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Chicken domestication: an updated perspective based on mitochondrial genomes

by Liang, J-P , Zhang, Y-P , Yu, N , Shen, Y-Y , Baig, M , Ouyang, Y-N , Mitra, B , Murphy, R W , Palanichamy, M G , Chaudhuri, T K , Yao, Y-G , Peng, M-S , Beja-Pereira, A , Miao, Y-W , Yang, Z-Y , Kong, Q-P , Wu, G-S , Pianchou, G

in Animals / Asia, Southeastern / Base Sequence / Breeding / Chickens / Chickens - classification / Chickens - genetics / Chromosomes / Deoxyribonucleic acid / DNA / DNA, Mitochondrial - classification / DNA, Mitochondrial - genetics / Domestication / Gallus gallus / Gallus gallus domesticus / Genetic diversity / Genetic Variation / Genome, Mitochondrial / Geographical distribution / Haplotypes / Mitochondrial DNA / Molecular Sequence Data / Original / Phylogenetics / Phylogeny / Phylogeography / Poultry / Sequence Analysis, DNA

2013

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Chicken domestication: an updated perspective based on mitochondrial genomes

2013

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2013

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Journal Article

Chicken domestication: an updated perspective based on mitochondrial genomes

Liang, J-P,

Zhang, Y-P,

Yu, N,

Shen, Y-Y,

Baig, M,

Ouyang, Y-N,

Mitra, B,

Murphy, R W,

Palanichamy, M G,

Chaudhuri, T K,

Yao, Y-G,

Peng, M-S,

Beja-Pereira, A,

Miao, Y-W,

Yang, Z-Y,

Kong, Q-P,

Wu, G-S,

Pianchou, G

2013

Overview

Domestic chickens (Gallus gallus domesticus) fulfill various roles ranging from food and entertainment to religion and ornamentation. To survey its genetic diversity and trace the history of domestication, we investigated a total of 4938 mitochondrial DNA (mtDNA) fragments including 2843 previously published and 2095 de novo units from 2044 domestic chickens and 51 red junglefowl (Gallus gallus). To obtain the highest possible level of molecular resolution, 50 representative samples were further selected for total mtDNA genome sequencing. A fine-gained mtDNA phylogeny was investigated by defining haplogroups A-I and W-Z. Common haplogroups A-G were shared by domestic chickens and red junglefowl. Rare haplogroups H-I and W-Z were specific to domestic chickens and red junglefowl, respectively. We re-evaluated the global mtDNA profiles of chickens. The geographic distribution for each of major haplogroups was examined. Our results revealed new complexities of history in chicken domestication because in the phylogeny lineages from the red junglefowl were mingled with those of the domestic chickens. Several local domestication events in South Asia, Southwest China and Southeast Asia were identified. The assessment of chicken mtDNA data also facilitated our understanding about the Austronesian settlement in the Pacific.

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Publisher

Springer Nature B.V,Nature Publishing Group

Subject

/ Chickens - classification

/ Chickens - genetics