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All Journal Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Jurnal Ilmu Ternak Veteriner
M. Syamsul Arifin Zein
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Veterinary

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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
Genetic diversity of Lombok chickens based on D-loop mitochondrial DNA sequences Arifin Zein, M. Syamsul; Sulandari, Sri
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 (65.558 KB) | DOI: 10.14334/jitv.v13i4.575

Abstract

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
Struktur Populasi Genetik Ayam Hutan Hijau Menggunakan Sekuen Hypervariable 1 D-Loop DNA Mitokondria Arifin Zein, M. Syamsul; Sulandari, Sri
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 | Full PDF (245.12 KB) | DOI: 10.24002/biota.v13i3.2573

Abstract

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.
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)

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 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)

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (65.558 KB) | DOI: 10.14334/jitv.v13i4.575

Abstract

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
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

Abstract

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.
Analisis Gen 12SrRNA Dari DNA Mitochondria Kelelawar Pemakan Buah Chironax Melanocephalus (Chiroptera: Pteropodidae) Di Taman Nasional Gunung Halimun M. Syamsul Arifin Zein; Maharadatunkamsi Maharadatunkamsi
Biota : Jurnal Ilmiah Ilmu-Ilmu Hayati Vol 8, No 1 (2003): February 2003
Publisher : Universitas Atma Jaya Yogyakarta

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24002/biota.v8i1.2787

Abstract

A study on genetic variation of the high mountain fruit bat (Chironax melanocephalus) was conducted in Gunung Halimun National Park. DNA total from liver tissues were extracted and fragment of the 12SrRNA gene region of mitochondrial DNA were amplified by Polymerase Chain Reaction (PCR). Nucleotide sequence of the PCR products were determined by automated sequencer. Seven haplotype were found among 20 individuals from 6 localities, namely: South Halimun Mountain, Kendeng Mountain, Botol Mountain, Pasir Cangkuang Mountain, Kencana Mountain, and Buligir Putih Mountain. Haplotype diversity and nucleotide diversity were 0.76 and 0.0222. DNA distances values ranged from 0.0028 to 0.0202.
Co-Authors Maharadatunkamsi Maharadatunkamsi Sri Sulandari SRI SULANDARI TIKE SARTIKA