Poultry, such as chickens, is an important source of animal protein, producing eggs and meat. Local chickens are able to adapt to the hot weather and become more resistant to disease. However, it has ...relatively slow growth and low egg production. These problems can be overcome through holding selection and crossing. Local chicken productivity is slow and low based on chicken growth. There is a need to examine the factors that influence growth and productivity. Therefore, this study aimed to evaluate crossbreed chicken growth performance, including body weight (BW), BW gain, feed intake, and feed conversion.
DNA was extracted from 40 chickens with the growth hormone (GH) gene and 40 chickens with the insulin-like growth factor 2 (IGF2) gene, followed by a polymerase chain reaction. Genotyping was performed using restriction fragment length polymorphism analysis. In animal selection and phenotypic data collection, 80 chickens from Sentul, Kampung, and Kedu were used to produce the second-generation three-crossbreed chickens (F2) using the GH gene.
Growth hormone is a very relevant gene in chicken performance traits. Growth hormone and IGF2 genes regulate chicken production. This study presents the second-generation growth features of three-crossbreed chickens derived from Sentul, Kampung, and Kedu, all of which are native to Indonesia (F2). A statistically significant (p = 0.05) improvement in BW, weight gain, feed intake, and feed conversion over a 12-week period was observed when the animals were allowed free access to regular feed. Analysis of variance results indicated a significant (p = 0.0001) interaction between the 12-week period and GH and IGF2 gene sensitivities of different chicken breeds.
Crossbreed chicken growth performance increased within 12 weeks. This study highlighted the need to improve the productivity and breeding of domestic crossbred chickens to contribute to the Indonesian conservation and genetic diversity program.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
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.
Myostatin plays a role in inhibiting skeletal muscle growth in vertebrates. This study aimed to investigate the full sequence of the myostatin gene in fast-growing and slow-growing chickens. Fast- ...and slow-growing chicken models were produced from F2 Kampung x broiler. The full sequence of the myostatin gene was identified using 24 pairs of primers covering about 8,000 bp. mRNA expression analysis of muscle tissue was performed to examine whether the expression levels of myostatin are affected by chicken lines, sex, or muscle type. The results showed 170 mutations in fast- and slow-growing chickens. One hundred and sixty-one of them are novel mutations. A total of five and twenty-two alleles were specific alleles found only in the fast-growing and slow-growing groups of chickens, respectively. There were no differences in amino acids and gene expression levels of myostatin between the fast- and slow-growing chickens. In summary, the results of this study showed that specific alleles for the fast-growing or slow-growing chicken groups were found, suggesting that these specific alleles potentially be used as genetic markers for muscle growth in chickens.
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.
Dudi D, Hilmia N, Khaerunnisa I, Mushawwir A. 2023. DGAT1 gene polymorphism and their association with fat deposition and carcass quality in Pasundan cattle of Indonesia. Biodiversitas 24: 4202-4208. ...The bovineAcyl-CoA: Diacylglycerol O-acyltransferase 1 (DGAT1) gene is crucial to milk and meat quality in cattle. The K232A DGAT1 mutation was broadly used as a milk and meat quality genetic marker. Pasundan cattle are Indonesian local cattle from West Java. These local cattle have adapted to the tropical environment, environmental factors are not obstructing their development. The DGAT1 gene polymorphism information and their contribution to fat deposition and carcass quality in Pasundan cattle is very limited. The objective of this study was to examine the genetic polymorphism of the K232A DGAT1 gene and its association with fat deposition and carcass quality in Pasundan cattle population. The gene polymorphisms were identified using PCR, and direct sequencing to discover a single nucleotide polymorphism (SNP). All sequencing results (ABI trace files) were analyzed in FinchTV, BioEdit, and Molecular Evolutionary Genetic Analysis (MEGA) 6.0. Genotyping was performed on 80 Pasundan cattle. In comparison, Ongole-Grade (n=5), Bali (n=2), Simmental (n=2), Limousin (n=2), Madura (n=2), and Pesisir (n=2) were also used in this study. Their association with fat deposition and carcass quality was evaluated on seven heads of AK genotype and 23 heads of KK genotype. According to the sequencing result, two SNPs were found at g.201G>A and g.202C>A, respectively. The K232A DGAT1 locus was polymorphic in Pasundan cattle population with the K and A allele frequencies of 0.956 and 0.044, respectively. In addition, DGAT1 gene polymorphisms are not associated with back fat thickness, longissimus dorsi area, rump area, and intramuscular fat.
Bali cattle (Bos javanicus) are a local breed from Indonesia with the potential for beef production, but its meat has been reported to be tough. This indicates that there is a need to develop various ...methods that can be used for assessment to improve the quality of the meat. One such method is muscle scoring (MS), which is often used to predict the amount of meat in the carcass from live animals, but the muscle microstructure contributing to the quality is often neglected. Therefore, this study aims to evaluate the correlation between the muscle score of Bali cattle and the quality of muscle microstructure in terms of myofibril morphometric and connective tissue composition using a histochemistry approach. The population consisted of 31 Bali cattle, and MS was performed by evaluating the muscle line using a range of 1 to 15. The three individuals with the highest scores (Hi) and the three with the lowest (Lo) were sampled for semitendinosus muscle microstructural observation. The results showed that cattle in the Hi group had a higher surface area of myofibril and sarcomere length, but had a significantly lower relative percentage of intramuscular collagen compared to others in the Lo group (p < 0.05). Generally, muscle score had a positive correlation with body weight, surface area of myofibril and sarcomere length. In all cattle, the fibres identified were similar, where the thick types were dominant in the epimysium and perimysium, followed by the thin variants. Furthermore, the endomysium prominently contained non‐fibrous or other types of fibre. This study can provide the basic data that can be used as a pilot for future studies of muscle score assessment in Indonesian cattle.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Sterol regulatory element-binding protein 1 (SREBP1) gene is a gene that encodes SREBP1, a family of transcription factors that have a key role in lipid homeostasis as well as fatty acid metabolisms. ...The present study aimed to detect the 84-bp indel polymorphism in the intron 5 of the SREBP1 gene (84-bp indel) in several cattle breeds in Indonesia. A total of 740 cattle of six breeds (Limousin, Simmental, Holstein-Friesian, Bali, Sumbawa, and Pasundan) from two National Artificial Insemination Centers (NAICs) and smallholder farmers were used in this study. The detection of 84-bp indel polymorphism was performed using the polymerase chain reaction (PCR) method and visualized through a gel agarose electrophoresis system. The study showed that the L allele (insertion-type) was common and is fixed in Holstein-Friesian, Bali, and Sumbawa cattle (1.00). Meanwhile, the S allele (deletion-type) was found in Limousin, Simmental, and Pasundan cattle with a frequency of 0.24, 0.16, and 0.01, respectively. The presence of the S allele in Pasundan cattle was only found in the form of the heterozygous LS genotype (0.03). In conclusion, the 84-bp indel of the SREBP1 gene was found to be polymorphic in Limousin, Simmental, and Pasundan cattle, but monomorphic in Holstein-Friesian, Bali, and Sumbawa cattle.
The prolactin (PRL) gene regulates the egg production and incubation in laying chickens. Local chickens' reproductive systems will disrupt as a result of the incubation period activity, and they will ...lay fewer eggs. This study aimed to determine the prolactin gene polymorphism in IPB-D1 hens and its relationship to egg production. The polymorphism of the exon 5 prolactin gene was examined on 112 samples of the IPB-D1 chicken DNA collection from the Division of Animal Genetics and Breeding, Faculty of Animal Sciences, IPB University. By performing the phenol-chloroform method, the genomic DNA was obtained. A polymerase chain reaction (PCR) product with a size of 557 bp was produced as a result of the DNA amplification. Three single-nucleotide sequences were discovered. Three single-nucleotide polymorphisms (SNPs), g.7835A
G, g.7886A
T, and g.8052T
C, were found in exon 5 of the PRL gene. Each mutation was polymorphic and in Hardy-Weinberg equilibrium. The point mutation g.8052T
C significantly impacted the egg production of IPB-D1 chickens, according to the SNP association analysis on egg production, and may serve as a marker to enhance the selection for the features of egg production in IPB-D1 chickens.
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.
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.
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