Genetic diversity analysis of Thai indigenous chickens based on complete sequences of mitochondrial DNA D-loop region
Objective Complete mtDNA D-loop sequences of four Thai indigenous chicken varieties, including Pra-dhu-hang-dam (PD), Leung-hang-khao (LK), Chee (CH), and Dang (DA) were explored for genetic diversity and relationships with their potential ancestor and possible associates to address chicken domestic...
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| Format: | Article |
| Language: | English |
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Asian-Australasian Association of Animal Production Societies
2018-06-01
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| Series: | Asian-Australasian Journal of Animal Sciences |
| Subjects: | |
| Online Access: | http://www.ajas.info/upload/pdf/ajas-31-6-804.pdf |
| _version_ | 1828381604480811008 |
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| author | Piyanat Teinlek Kannika Siripattarapravat Chanin Tirawattanawanich |
| author_facet | Piyanat Teinlek Kannika Siripattarapravat Chanin Tirawattanawanich |
| author_sort | Piyanat Teinlek |
| collection | DOAJ |
| description | Objective Complete mtDNA D-loop sequences of four Thai indigenous chicken varieties, including Pra-dhu-hang-dam (PD), Leung-hang-khao (LK), Chee (CH), and Dang (DA) were explored for genetic diversity and relationships with their potential ancestor and possible associates to address chicken domestication in Thailand. Methods A total of 220 complete mtDNA D-loop sequences of the four Thai indigenous chicken varieties were obtained by Sanger direct sequencing of polymerase chain reaction amplicons of 1,231 to 1,232 base pair in size. A neighbor-joining dendrogram was constructed with reference complete mtDNA D-loop sequences of Red Junglefowl (RJF) and those different chicken breeds available on National Center for Biotechnology Information database. Genetic diversity indices and neutrality test by Tajima’s D test were performed. Genetic differences both within and among populations were estimated using analysis of molecular variance (AMOVA). Pairwise fixation index (FST) was conducted to evaluated genetic relationships between these varieties. Results Twenty-three identified haplotypes were classified in six haplogroups (A–E and H) with the majority clustered in haplogroup A and B. Each variety was in multiple haplogroups with haplogroups A, B, D, and E being shared by all studied varieties. The averaged haplotype and nucleotide diversities were, respectively 0.8607 and 0.00579 with non-significant Tajima’s D values being observed in all populations. Haplogroup distribution was closely related to that of RJF particularly Gallus gallus gallus (G. g. gallus) and G. g. spadiceus. As denoted by AMOVA, the mean diversity was mostly due to within-population variation (90.53%) while between-population variation (9.47%) accounted for much less. By pairwise FST, LK was most closely related to DA (FST = 0.00879) while DA was farthest from CH (FST = 0.24882). Conclusion All 4 Thai indigenous chickens are in close relationship with their potential ancestor, the RJF. A contribution of shared, multiple maternal lineages was in the nature of these varieties, which have been domesticated under neutral selection. |
| first_indexed | 2024-12-10T04:17:01Z |
| format | Article |
| id | doaj.art-2c57318d25c54ff3a6ff8f6b786bfd63 |
| institution | Directory Open Access Journal |
| issn | 1011-2367 1976-5517 |
| language | English |
| last_indexed | 2024-12-10T04:17:01Z |
| publishDate | 2018-06-01 |
| publisher | Asian-Australasian Association of Animal Production Societies |
| record_format | Article |
| series | Asian-Australasian Journal of Animal Sciences |
| spelling | doaj.art-2c57318d25c54ff3a6ff8f6b786bfd632022-12-22T02:02:33ZengAsian-Australasian Association of Animal Production SocietiesAsian-Australasian Journal of Animal Sciences1011-23671976-55172018-06-0131680481110.5713/ajas.17.061123911Genetic diversity analysis of Thai indigenous chickens based on complete sequences of mitochondrial DNA D-loop regionPiyanat Teinlek0Kannika Siripattarapravat1Chanin Tirawattanawanich2 Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, ThailandObjective Complete mtDNA D-loop sequences of four Thai indigenous chicken varieties, including Pra-dhu-hang-dam (PD), Leung-hang-khao (LK), Chee (CH), and Dang (DA) were explored for genetic diversity and relationships with their potential ancestor and possible associates to address chicken domestication in Thailand. Methods A total of 220 complete mtDNA D-loop sequences of the four Thai indigenous chicken varieties were obtained by Sanger direct sequencing of polymerase chain reaction amplicons of 1,231 to 1,232 base pair in size. A neighbor-joining dendrogram was constructed with reference complete mtDNA D-loop sequences of Red Junglefowl (RJF) and those different chicken breeds available on National Center for Biotechnology Information database. Genetic diversity indices and neutrality test by Tajima’s D test were performed. Genetic differences both within and among populations were estimated using analysis of molecular variance (AMOVA). Pairwise fixation index (FST) was conducted to evaluated genetic relationships between these varieties. Results Twenty-three identified haplotypes were classified in six haplogroups (A–E and H) with the majority clustered in haplogroup A and B. Each variety was in multiple haplogroups with haplogroups A, B, D, and E being shared by all studied varieties. The averaged haplotype and nucleotide diversities were, respectively 0.8607 and 0.00579 with non-significant Tajima’s D values being observed in all populations. Haplogroup distribution was closely related to that of RJF particularly Gallus gallus gallus (G. g. gallus) and G. g. spadiceus. As denoted by AMOVA, the mean diversity was mostly due to within-population variation (90.53%) while between-population variation (9.47%) accounted for much less. By pairwise FST, LK was most closely related to DA (FST = 0.00879) while DA was farthest from CH (FST = 0.24882). Conclusion All 4 Thai indigenous chickens are in close relationship with their potential ancestor, the RJF. A contribution of shared, multiple maternal lineages was in the nature of these varieties, which have been domesticated under neutral selection.http://www.ajas.info/upload/pdf/ajas-31-6-804.pdfThai Indigenous ChickenMitochondrial DNA D-loopGenetic DiversityDomestication |
| spellingShingle | Piyanat Teinlek Kannika Siripattarapravat Chanin Tirawattanawanich Genetic diversity analysis of Thai indigenous chickens based on complete sequences of mitochondrial DNA D-loop region Asian-Australasian Journal of Animal Sciences Thai Indigenous Chicken Mitochondrial DNA D-loop Genetic Diversity Domestication |
| title | Genetic diversity analysis of Thai indigenous chickens based on complete sequences of mitochondrial DNA D-loop region |
| title_full | Genetic diversity analysis of Thai indigenous chickens based on complete sequences of mitochondrial DNA D-loop region |
| title_fullStr | Genetic diversity analysis of Thai indigenous chickens based on complete sequences of mitochondrial DNA D-loop region |
| title_full_unstemmed | Genetic diversity analysis of Thai indigenous chickens based on complete sequences of mitochondrial DNA D-loop region |
| title_short | Genetic diversity analysis of Thai indigenous chickens based on complete sequences of mitochondrial DNA D-loop region |
| title_sort | genetic diversity analysis of thai indigenous chickens based on complete sequences of mitochondrial dna d loop region |
| topic | Thai Indigenous Chicken Mitochondrial DNA D-loop Genetic Diversity Domestication |
| url | http://www.ajas.info/upload/pdf/ajas-31-6-804.pdf |
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