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All Journal Tarjih Tropical Livestock Journal
Sari, Apriliana Putri Zahara Nafsina Luvita
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Agriculture, Biological Sciences & Forestry Veterinary

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First Screening of Heat Shock 70kDa Protein 1A (HSPA1A) Gene Polymorphisms in Indonesian Local Sheep Sari, Apriliana Putri Zahara Nafsina Luvita; Ibrahim, Alek; Tribudi, Yuli Arif; Maulana, Yasin Pradana
Tarjih Tropical Livestock Journal Vol. 4 No. 2 (2024): Tarjih-Tropical Livestock Journal
Publisher : Program Studi Peternakan Fakultas Sains dan Teknologi Universitas Muhammadiyah Sinjai

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.47030/trolija.v4i2.862

Abstract

Heat shock proteins (HSPs) are a collection of proteins that promote thermotolerance in cells and protect against environmental stress. This study was a preliminary analysis to identify the nucleotide variant within the partial heat shock 70kDa protein 1A (HSPA1A) gene in several Indonesian sheep breeds. The blood samples were collected from five breeds of Indonesian sheep (Sapudi, Batur, Sakub, Wonosobo, and Garut) to be analyzed and amplified using a specific primer. The sequences were aligned using Clustal Omega to identify the single nucleotide polymorphism (SNP). An ExPasy program was used to detect the amino acid changes. The genotyping was done by direct examination of the peak of the electropherogram. As a result, based on the sequence alignment and direct observation of the electropherograms, three variants were found: SNP c.286A>G, c.503A>G, and c.733A>G. All SNPs were categorized as synonymous mutations since they did not alter the amino acid. The genotyping of samples showed two types of genotypes (AG and GG) from each SNP. In conclusion, our study suggests exploring other regions of the HSPA1A gene to find candidate mutations for further genetic analysis.
Identification of Single-Nucleotide Polymorphism, Linkage Disequilibrium, and Restriction Enzyme Analysis of the Growth Hormone Gene in Kampung Super Chicken Sari, Apriliana Putri Zahara Nafsina Luvita; Maharani, Dyah; Febrianto, Firman; Maulana, Yasin Pradana; Tribudi, Yuli Arif
Tarjih Tropical Livestock Journal Vol. 5 No. 1 (2025): Tarjih Tropical Livestock Journal
Publisher : Program Studi Peternakan Fakultas Sains dan Teknologi Universitas Muhammadiyah Sinjai

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.47030/trolija.v5i1.936

Abstract

This study aimed to investigate single-nucleotide polymorphisms (SNPs) and haplotype diversity within the growth hormone (GH) gene of Kampung Super chickens, a hybrid breed derived from KUB males and commercial layer hens. In this study, thirty-eight blood samples of Kampung Super chicken were collected and analyzed. A total of 11 SNPs were identified within intronic regions of the GH gene. Despite their non-coding location, these variants may influence gene regulation through mechanisms such as alternative splicing, mRNA transport, or chromatin accessibility. Linkage disequilibrium (LD) analysis revealed several strong associations among SNP pairs, indicating the presence of conserved haplotype blocks potentially under stabilizing selection. In silico restriction enzyme analysis showed that five SNPs displayed three genotypic classes, and four of them could be effectively genotyped using PCR-RFLP, while one SNP (g.3018G/A) lacked suitable restriction sites. The SNP g.3094C/T exhibited high diagnostic potential using multiple enzymes (StuI, MspI, XmaI), while g.3129A/T was distinguishable using TaqI, although the adjacent SNP overlap limited interpretability. Two SNPs (g.3261C/T and g.3268G/A) were digestible by enzymes with multiple cut sites, complicating gel-based resolution. These findings provide a foundation for future functional and association studies and support the use of GH gene polymorphisms in marker-assisted selection strategies for growth-related traits in Kampung Super chicken.
Co-Authors Alek Ibrahim Dyah Maharani Febrianto, Firman Maulana, Yasin Pradana Yuli Arif Tribudi