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

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

Detection and Host Range Study of Virus Associated with Pepper Yellow Leaf Curl Disease SRI SULANDARI; RUSMILAH SUSENO; SRI HENDRASTUTI HIDAYAT; JUMANTO HARJOSUDARMO; SOEMARTONO SOSROMARSONO
HAYATI Journal of Biosciences Vol. 13 No. 1 (2006): March 2006
Publisher : Bogor Agricultural University, Indonesia

High incidence of Pepper yellow leaf curl virus (PepYLCV) was observed in Indonesia since early 2000. Disease incidence in Yogyakarta, Central and West Java reached 100% on Capsicum frutescens, but only 10-35% on C. annuum. As an exception, the disease incidence on C. annuum cv. TM 999 was in the range of 70-100%. The causal agent of the disease, PepYLCV, was detected by polymerase chain reaction. Viral specific DNA fragment of the size ~1600 bp and ~550 bp was amplified from infected plants using two pairs of geminivirus universal primers pAL1v1978/pAL1c715, and pAv494/pAc1048, respectively. The PepYLCV has an intermediate host range including plants belonging to the family of Solanaceae, Leguminosae, and Compositae. The species belonging to the families of Cucurbitaceae, Malvaceae, Chenopodiaceae, and Amaranthaceae were resistant to the virus. Physalis floridana, is very prospective as a propagation host for the geminivirus infecting pepper. Nicotiana spp., cucumber, watermelon, cotton, and Sida sp. could be used as a differential host. Besides, Capsicum frutescens cv. Cakra, tomato, N. benthamiana, N. glutinosa, and Ageratum conyzoides could be used as indicator plants for the geminivirus infecting pepper. Key words: Pepper yellow leaf curl virus, disease incidence, host range

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

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 diversity of Lombok chickens based on D-loop mitochondrial DNA sequences M. Syamsul Arifin Zein; Sri Sulandari
Jurnal Ilmu Ternak dan Veteriner Vol 13, No 4 (2008): DECEMBER 2008
Publisher : Indonesian Center for Animal Research and Development (ICARD)

Mitochondrial DNA (mtDNA) displacement (D)-loop sequences were used to study the genetic diversity and relationship of Lombok chickens. A total of 45 individuals were sampled. The D-loop segment was PCR amplified and subsequently sequenced. The sequences of the 785 nucleotides were used for analysis. Twelve haplotypes were identified from 25 polymorphic sites with polymorphism between nucleotides 200 and 400 contributing to 80% of the variation. Fu’s Fs value was - 8.768 (all samples, P = 0), indicating high genetic diversity and population expansion, a conclusion supported by a neighbor– joining analysis of the haplotypes. Nucleotides diversity of the Lombok chicken were 0.00221 and haplotype diversity were 0.654 + 0.08. The dominant haplotype found among the Lombok chickens was haplotype B (62%) and genetic distances value ranged from 0.001 to 0.017. Key Words: Mtdna, D-Loop, Genetic Diversity, Haplotype, Lombok Chicken

Nunukan Chicken: Genetic Characteristics, Phenotype and Utilization Tike Sartika; Sri Sulandari; M S A Zein; Sri Paryanti
WARTAZOA, Indonesian Bulletin of Animal and Veterinary Sciences Vol 16, No 4 (2006): DECEMBER 2006
Publisher : Indonesian Center for Animal Research and Development

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

Investigasi Asal Usul Ayam Indonesia Menggunakan Sekuens Hypervariable-1 D-loop DNA Mitokondria Moch Syamsul Arifin Zein; Sri Sulandari
Jurnal Veteriner Vol 10 No 1 (2009)
Publisher : Faculty of Veterinary Medicine, Udayana University and Published in collaboration with the Indonesia Veterinarian Association

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Chicken taxonomy and pedigree investigation are important parts to understand the domesticationprocess occurred on chicken in Indonesia. The Indonesian native chickens have very different clade with thechickens from other Asian countries and others. This study was conducted to construct phylogeny junglefowls (red and green jungle fowls) and Indonesian native chickens, in order to know their relationship.Among the available DNA marker, the region D-loop on DNA mitochondria is the most effective markerused in the investigation. Mitochondrial DNA D-loop (hypervariable-1 segment) was PCR amplified andsubsequently sequenced for a total 33 individuals of green jungle fowls (Gallus varius), 9 individuals of redjungle fowls (Gallus g. gallus) from Indonesia, and 30 individuals of Indonesian native chickens (Lombok,Cemani, Kedu, Kedu Putih, Nunukan, Kate, Pelung, Gaok, Merawang, dan Sentul). Seventy two (72)sequences were used for analysis. Seven (7) published reference D-loop sequences of genus Gallus fromGenBank were also included in the analysis: Gallus varius (GenBank accession number D64163 danD82912), Gallus gallus (GenBank accession number AB098668), G. gallus spadiceus (GenBank accessionnumber AB007721), Gallus gallus bankiva (GenBank accession number AB007718), Gallus lafayetti(GenBank accession number D66893), and Gallus sonneratii (GenBank accession number D66892). Phylogenyanalysis indicates that Indonesia jungle fowls can be grouped into two clades (clades of red jungle fowls/Indonesia native chicken and green jungle fowls). Monophyletic phylogeny trees of jungle fowls from Indonesiawere shown in this study for pedigree investigation of domesticated chickens.

Keragaman Fenotipik dan Pendugaan Jarak Genetik pada Ayam Lokal dan Ayam Broiler Menggunakan Analisis Morfologi (PHENOTYPIC VARIATION AND ESTIMATION GENETIC DISTANCE BETWEEN LOCAL CHICKEN AND BROILER CHICKEN USING MORPHOLOGICAL ANALYSIS) Harini Nurcahya Mariandayani; Dedy Duryadi Solihin; Sri Sulandari; Cece Sumantri
Jurnal Veteriner Vol 14 No 4 (2013)
Publisher : Faculty of Veterinary Medicine, Udayana University and Published in collaboration with the Indonesia Veterinarian Association

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This aim of the research was to study the morphological characteristic and estimating genetic distancebetween local chicken and broiler chicken with discriminant and canonical analysis. This research washeld in Faculty of Animal Husbandry, Bogor Agricultural University, using 25 sentul chickens, 25 kampongchickens, 25 kedu chickens , 25 pelung chickens and 25 broiler chickens. The variable as the length ofshank, beak length, back length, chest depth and chest width were measured in this study. The collecteddata were analyzed by using SAS and SPSS package program. Kampung chickens were mixed with sentulchickens (17.60 %) and kedu chickens (17,70 %). Kedu, kampong, and sentul chickens have a relativelyclose genetic distance compared the genetic distance to pelung chickens with the kampung, sentul, andkedu chickens. Fenogram tree show that there were three separate groups of chickens at the age of eightweeks i.e. : (1) pelung chickens (2), kedu, kampong, and sentul chickens, (3) broiler chickens. Fenogram treealso shows two separate groups : (1) pelung chickens (2) kedu, kampong, and Sentul chickens (at the age of28 weeks chicken). The crossbreed between kedu and sentul chickens, also have a relatively close geneticdistance. The phenotypic size of chickens giving a strong influence on the distinction variable of chickengroups were body length and chest circumference.

Genetic Polymorphisms of The Chicken Antiviral Mx Gene in A Variety of Indonesian Indigenous Chicken Breeds Sri Sulandari; Moch Syamsul Arifin Zein; Dwi Astuti; Tike Sartika
Jurnal Veteriner Vol 10 No 2 (2009)
Publisher : Faculty of Veterinary Medicine, Udayana University and Published in collaboration with the Indonesia Veterinarian Association

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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.

Sidik Jari DNA dan Fenotipe pada Populasi Kambing Gembrong dengan Status Kritis di Karangasem, Bali (DNA FINGERPRINT AND PHENOTYPE ON THE CRITICAL POPULATION STATUS OF GEMBRONG GOAT IN KARANGASEM REGENCY, BALI) Moch Syamsul Arifin Zein; Sri Sulandari
Jurnal Veteriner Vol 15 No 2 (2014)
Publisher : Faculty of Veterinary Medicine, Udayana University and Published in collaboration with the Indonesia Veterinarian Association

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Gembrong goat is animal genetic resources which endemic in Bali island and only exists in Karangasemregency. The current population status of the gembrong goat is critical. Therefore, the population developmentof in-situ or ex-situ needs to be conducted. Close relative mating tend to occur in conditions such as in asmall population, critical status or limited distribution. Low degree of genetic variability is often found insuch conditions. Mating arrangements based on DNA data of fingerprint was developed in this study toavoid mating between close relatives (inbreeding). Pedigree detection was analyzed using fifteen (15)microsatellite markers as recommended by ISAP/FAO. The results showed that polymorphic alleles foundin the microsatellite markers of SRCRSP3, ILSTS005, MCM527 (4 alleles), followed BM1818 (3 alleles),and ILSTS029, BMS1494, MAF035, OARFCB20, OARE54, MAF70, ILSTS11, ETH10 (2 alleles).Monomorphic allele (1 allele) was also found in microsatellite markers of SPS113, CSRD247, INRA0132.DNA fingerprint of the gembrong goat population was created by genetic distance between individuals,and indicated six clades / haplogroups. It is suggested from this study that mating arrangements betweendifferent clades should be applied to increase genetic diversity. Description of morphologies such as haircolor and body size, were used as basic considerations in determining the authenticity of gembrong goat.Among the population of gembrong goat in this study, hair color of the goat showed white (78.95%), amixture of light brown and white (15.79%), and a mixture of brown and black (5.26%). Gembrong goat bodysize in this study was still in the range of the previous studies. The analysis results of DNA fingerprintsand phenotypes can be used as a basis for rescue and development of gembrong goats, in an attempt toform a large gene pool with high viability for the conservation, development and sustainable uses.

Struktur Populasi Genetik Ayam Hutan Hijau Menggunakan Sekuen Hypervariable 1 D-Loop DNA Mitokondria M. Syamsul Arifin Zein; Sri Sulandari
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 13, No 3 (2008): October 2008
Publisher : Universitas Atma Jaya Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24002/biota.v13i3.2573

Thirty-three individuals from four populations of green junglefowl (Gallus varius) were collected throughout Indonesia: 14 from Central Java, 4 from Eastern Java, 3 from Sumbawa island and 12 from Flores island. The mitochondrial DNA D-loop the samples were analysed for sequence diversity. Twenty-five haplotypes with 28 polymorphic sites were identified within the first hypervariable-1 fragment (397 bp) of the D-loop. Fu’s Fs value was -25.96 (all samples, P=0), indicating high genetic diversity and population expansion; a conclusion supported by a neighbor–joining analysis of the haplotypes. Though sample size per population varied between 3 and 14, the Fs values for the four populations, between -2.20 and -10.76, were all significant (P=0). Only one haplotype was shared between three populations (Central Java, Sumbawa island, and Flores island) by a total of seven individuals. Within populations, only three haplotypes were shared by three individuals. The remaining haplotypes were unique, indicating genetic differentiation between populations as confirmed by significant pairwise Fst values at P=0.05 in four out of the six population pairs (except two pairs of Central Java & Sumbawa island and Flores island & Sumbawa island). The diversity pattern observed at the mtDNA of the green junglefowl provides a baseline which may help to understand the recent population expansions of domesticated chickens from multiple centres of domestications. Our observations also suggest careful interpretation of the results of genetic characterization may be needed when applied to the management and conservation of species like the green junglefowl. As in other multiparous birds and mammals with a short reproductive interval, green junglefowl may have established distinct genetic entities in metapopulations across its geographic distribution.

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