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M Syamsul Arifin Zein

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Author-ID : 232581

Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Veterinary

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Genetic diversity and haplogroups distributions of Kampung chickens using hypervariable-I mitochondrial DNA control region Arifin Zein, M Syamsul; Sulandari, S
Indonesian Journal of Animal and Veterinary Sciences Vol 17, No 2 (2012)
Publisher : Indonesian Animal Sciences Society

Until now no studies evaluating the position of Kampung chickens in chicken clade of Asia. Thus studies based on molecular DNA sequence hipervariable-I on Kampung chicken is needed. Molecular studies based on DNA sequences hyper variable-I of Kampong chicken was done to confirm the results of previous evaluations conducted on 15 families of local chickens of Indonesia. An analysis of 210 individuals Kampung chicken (Aceh, North Sumatra, Lampung, Banten, Central Java, Lombok, Sulawesi, Ternate, Morotai and Halmahera) resulted in 51 haplotypes derived from 62 polymorphic sites. Polymorphic sites among the highest seen at 112-397 (93.22%). The highest haplotype frequencies contained in the haplotype H-4 (36.19%), followed by H-1 (18.57%) and H-5 (10, 95%). Kampung chicken phylogeny analysis formed four haplogroups/clade from 7 references of Asian chicken clade. Four haplogroups are clade II = 84.31% (43 haplotypes), clade IIIC = 1.96% (1 haplotype), clade IIID = 3.92% (2 haplotypes), clade IV = 7.84% (4 haplotypes). The results prove of that Indonesian local and indigenous chickens were equally dominated clade II. Analysis of genetic diversity showed haplotype diversity of 0.825 Â± 0.021, nucleotide diversity of 0.00600 on average, the genetic distance between populations ranged from 0.003 to 0.011, and the genetic distance within populations ranged from 0.00395 to 0.01031. Genetic distance between individuals in all populations of Kampung chickens was significantly different (P < 0.01). Fus Fs values was negative, indicating high genetic diversity and population expansion on native chicken in Indonesia. Other important result was shown with the major haplotype spread from western to eastern Indonesia, and had strengthened the position of Indonesia as one of the centers of domestication of the chicken. Key Words: Kampung Chicken, Hypervariable-I, Control Region, Mitochondrial DNA, Haplotype, Clade

Genetic diversity and haplogroups distributions of Kampung chickens using hypervariable-I mitochondrial DNA control region M Syamsul Arifin Zein; S Sulandari
Jurnal Ilmu Ternak dan Veteriner Vol 17, No 2 (2012): JUNE 2012
Publisher : Indonesian Center for Animal Research and Development (ICARD)

Until now no studies evaluating the position of Kampung chickens in chicken clade of Asia. Thus studies based on molecular DNA sequence hipervariable-I on Kampung chicken is needed. Molecular studies based on DNA sequences hyper variable-I of Kampong chicken was done to confirm the results of previous evaluations conducted on 15 families of local chickens of Indonesia. An analysis of 210 individuals Kampung chicken (Aceh, North Sumatra, Lampung, Banten, Central Java, Lombok, Sulawesi, Ternate, Morotai and Halmahera) resulted in 51 haplotypes derived from 62 polymorphic sites. Polymorphic sites among the highest seen at 112-397 (93.22%). The highest haplotype frequencies contained in the haplotype H-4 (36.19%), followed by H-1 (18.57%) and H-5 (10, 95%). Kampung chicken phylogeny analysis formed four haplogroups/clade from 7 references of Asian chicken clade. Four haplogroups are clade II = 84.31% (43 haplotypes), clade IIIC = 1.96% (1 haplotype), clade IIID = 3.92% (2 haplotypes), clade IV = 7.84% (4 haplotypes). The results prove of that Indonesian local and indigenous chickens were equally dominated clade II. Analysis of genetic diversity showed haplotype diversity of 0.825 ± 0.021, nucleotide diversity of 0.00600 on average, the genetic distance between populations ranged from 0.003 to 0.011, and the genetic distance within populations ranged from 0.00395 to 0.01031. Genetic distance between individuals in all populations of Kampung chickens was significantly different (P < 0.01). Fu's Fs values was negative, indicating high genetic diversity and population expansion on native chicken in Indonesia. Other important result was shown with the major haplotype spread from western to eastern Indonesia, and had strengthened the position of Indonesia as one of the centers of domestication of the chicken. Key Words: Kampung Chicken, Hypervariable-I, Control Region, Mitochondrial DNA, Haplotype, Clade

Genetic diversity and phylogenetic relationship of Indonesian Local goats using microsatellite DNA markers M Syamsul Arifin Zein; S Sulandari; Muladno .; Subandriyo .; Riwantoro .
Jurnal Ilmu Ternak dan Veteriner Vol 17, No 1 (2012): MARCH 2012
Publisher : Indonesian Center for Animal Research and Development (ICARD)

Genetic diversity is important information in the process of conservation and sustainable utilization of animal genetic resources. Thirteen microsatellite markers were used to estimate the degree of genetic diversity on five Indonesian local goats. Results showed the highest average allele diversity present in the locus MAF70 (5.6 ± 2.9), and the lowest was in the locus MAF035 (1.6 ± 0.6), the average number of alleles per locus was 6 ± 2.3. The lowest average alleles diversity present was in the Gembrong goat (2.2 ± 1.1) and the highest was in the Jawarandu goat (4.9 ± 2.2). There is a unique alleles at loci MCM527 and present in all Indonesian local goat with the highest allele frequency on Peranakan Etawa (37.2%) and lowest in Gembrong goat (7.9%). H0 ranged from 0.372 ± 0.173 (Gembrong) to 0.540 ± 0.204 (Peranakan Etawa), and HE ranging from 0.249 ± 0.196 (Gembrong) to 0.540 ± 0.212 (Peranakan Etawa).The genetic differentiation for inbreeding among population (FIS), within population (FIT), and average genetic differention (FST) were 0,0208 (2,08%), 0,1532 (15,32%), and 0,1352 (13,52%), respectively. Locus ILSTS029, BMS1494, MAF035 and INRA0132 had a low PIC value (PIC < 0.25), locus SRCRSP3, OARFCB20, ILSTS005, SPS113, MCM527, and ETH10 provide moderate (PIC = 0.25 to 0.5), and locus CSRD247, MAF70, and ILSTS11 had high value PIC > 0.5. Phylogenetic relationship was consistent with the history of its development based on Kacang goat except was for Gembrong Goat. This research information can be used for conservation strategies and breeding programs on each population of Indonesian local goat. Key Words: Local Goat, Indonesia, Microsatellites, Genetic Diversity, PIC

KAJIAN KARAKTERISTK GENETIK RUSA TIMOR (Cervus timorensis timorensis Blanville, 1822) M Syamsul Arifin Zein; Bambang Surjobroto; Dedy D Solihin; Siti N Prijono
BERITA BIOLOGI Vol 4, No 4 (1998)
Publisher : Research Center for Biology-Indonesian Institute of Sciences

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14203/beritabiologi.v4i4.1261

A study on characteristic of genetic of the Timor deer (Cervus timorensis timorensis)was conducted during the periode of June - November 1997.Twenty four blood samples from Timor, Semau, Pantar, and Alor Island,Nusa Tenggara Timur Province were examined for this study.Restriction site analysis of part of ribosomeRNA mitochondrial DNA (447 bp),using restriction endonucleasis Haelll and Mbol showed that there were two haplotype variation.

Co-Authors Bambang Surjobroto Dedy D Solihin Riwantoro . S Sulandari Siti N Prijono Subandriyo .

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