selection for the characteristics of egg production in IPB-D1 chickens.
Polymorphisms of the Thy1 (Thymocyte Differentiation Antigen 1) Gene in Candidate IPB D2 Chicken Line Nensy Tri Putri; Sri Murtini; Niken Ulupi; Isyana Khaerunnisa; Cece Sumantri
Jurnal Ilmu Ternak dan Veteriner Vol 27, No 4 (2022): December 2022
Publisher : Indonesian Center for Animal Research and Development (ICARD)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14334/jitv.v27i4.3029

Abstract

The Thy1 gene is a member of the immunoglobulin superfamily, which is found in many different animals. This gene encodes a Thy1 protein (CD90) which measures 25–37 kDa. Although the function of the Thy1 gene is unknown, it is thought to play a crucial role in the immunological response, particularly in the activation of T cells. The goal of this study was to find a variation in the Thy1 gene in IPB D2  chickens that might be utilized as candidates for immunoresistance genetic markers. A total of 123 samples from IPB D2 chickens consisting of 38 samples from IPB D2 G0 (basic generation) chickens and 85 samples from IPB D2 G2 (second generation) chickens were used in this study. PCR methods and direct-DNA sequencing were used in this study. Data analysis in this study consisted of genotype frequency, allele frequency, observed heterozigosity, expected heterozygosity, and Hardy-Weinberg equilibrium. The results of the study  discovered two SNPs on the intron (g.2139 CT and g.2542 AG). Four haplotypes were created by combining two SNPs. The g.2139 CTand g.2542 AG were polymorphic, but not in the Hardy-Weinberg equilibrium.
Co-Authors Armyn Hakim Daulay Cahyo Budiman Cece Sumantri Ferdy Saputra Fuad Hasan Irma Isnafia Arief Jakaria Jakaria Lailatul Rohmah Masrurah Masrurah Nensy Tri Putri Niken Ulupi Sri Darwati sri murtini .