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 domesti...
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 ($F_{ST}$) 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 $F_{ST}$, LK was most closely related to DA ($F_{ST}=0.00879$) while DA was farthest from CH ($F_{ST}=0.24882$). 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.
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 ($F_{ST}$) 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 $F_{ST}$, LK was most closely related to DA ($F_{ST}=0.00879$) while DA was farthest from CH ($F_{ST}=0.24882$). 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.
* AI 자동 식별 결과로 적합하지 않은 문장이 있을 수 있으니, 이용에 유의하시기 바랍니다.
문제 정의
Exploration of background genetic relationships among chickens in the region might provide traits of humanchicken, human-human and chicken-chicken interactions going on since the prehistoric era and could lead to the identification of an ancestral area as a center of chicken domestication[20,21]. This study presents molecular genetic evidences in supporting the illustration of matrilineal characters and genetic diversity of Thai indigenous chickens as well as their genetic relationships with RJF and other potential associated indigenous chickens.
제안 방법
The PCR reaction was performed in a 50 μL reaction volume containing 25 μL of 2× Phusion Blood Direct PCR Master Mix (Thermo Scientific, Waltham, MA, USA), 1 pmol/μL of each primer, 1 μL of the whole blood sample and 22 μL of dH2O.
The PCR was conducted in a thermal cycler (ARKTIK Thermal Cycler, Thermo Scientific, USA) with the conditions of 5 min initial denaturation at 98°C, followed by 35 cycles, each consisting of 1 s denaturation at 98°C, 5 s annealing at 62°C and 1 min extension at 72°C cycle, and then final extension step at 72°C for 5 min.
5× Tris-acetateethylenediaminetetraacetic acid (TAE) buffer. The amplified products were visualized under ultraviolet light and purified using GeneJET PCR Purification Kit (Thermo Scientific, USA) before sending for direct sequencing on both strands at 1st BASE sequencing service (Singapore).
The complete sequence of mtDNA D-loop region has been successfully used in genetic study especially to determine phylogenetic relationships, including genetic distance and genetic variability within and among populations [5,7,15]. We therefore explored the complete mtDNA D-loop sequences of Thai indigenous chickens, including Pradhu-hang-dam (PD), Lueng-hang-khao (LK), Chee (CH), and Dang (DA) for genetic diversity and their relationships with other reference sequences of RJF and domestic chickens. We anticipated gaining significant evidences to better understand chicken domestication in Thailand, which is proposed to be the origin of chicken domestication [2].
이론/모형
0 [19]. An unrooted neighbor-joining (NJ) tree was constructed using Kimura 2-parameter model. Bootstrap values of the phylogenetic tree were estimated with 1,000 repetitions.
5 [18]. To evaluate the sequence variation among and within the population, analysis of molecular variance (AMOVA) and pairwise fixation index (FST) were computed using Arlequin version 3.5 [18].
mtDNA D-loop diversity indices, including the number of haplotype (H), haplotype diversity (Hd), and nucleotide (π) diversity and Tajima’s D test were estimated using DnaSP version 5.10 [17] and Arlequin version 3.5 [18].
성능/효과
The diversity indices calculated for all experimental individuals are presented in Table 3. A total number of haplotypes of all studied populations was 23, of which 16 (69.57%) were singletons and only 7 (30.43%) were shared between the Thai indigenous chickens. The highest number of haplotypes was found in LK representative population while the lowest number detected was in CH (13 and 4 haplotypes, respectively).
The highest number of haplotypes was found in LK representative population while the lowest number detected was in CH (13 and 4 haplotypes, respectively). The Hd of the Thai indigenous chickens was found ranging from 0.6399 to 0.8320 with the highest diversity being estimated in PD population and the lowest diversity in CH population. The averaged haplotype diversity of all population was approximately 0.
The complete mtDNA D-loop sequences of the studied samples were found to be 1,231 to 1,232 bp in length with a total number of 38 variable sites being identified (Table 2). All variable sites were in transition excepting position 391 that was in transversion and position 859 that was single nucleotide insertion/deletion.
43%) were shared between the Thai indigenous chickens. The highest number of haplotypes was found in LK representative population while the lowest number detected was in CH (13 and 4 haplotypes, respectively). The Hd of the Thai indigenous chickens was found ranging from 0.
91%. The majority of the PD and CH representative populations were clustered in haplogroup B, and that of LK and DA were in haplogroup A with frequencies of 53.75% and 67.65%, and 42.11% and 56.67%, respectively. The second major haplogroup of the PD and CH was haplogroup A being accounted respectively for 28.
67%, respectively. The second major haplogroup of the PD and CH was haplogroup A being accounted respectively for 28.75% and 17.65% while that of LK and DA was haplogroup B for 27.63% and 20%.
1 Darwin C The variation of animals and plants under domestication 1st ed London, UK John Murray 1868
2 Fumihito A Miyake T Sumi S One subspecies of the red junglefowl ( Gallus gallus gallus ) suffices as the matriarchic ancestor of all domestic breeds Proc Natl Acad Sci USA 1994 91 12505 9 7809067
8 Hoque MR Seo DW Jo C Reconstruction of phylogenetic relationships of korean chickens using mitochondrial D–loop sequences J Fac Agr, Kyushu Univ 2013 58 287 93
9 Kanginakudru S Metta M Jakati RD Nagaraju J Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken BMC Evol Biol 2008 8 174 18544161
10 Muchadeyi FC Eding H Simianer H Mitochondrial DNA D-loop sequences suggest a Southeast Asian and Indian origin of Zimbabwean village chickens Anim Genet 2008 39 615 22 19032252
11 Sulandari SRI Zein MSA Sartika T Molecular characterization of Indonesian indigenous chickens based on mitochondrial DNA Displacement (D)-loop sequences HAYATI J Biosci 2008 15 145 54
12 Kawabe K Worawut R Taura S Genetic diversity of mtDNA D-loop polymorphisms in laotian native fowl populations Asian-Australas J Anim Sci 2014 27 19 23 25049921
13 Cuc NTK Simianer H Groeneveld LF Weigend S Multiple maternal lineages of vietnamese local chickens inferred by mitochondrial DNA D-loop sequences Asian-Australas J Anim Sci 2011 24 155 61
14 Brown WM Matthew George J Wilson AC Rapid evolution of animal mitochondrial DNA Proc Natl Acad Sci USA 1979 76 1967 71 109836
15 Osman SAM Nishibori M Phylogenetic analysis of South East Asian countries chickens based on mitochondrial DNA variations J Poult Sci 2014 51 248 61
16 Nishibori M Hayashi T Tsudzuki M Yamamoto Y Yasue H Complete sequence of the Japanese quail ( Coturnix japonica ) mitochondrial genome and its genetic relationship with related species Anim Genet 2001 32 380 5 11736810
18 Excoffier L Lischer HE Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows Mol Ecol Resour 2010 10 564 7 21565059
20 Bhuiyan MS Chen S Faruque S Bhuiyan AK Beja-Pereira A Genetic diversity and maternal origin of Bangladeshi chicken Mol Biol Rep 2013 40 4123 8 23640100
21 Silva P Guan X Ho-Shing O Mitochondrial DNA-based Analysis of genetic variation and relatedness among Sri Lankan indigenous chickens and the Ceylon junglefowl ( Gallus lafayetti ) Anim Genet 2009 40 1 9 18945292
22 Liao Y Mo G Sun J Wei F Liao DJ Genetic diversity of Guangxi chicken breeds assessed with microsatellites and the mitochondrial DNA D-loop region Mol Biol Rep 2016 43 415 25 27038171
25 Komiyama T Ikeo K Tateno Y Gojobori T Japanese domesticated chickens have been derived from Shamo traditional fighting cocks Mol Phylogenet Evol 2004 33 16 21 15324835
※ AI-Helper는 부적절한 답변을 할 수 있습니다.