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Molecular Characterization of Indonesian Indigenous Chickens based on Mitochondrial DNA Displacement (D)-loop Sequences SULANDARI, SRI; ZEIN, MOCH SYAMSUL ARIFIN; SARTIKA, TIKE
HAYATI Journal of Biosciences Vol 15, No 4 (2008): December 2008
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (520.93 KB) | DOI: 10.4308/hjb.15.4.145

Abstract

The Mitochondrial DNA (mtDNA) displacement (D)-loop sequences were used to study the genetic diversity and relationship of Indonesian indigenous chickens. A total of 483 individuals belonging to 15 population breeds and 43 individuals belonging to 6 populations of jungle fowl (2 populations of Gallus gallus and 4 populations of Gallus varius) were sampled. The hypervariable I (HVI) segment of the D-loop was PCR amplified and subsequently sequenced. The sequences of the first 397 nucleotides were used for analysis. Sixty nine haplotypes were identified from 54 polymorphic sites with polymorphism between nucleotides 167 and 397 contributing to 94.5% of the sequence variation. Phylogenetic analysis indicates that Indonesian indigenous chickens can be grouped into five distinct 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 indigenous chickens. Fifty haplotypes belong to clade II, seven haplotypes are in clade IV, six are in clade IIId, three are in clade I and one haploype is in clade IIIc. There was no breed-specific clade. Analysis of Molecular Variance (AMOVA) based on partial D-loop sequences of Indonesian chicken indicates that 67.85% of the total sequence variation between haplotypes was present within the population and 32.15% between populations. One of the haplotypes (represented by PLC4) was shared by all populations, suggesting that these populations may share the same maternal ancestor. These results show a high mitochondrial D-loop diversity and indicate multiple maternal origins for Indonesian indigenous chickens. Key words: Indonesian indigenous chicken, mitochondrial DNA, D-loop, haplotype, phylogenetic analysis and clade
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 : Jurnal Veteriner

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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
Analysis of genetic relationship among Indonesian native chicken breeds based on 335 D-loop sequences Sulandari, Sri; Arifin Zein, M. Syamsul; Sartika, Tike
Jurnal Ilmu Ternak dan Veteriner Vol 13, No 4 (2008): DECEMBER 2008
Publisher : Indonesian Center for Animal Research and Development (ICARD)

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
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
Jurnal Ilmu Ternak dan Veteriner Vol 9, No 2 (2004): JUNE 2004
Publisher : Indonesian Center for Animal Research and Development (ICARD)

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
MANAJEMEN RANTAI PASOK KOMODITAS TELUR AYAM KAMPUNG Saptana, Saptana; Sartika, Tike
Jurnal Manajemen & Agribisnis Vol 11, No 1 (2014): Vol. 11 No. 1, Maret 2014
Publisher : Graduate Program of Management and Business Bogor Agricultural University

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Abstract

ABSTRACTThe studied aimed to formulate an integrated policy of supply chain management development of native chicken eggs. In detail, the research objectives were: 1) to describe the actors of supply chain of native chicken eggs, 2) to analyze the Institutions of supply chain management of native chicken eggs, and 3) to analyze the value chain of native chicken eggs. The data were obtained from interviewed with breeder of native chicken and group discussion with actors of supply chain in the province of West Java, East Java and South Kalimantan. Quantitative data were analyzed using analysis of R/C ratio, marketing margin system and value chain analysis, while qualitative information with a descriptive analysis was focus on institutions of supply chain management. The results showed that: 1) The eight main actors in supply chain of native chicken eggs commodity were: government, breeding industry, breeders, farmers groups, associations of farmers groups, traders at the centers of production, traders at the centers of consumption, and industrial of cake/bread; 2) most strategic institutional in the whole of supply chain of native chicken eggs was the institutionalization of distribution and marketing, and 3) cake/ bread industrial received the largest of value-added per unit of output, while the large traders in the center of production and consumption received the greatest value in the aggregate. The overall study of policy recommendations of `the development of agribusiness of native chicken eggs was the integration of all factors connected in supply chain.Keywords: institutional , agribusiness, value chain, eggs, economic sociaty   ABSTRAKSecara umum penelitian ini bertujuan merumuskan kebijakan pengembangan manajemen rantai pasok komoditas telur ayam  kampung secara terpadu. Secara rinci tujuan penelitian adalah 1) mendeskripsikan pelaku  rantai pasok komoditas telur ayam  kampung; 2) menganalisis kelembagaan manajemen rantai pasok komoditas telur ayam  kampung; dan 3) menganalisis rantai nilai komoditas telur ayam  kampung. Data yang digunakan bersumber dari hasil wawancara terstruktur dengan peternak ayam  kampung petelur serta wawancara kelompok dengan para pelaku rantai pasok di Provinsi Jawa Barat, Jawa Timur, dan Kalimantan Selatan. Data kuantitatif dianalisis menggunakan analisis R/C ratio, margin tata niaga dan analisis rantai nilai, sementara informasi kualitatif dengan analisis deskriptif dengan fokus pada kelembagaan manajemen rantai pasok. Hasil penelitian menunjukkan bahwa: 1) terdapat delapan pelaku utama rantai pasok komoditas telur ayam  kampung,  yaitu pemerintah, industri perbibitan, peternak, kelompok peternak, asosiasi peternak, pedagang di sentra produksi, pedagang di sentra konsumsi, dan industri kue/roti; 2) kelembagaan yang paling strategis dalam keseluruhan rantai pasok komoditas telur ayam  kampung adalah kelembagaan distribusi dan pemasaran; dan 3) industri kue/roti menerima nilai tambah terbesar per  unit output, sedangkan pedagang besar di pusat produksi dan pedagang besar di pusat konsumsi menerima nilai terbesar secara agregat. Rekomendasi kebijakan yang dihasilkan adalah pengembangan agribisnis komoditas telur ayam  kampung harus dilakukan secara terpadu dalam keseluruhan rantai pasok. Kata kunci: kelembagaan, tata niaga,  rantai nilai, telur, ayam kampung
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 | 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