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IDENTIFIKASI KERAGAMAN GEN KALPASTATIN (CAST) PADA AYAM LOKAL INDONESIA (IDENTIFICATION OF POLYMORPHISM CALPASTATINE GENE IN LOCAL CHICKEN) Harahap, Ahmad Saleh; Sumantri, Cece; Ulupi, Niken; Darwati, Sri; Sartika, Tike
Jurnal Veteriner Vol 18 No 2 (2017)
Publisher : Faculty of Veterinary Medicine, Udayana University and Published in collaboration with the Indonesia Veterinarian Association

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (350.216 KB) | DOI: 10.19087/jveteriner.2017.18.2.192

Abstract

Calpastatin (CAST) gene is one of the genes that play a role in the process of tenderization of meat. CAST gene serves as an inhibitor of meat tenderness. The purpose of this study was to identify Single Nucleotide Polymorphisms (SNP) in the CAST gene of kampong chickens. A total of 61 kampong chickens used were used in the study including strain cobb, F1 of strain cobb-kampong, merawang, sentul, nunukan, and pelung, respectively. The method used is extracted DNA from blood samples, then amplified by Polymerase Chain Reaction (PCR) and then genotyping by DNA sequencing. The results showed that SNP was identified at position g.42988G> T in the intron 11 CAST gene of merawang chicken with genotype GG and GT. SNP was not identified in kampong chicken, strain cobb, F1 of strain cobb-kampong, sentul, nunukan, and pelung chicken, respectively. In conclusion, the intron 11 CAST gene region with 482 of product length of merawang chicken is polymorphic, whereas the other chicken species is monomorphic.   ABSTRAK Gen Calpastatin (CAST) merupakan salah satu gen yang berperan dalam proses keempukan pada daging. Gen CAST berfungsi sebagai inhibitor (penghambat) keempukan daging. Tujuan dari penelitian ini adalah mengidentifikasi Single Nucleotide Polymorphisms (SNP) gen CAST pada ayam kampung. Jumlah ayam yang digunakan 61 ekor ayam kampung, ayam strain cobb, F1 ayam strain cobb-kampung, ayam merawang, ayam sentul, ayam nunukan, dan ayam pelung. Metode yang dilakukan adalah ekstrasi DNA dari sampel darah, kemudian dilakukan amplifikasi menggunakan mesin Polymerase Chain Reaction (PCR) dan selanjutnya dilakukan genotiping melalui DNA sequencing. Hasil penelitian menunjukkan bahwa gen CAST intron 11 pada ayam pengamatan ditemukan SNP posisi g.42988G>T pada ayam merawang dengan genotip GG dan GT, sedangkan pada ayam kampung, ayam strain cobb, F1 ayam kampung dengan strain cobb, ayam sentul, ayam nunukan, ayam merawang dan ayam pelung tidak ditemukan SNP. Simpulan dari penelitian ini memperlihatkan gen CAST daerah intron 11 dengan panjang produk 482 pada ayam merawang bersifat polimorfik, sedangkan jenis ayam yang lain bersifat monomorfik.  
GENETIC POLYMORPHISMS OF THE CHICKEN ANTIVIRAL MX GENE IN A VARIETY OF INDONESIAN INDIGENOUS CHICKEN BREEDS Sulandari, Sri; Syamsul Arifin Zein, Moch; Astuti, Dwi; Sartika, Tike
Jurnal Veteriner Vol 10 No 2 (2009)
Publisher : Faculty of Veterinary Medicine, Udayana University and Published in collaboration with the Indonesia Veterinarian Association

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (165.533 KB)

Abstract

It has previously been demonstrated that a G/A Single Nucleotide Polymorphism (SNP) at nucleotideposition 1,892 of coding sequence of chicken Mx gene confers susceptibility/resistance to avian viral diseases.The aim of this study was to assess the geographical distribution of G/A alleles in relation to differentgenetic backgrounds of a wide range of chicken populations. Using Polymerase Chain Reaction- RestrictionFragment Length Polymorphism (PCR-RFLP) methods, 492 samples from 15 breeds of indigenous chickenpopulations from Java, Sumatera, Kalimantan and Sulawesi islands were genotyped. Allele and genotypefrequencies of each population were calculated. Deviations from Hardy-Weinberg equilibrium were testedand inbreeding coefficient FIS estimated. Overall, the susceptible allele G had a frequency of 37.27% whilethe resistant allele A had a corresponding frequency of 62.73%. No clear relation of the geographicaldistribution of the G/A alleles to genetic backgrounds was found. The distribution of this SNP acrosspopulations seems to be affected by genetic drift rather than selection.
Broodiness Trait of Chicken Through Molecular Investigation Sartika, Tike
WARTAZOA. Indonesian Bulletin of Animal and Veterinary Sciences Vol 15, No 4 (2005): DECEMBER 2005
Publisher : Indonesian Center for Animal Research and Development

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (757.769 KB) | DOI: 10.14334/wartazoa.v15i4.819

Abstract

Incubation behavior of Kampung chicken is associated with the cessation of egg laying, and intensity of broodiness trait depends on genetic and environmental factors such as breed, management system, type of cages and photo periodicity. In this review, broodiness trait was investigated through molecular analysis. The result of the study concluded that there are two hypothesis of genetic incubation behavior. Some authors agreed that the incubation behavior is controlled by a major gene sexlinked on the Z chromosome. The prolactin receptor (PRLR) gene is a candidate gene for broodiness trait on the Z chromosome. However, the expression of broodiness in White Leghorn and Bantam hens cannot be explained by differences in the amounts of PRLR mRNA in the transcription or gross structure of the PRLR gene. The other hypothesis concluded that the incubation behavior is controlled by a small number of dominant autosomal genes with no sex linkage. Prolactin promoter (PRLp) gene is the major gene autosomal as starting point to express prolactin gene on the 2 chromosome. Prolactin promoter gene could be represented by the broodiness bands. Genotype AA and AC is identified as the broody genotype and BB as the non broody genotype. Key words: Broodiness, prolactin receptor, prolactin promoter, Kampung chicken
Broodiness Trait of Chicken Through Molecular Investigation Sartika, Tike
Indonesian Bulletin of Animal and Veterinary Sciences Vol 15, No 4 (2005)
Publisher : Indonesian Animal Sciences Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (757.769 KB) | DOI: 10.14334/wartazoa.v15i4.819

Abstract

Incubation behavior of Kampung chicken is associated with the cessation of egg laying, and intensity of broodiness trait depends on genetic and environmental factors such as breed, management system, type of cages and photo periodicity. In this review, broodiness trait was investigated through molecular analysis. The result of the study concluded that there are two hypothesis of genetic incubation behavior. Some authors agreed that the incubation behavior is controlled by a major gene sexlinked on the Z chromosome. The prolactin receptor (PRLR) gene is a candidate gene for broodiness trait on the Z chromosome. However, the expression of broodiness in White Leghorn and Bantam hens cannot be explained by differences in the amounts of PRLR mRNA in the transcription or gross structure of the PRLR gene. The other hypothesis concluded that the incubation behavior is controlled by a small number of dominant autosomal genes with no sex linkage. Prolactin promoter (PRLp) gene is the major gene autosomal as starting point to express prolactin gene on the 2 chromosome. Prolactin promoter gene could be represented by the broodiness bands. Genotype AA and AC is identified as the broody genotype and BB as the non broody genotype. Key words: Broodiness, prolactin receptor, prolactin promoter, Kampung chicken
Nunukan Chicken: Genetic Characteristics, Phenotype and Utilization Sartika, Tike; Sulandari, Sri; Zein, M S A; Paryanti, Sri
Indonesian Bulletin of Animal and Veterinary Sciences Vol 16, No 4 (2006)
Publisher : Indonesian Animal Sciences Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (922.236 KB) | DOI: 10.14334/wartazoa.v16i4.843

Abstract

Nunukan chicken is a local chicken from East Kalimantan which spreads out in Tarakan and Nunukan Islands . The chicken has a specific buff color and Columbian type feather and also has very late feathering (VLF) trait . The Nunukan cocks and hens have no wing and tail primary feather; the tail feathers are short and fragile . The VLF trait is known to have association with a K gene on the Z chromosome. The chicken is efficient in protein metabolism . Sulfur amino acids (cystine and methionine) that needed for feather growth, could be utilized for meat and egg production . The egg production of Nunukan chicken was better than the Kampung chicken . The average of hen day, hen house and peak production of Nunukan chicken was 45 . 39.1 and 62%, respectively, while the Kampung chicken was 35 .9, 30 .9 and 48%, respectively . Based on genetic analysis, the external genotype characteristic of the Nunukan chicken is ii ce ss Idld pp. It means that the phenotype appearance of the Nunukan chicken was columbian and gold feathering type, yellow and white shank color and single comb type. This phenotype is similar to Merawang Chicken . The genetic introgression of the Nunukan chicken is affected by the Rhode Island Red with the genetic introgression value of 0.964 . Key words: Nunukan chicken, character, genetic; phenotype characteristics, utilization
Crossbreeding between male pelung and female selected native chicken at second generation (G2) Gunawan, Benny; Sartika, Tike
Indonesian Journal of Animal and Veterinary Sciences Vol 6, No 1 (2001)
Publisher : Indonesian Animal Sciences Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (124.002 KB) | DOI: 10.14334/jitv.v6i1.214

Abstract

  The experiment aimed to produce native chicken with faster growth rate that is to achieve body weight of more than 1 kg at 3 months of age. Three hundreds and thirty three crossbreeds (PK) day old chicken from the results of artificial insemination between male Pelung and second generation of selection of female native chicken, were used in this experiment. One hundred and eighty purebreds native chickens were also used as control population. They were put in grower cages with density of 10 birds per cage and each cage was treated as a single unit of replication. Feeds during experiment were given and divided into 3 phases that is Starter Feeds I (Protein 21% and Energy 3000 kcal/kg) for chicken between 0-21 days of age, Starter Feeds II (Protein 19% and Energy 2900 kcal/kg) for chicken between 22-42 days and Grower Feeds (Protein 17% and Energy 2900 kcal/kg) for chicken between 43-84 days. Variables which were recorded were weekly body weight until 12 weeks of age, feed consumption, feed conversion, mortality, carcass weight and simple economic ratio (B/C ratio). The results of the experiment showed that body weight at 12 weeks of crossbred (PK) was significantly higher than the pure native chicken (1000 vs 923 g) (P<0.05). Feed consumption was not significantly different (3037 vs 3036 g/bird/12 weeks), but the feed conversion of the crossbred was significantly better than the purebred (3.09 vs 3.4) (P<0.05). Carcass weight and carcass components were not significantly different between the two breeds, but they were different between sexes (P<0.05). Simple economic calculation showed that crossbreeds produced higher profit than purebreds with the benefit cost ratio were 1.31 for crossbred (PK) and 1.2 for purebred native chicken. The mortality rate during the experiment was low, that is 5.5% for crossbred and 6.36% for purebred.   Key words: Crossbreeding, male Pelung, female native chicken
Genetic relationships of Kampung, Pelung, Sentul and Black Kedu Chicken using Microsatellite DNA Markers: I. Lingkage group of macro chromosome Sartika, Tike; Iskandar, S; Prasetyo, L.H; Takahashi, H; Mitsuru, M
Indonesian Journal of Animal and Veterinary Sciences Vol 9, No 2 (2004)
Publisher : Indonesian Animal Sciences Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (165.359 KB) | DOI: 10.14334/jitv.v9i2.413

Abstract

Genetic relationships of Kampung, Pelung, Sentul and Black Kedu chickens were studied on the basis of microsatellite DNA polymorphism. DNA samples were analyzed using nine microsatellite markers which chosen from linkage group of macrochromosome (chromosome 1-8) such as, locus ABR 258, ABR359, ABR 297, ABR 339, ABR 75, ABR 209, ABR 28, ABR 419 and ABR 604. Analyses of amplified DNA fragments were performed using Gene Mapper 2.0 software (PE, Applied Biosystems). The allele frequencies in each breed estimated by direct counting. Since all nine microsatellite markers were polymorphic, genetic distance between the breeds could be calculated based on the frequencies of alleles of the microsatellite. Genetic relationships between the breeds could be constructed. The results indicated that a total of 73 allele were detected while typing all the four breeds of local chicken and one breed of White Leghorn as outgroup breed acrossed nine loci. The number of alleles was observed in all of the breed ranged 3-17 alleles according to the microsatellite under scrutiny. Highest observed number of alleles was found in Kampung Chicken 60 alleles (82.2%). The UPGMA method for dendogram based on Nei genetic distances indicated that the local chickens have the same of ancestor, while Kampung and Sentul chicken have the same cluster followed by Black Kedu and Pelung Chicken.   Key words: Local chicken, microsatellite, macrochromosome, genetic distance
Prolactin promoter gene as marker assisted selection (MAS) for the control of broodiness of Kampung chicken Sartika, Tike; Mansjoer, S.S; Saefuddin, A; Martojo, H
Indonesian Journal of Animal and Veterinary Sciences Vol 9, No 4 (2004)
Publisher : Indonesian Animal Sciences Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (187.539 KB) | DOI: 10.14334/jitv.v9i4.433

Abstract

Preliminary research about MAS (Marker Assisted Selection) was conducted to detect broodiness trait of Kampung chicken. MAS currently is very important in situations, where the accuracy of selection is low, such as, traits with low heritability, e.g. broodiness trait and egg production. Prolactin promoter was selected as a marker gene for broodiness because it plays a critical part in the neuroendocrine cascade which is triggered at the onset of broodiness. DNA samples were collected from low and highbroodiness samples on basic population (G0) each 24 samples, and from selected population (G3) each 28 samples. As control population without broody behavior was used 16 samples White Leghorn (WL) chicken. Prolactin promoter gene was amplified using polymerase chain reaction (PCR). PCR product was analyzed using electrophoresis agarose gel 2%. The results showed four types of bands represent in the Kampung chicken, three types called as wild type band and one type as the WL band. The chickens with low and high broodiness on G0 generation have 75 and 87.5% of wild type band while in the G3 generation was decreased to 25 and 75%. Conclusions of the research indicated that the selected breed of the Kampung chicken on G3 generation increased WL band like White Leghorn chicken as much as 31,25% from the G0 generation.   Key words: Kampung chicken, prolactin promoter, MAS
Genetic diversity of native chicken based on analysis of D-Loop mtDNA marker Sartika, Tike; Duryadi, D; Mansjoer, S.S; Gunawan, B
Indonesian Journal of Animal and Veterinary Sciences Vol 5, No 2 (2000)
Publisher : Indonesian Animal Sciences Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (536.415 KB) | DOI: 10.14334/jitv.v5i2.205

Abstract

Production was carried out using control region/D-loop mtDNA marker. The base population of native chicken was selected from subpopulation at Cianjur, Jatiwangi, Depok, Bogor I, and Bogor 2. Samples from each population was 10 heads and 2 samples Green Jungle Fowl (Gallus various) from East Java as out Group samples. Two primers binding conserved tRNA Phenylalanine gene and tRNA Glutamine gene were DNA Heavy stranded HI255 (5-CATCTTGGCATCTTCAGTGCC-3) and DNA Light stranded Ll6750 (5-AGGACTACGGCTTGAAAAGC-3) was used to amplify D-Ioop mtDNA chicken. PCR-RFLP methods with 6 restriction enzymes 4 cutter such as, Alul (AG↓CT), Hpall (C↓CGG), Mbol (↓GATC), Rsal (GT↓AC), NlaIII (CATG↓) and HaeIII (GG↓CC) were used to detect polymorphism within and between subpopulation. Result of experiment show that mtDNA which was amplified by PCR was 1320 bp, consist of 1227 bp control region/D-loop, 45 bp tRNA Glutamine gene and 48 bp tRNA Phenylalananine gene. PCR product which were digested from 6 endonucleases enzyme show that native chicken within and between population was monomorphic and if its compare with Green Jungle Fowl was polymorphic.   Key words: Native chicken, genetic diversity, mtDNA
Analysis of genetic relationship among Indonesian native chicken breeds based on 335 D-loop sequences Sulandari, Sri; Arifin Zein, M. Syamsul; Sartika, Tike
Indonesian Journal of Animal and Veterinary Sciences Vol 13, No 4 (2008)
Publisher : Indonesian Animal Sciences Society

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (219.112 KB) | DOI: 10.14334/jitv.v13i4.574

Abstract

The Mitochondrial DNA (mtDNA) D-loop segment was PCR amplified and subsequently sequenced for a total of 335 individuals from Indonesian native chicken. The individuals were drawn from sixteen populations of native chicken and three individuals of green jungle fowls (Gallus varius). Indonesian native chicken populations were: Pelung Sembawa, PL (n = 18), Pelung Cianjur, PLC (n = 29) and Arab Silver, ARS (n=30), Cemani, CM (n = 32), Gaok, GA (n = 7), Kedu Hitam, KDH (n = 11), Wareng, T & TW (n = 10), Cemani, CMP (n = 2), Kedu, KD (n=26), Kedu Putih, KDP (n = 15), Sentul Jatiwangi, STJ (n = 27), Ayam Kate, KT (n = 29), Ayam Sentul, STC (n = 15), Arab Golden, ARG (n = 26), Ayam Merawang, MR (n = 28), Kedu Putih Jatiwangi, KDPJ (n=6) and Kapas, KPS (n = 21). Green jungle fowls were: two individuals from Flores island (FL5 and FL57) and one individual (BD42) from Sumbawa island. The sequences of the first 530 nucleotides were used for analysis. Eighty two haplotypes were identified from 78 polymorphic sites for the 335 individuals. Seventy nine haplotypes were identified in native chicken from 57 polymorphic sites while three were of jungle fowls. Phylogenetic analysis indicates that Indonesian native chicken can be grouped into five clades (Clade I, II, IIIc, IIId and IV) of the previously identified seven clades (Clade I, II, IIIa, IIIb, IIIc, IIId and IV) in Asian domestic chicken. Haplotypes CM10 and CM32 fall to a different category while STC12 is also on its own. Interestingly STC12 clusters together with Gallus gallus gallus (GenBank accession No. SULANDARI et al. Analysis of genetic relationship among Indonesian native chicken breeds based on 335 D-loop sequences 296 AB007720). When CM10 (same as CM14), CM32 and STC12 were removed, 77 haplotypes of domestic chicken were identified from 53 polymorphic sites. All the green jungle fowls are clustered to one clade of their own. The clades of domestic chicken are: Clade I which has three haplotypes, Clade II has 52 haplotypes, Clade IIIc has one haplotype (represented by ARS30), Clade IIId has nine haplotypes while Clade IV has eleven haplotypes. The phylogenetic relationship between chicken populations has no link to the geographic locations. Analysis of molecular variance showed that the genetic variation within populations was 67.42% while 32.58% accounted for the genetic differentiation between populations. Key Words: Native Chiken, Green Jungle Fowls, D-Loop DNA Mitochondria, HV-1, Clade, Haplotype, Phylogenetic, Genetic Variation