Unraveling the history of the genus Gallus through whole genome sequencing

Mariadassou, Mahendra; Suez, Marie; Sathyakumar, Sanbadam; Vignal, Alain; Arca, Marcella; Nicolas, Pierre; Faraut, Thomas; Esquerré, Diane; Nishibori, Masahide; Vieaud, Agathe; Chen, Chih‐Feng; Phạm, Hùng Mạnh; Roman, Yannick; Hospital, Frederic F.; Zerjal, Tatiana; Rognon, Xavier; Tixier‐Boichard, Michèle

doi:10.1016/j.ympev.2020.107044

Cited by 11 publications

(18 citation statements)

References 51 publications

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“…2). Interestingly, the species relationship of topology T9, also highly supported in Lawal et al (2020), is the one favoured in the recent genome-wide study of Mariadassou et al (2020). The dating of shared ancestry between the species lineages is also uncertain, with more ancient divergence times than those in Lawal et al (2020), reported in other studies (see TimeTree, www.timetree.org).…”

Section: Introductionmentioning

confidence: 93%

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Domestic chicken diversity: Origin, distribution, and adaptation

Lawal

Hanotte

2021

Animal Genetics

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Summary Chicken is the most numerous among the domesticated livestock species. Across cultures, religions, and societies, chicken is widely accepted with little or no taboo compared to other domestic animals. Its adaptability to diverse environmental conditions and demonstrated potential for breeding improvement provide a unique genetic resource for addressing the challenges of food security in a world impacted by climatic change and human population growth. Recent studies, shedding new knowledge on the chicken genomes, have helped reconstruct its past evolutionary history. Here, we review the literature concerning the origin, dispersion, and adaptation of domestic chicken. We highlight the role of human and natural selection in shaping the diversity of the species and provide a few examples of knowledge gaps that may be the focus of future research.

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Section: Introductionmentioning

confidence: 93%

“…(2020), is the one favoured in the recent genome‐wide study of Mariadassou et al . (2020). The dating of shared ancestry between the species lineages is also uncertain, with more ancient divergence times than those in Lawal et al .…”

Section: Phylogeny and Divergence Between Speciesmentioning

confidence: 99%

Domestic chicken diversity: Origin, distribution, and adaptation

Lawal

Hanotte

2021

Animal Genetics

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“…High-quality resequencing datasets of 89 chicken individuals from other BBC, commercial chicken lines, and other distinctive chicken breeds with a coverage >20x were selected and obtained from ENA (Europen Nucleotide Archive) and (KNABIC) Korean National Agricultural Biotechnology Information Center (https://nabic.rda.go.kr/). Hence, we analyze a dataset of 101 individuals (89 public + 12 sequenced as part of this study) from different breeds (see Table 2 for more details) 20,21,25,40,[62][63][64][65][66][67] .…”

Section: Population Samplingmentioning

confidence: 99%

“…More widespread geographic sampling and analysis of allele sharing patterns may provide a definitive answer regarding the origin of BBC. Unlike the initial domestication of the chicken, which may have occurred independently 39,40 in several locations, the BBC has a single origin linked to the rearrangement at the FM locus. Irrespective of the source of all BBC, we identify several Kadaknath-specific genetic changes caused due to selection and introgression events.…”

Section: Did Black-bone Chicken Originate In India?mentioning

confidence: 99%

Hitchhiking of bactericidal/permeability-increasing protein-like gene with the fibromelanosis locus in Kadaknath black-bone-chicken

Shinde

Sharma

Vijay

2022

Preprint

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Black-bone-chicken (BBC) breeds are famous for their distinctive meat texture and taste. However, the relationship between BBC breeds, especially the Kadaknath breed native to India, is poorly understood. Here, we establish that all BBC breeds, including Kadaknath, share a common complex chromosomal rearrangement at the FM locus on the 20th chromosome, which is responsible for the melanin hyperpigmentation throughout the body. While we find breed-specific gene flow between BBC and commercial breeds, the shared ancestry of all BBC breeds and pattern of isolation by distance suggest Kadaknath is closely related to Tibetan BBC. Interestingly, two FM locus proximal regions (~70Kb and ~300 Kb) have signatures of selection unique to Kadaknath. These regions harbor several genes with protein-coding changes, with the Bactericidal/permeability-increasing-protein-like (BPIL) gene having two Kadaknath-specific changes within the protein domains. The absence of these changes in other BBC breeds suggests this variation arose after the separation of these breeds. Our results indicate that the rearrangement at the FM locus and protein-coding changes in the BPIL gene were selected simultaneously in Kadaknath due to close physical linkage. The identification of this FM locus proximal selective sweep sheds light on the distinctiveness of Kadaknath compared to other BBC.

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“…Early studies reconstructing the matrilineal history of domestic chickens based on mitochondrial DNA (mtDNA) analysis supported a monophyletic origin of the red junglefowl (RJF), which serves as the primary wild ancestor of domestic chickens 26 , 27 . However, from the early twenty-first century, numerous mtDNA analyses suggested multiple domestication events 7 , 8 , 28 and the possibility of different Gallus species contributing to the genetic makeup of domestic chickens 20 , 22 , 29 , 30 . Moreover, recent genome-wide data linked domestic chickens most closely to the Southeast Asian subspecies G. g. spadiceus , which locally interbred with other subspecies across South and Southeast Asia 11 .…”

Section: Introductionmentioning

confidence: 99%

Unveiling new perspective of phylogeography, genetic diversity, and population dynamics of Southeast Asian and Pacific chickens

Godinez

Layos

Yamamoto

et al. 2022

Sci Rep

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The complex geographic and temporal origins of chicken domestication have attracted wide interest in molecular phylogeny and phylogeographic studies as they continue to be debated up to this day. In particular, the population dynamics and lineage-specific divergence time estimates of chickens in Southeast Asia (SEA) and the Pacific region are not well studied. Here, we analyzed 519 complete mitochondrial DNA control region sequences and identified 133 haplotypes with 70 variable sites. We documented 82.7% geographically unique haplotypes distributed across major haplogroups except for haplogroup C, suggesting high polymorphism among studied individuals. Mainland SEA (MSEA) chickens have higher overall genetic diversity than island SEA (ISEA) chickens. Phylogenetic trees and median-joining network revealed evidence of a new divergent matrilineage (i.e., haplogroup V) as a sister-clade of haplogroup C. The maximum clade credibility tree estimated the earlier coalescence age of ancestral D-lineage (i.e., sub-haplogroup D2) of continental chickens (3.7 kya; 95% HPD 1985–4835 years) while island populations diverged later at 2.1 kya (95% HPD 1467–2815 years). This evidence of earlier coalescence age of haplogroup D ancestral matriline exemplified dispersal patterns to the ISEA, and thereafter the island clade diversified as a distinct group.

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Unraveling the history of the genus Gallus through whole genome sequencing

Cited by 11 publications

References 51 publications

Domestic chicken diversity: Origin, distribution, and adaptation

Domestic chicken diversity: Origin, distribution, and adaptation

Hitchhiking of bactericidal/permeability-increasing protein-like gene with the fibromelanosis locus in Kadaknath black-bone-chicken

Unveiling new perspective of phylogeography, genetic diversity, and population dynamics of Southeast Asian and Pacific chickens

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