Molecular Characterization of Indonesian Indigenous Chickens based on Mitochondrial DNA Displacement (D)-loop Sequences
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 Gallu...
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| Format: | Article |
| Language: | English |
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Bogor Agricultural University
2008-12-01
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| Series: | Hayati Journal of Biosciences |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1978301916302844 |
| _version_ | 1818822178024456192 |
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| author | SRI SULANDARI MOCH SYAMSUL ARIFIN ZEIN TIKE SARTIKA |
| author_facet | SRI SULANDARI MOCH SYAMSUL ARIFIN ZEIN TIKE SARTIKA |
| author_sort | SRI SULANDARI |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-18T23:19:57Z |
| format | Article |
| id | doaj.art-8d07f1e941cc4203a21fe56effeda01e |
| institution | Directory Open Access Journal |
| issn | 1978-3019 |
| language | English |
| last_indexed | 2024-12-18T23:19:57Z |
| publishDate | 2008-12-01 |
| publisher | Bogor Agricultural University |
| record_format | Article |
| series | Hayati Journal of Biosciences |
| spelling | doaj.art-8d07f1e941cc4203a21fe56effeda01e2022-12-21T20:48:01ZengBogor Agricultural UniversityHayati Journal of Biosciences1978-30192008-12-0115414515410.4308/hjb.15.4.145Molecular Characterization of Indonesian Indigenous Chickens based on Mitochondrial DNA Displacement (D)-loop SequencesSRI SULANDARI0MOCH SYAMSUL ARIFIN ZEIN1TIKE SARTIKA2Research Center for Biology-LIPIWidyasatwaloka Building, Cibinong Science Center, Jalan Raya Jakarta Bogor Km. 46, Cibinong 16911, IndonesiaResearch Center for Biology-LIPIWidyasatwaloka Building, Cibinong Science Center, Jalan Raya Jakarta Bogor Km. 46, Cibinong 16911, IndonesiaCentre for Animal Research and Development, Widyasatwaloka Building, Cibinong Science Center, Jalan Raya Jakarta Bogor Km. 46, Cibinong 16911, IndonesiaThe 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.http://www.sciencedirect.com/science/article/pii/S1978301916302844Indonesian indigenous chickenmitochondrial DNAD-loophaplotypephylogenetic analysis and clade |
| spellingShingle | SRI SULANDARI MOCH SYAMSUL ARIFIN ZEIN TIKE SARTIKA Molecular Characterization of Indonesian Indigenous Chickens based on Mitochondrial DNA Displacement (D)-loop Sequences Hayati Journal of Biosciences Indonesian indigenous chicken mitochondrial DNA D-loop haplotype phylogenetic analysis and clade |
| title | Molecular Characterization of Indonesian Indigenous Chickens based on Mitochondrial DNA Displacement (D)-loop Sequences |
| title_full | Molecular Characterization of Indonesian Indigenous Chickens based on Mitochondrial DNA Displacement (D)-loop Sequences |
| title_fullStr | Molecular Characterization of Indonesian Indigenous Chickens based on Mitochondrial DNA Displacement (D)-loop Sequences |
| title_full_unstemmed | Molecular Characterization of Indonesian Indigenous Chickens based on Mitochondrial DNA Displacement (D)-loop Sequences |
| title_short | Molecular Characterization of Indonesian Indigenous Chickens based on Mitochondrial DNA Displacement (D)-loop Sequences |
| title_sort | molecular characterization of indonesian indigenous chickens based on mitochondrial dna displacement d loop sequences |
| topic | Indonesian indigenous chicken mitochondrial DNA D-loop haplotype phylogenetic analysis and clade |
| url | http://www.sciencedirect.com/science/article/pii/S1978301916302844 |
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