Genetic Diversity of Mitochondrial DNA of Chinese Black-bone Chicken

Zhang, T; Du, Wei; Lu, Hongzhao; Wang, L

doi:10.1590/1806-9061-2018-0739

Cited by 6 publications

(5 citation statements)

References 15 publications

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“…Studies of BBCs have focused on the chemical properties of the meat (Jaturasitha et al 2008;Tian et al 2011), distribution of melanin pigmentation (Nganvongpanit et al 2020), molecular mechanism underlying melanin deposition (Dorshorst et al 2011;Shinomiya et al 2012;Yu et al 2018;Li et al 2019), as well as the origin and evolution of fibromelanosis (Dharmayanthi et al 2017;Sohn et al 2018). Additionally, genetic analyses based on genetic markers, such as microsatellites (Tang et al 2005;Qu et al 2006;Yu et al 2006) and mitochondrial DNA (mtDNA) (Zhu et al 2014;Guo et al 2017;Jia et al 2017;Zhang et al 2018;Liu et al 2018;Weng et al 2019) have attempted to unravel the population genetic history of BBCs. However, the scarcity of sampled breeds is a major limitation of these studies, and this issue is further compounded by the complexity of chicken demographics and domestication histories (Tixier-Boichard et al 2011;Miao et al 2013;Lan et al 2017;Huang et al 2018a).…”

Section: Introductionmentioning

confidence: 99%

Mitochondrial DNA diversity and demographic history of Black-boned chickens in China

Huang

Weng

et al. 2021

Mitochondrial DNA Part B

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Black-boned chickens (Gallus domesticus, herein abbreviated BBCs) are well known for their unique appearance and medicinal properties and have a long breeding history in China. However, the genetic diversity and demographic history of BBCs remain unclear. In this study, we analyzed 844 mitochondrial DNA D-loop sequences, including 346 de novo sequences and 498 previously published sequences from 20 BBC breeds. We detected a generally high level of genetic diversity among the BBCs, with average haplotype and nucleotide diversities of 0.917 ± 0.0049 and 0.01422, respectively. Nucleotide diversity was highest in populations from Southwest China (0.01549 ± 0.00026), particularly in Yunnan Province (0.01624 ± 0.00025). Significant genetic divergence was detected between most breeds, particularly between Yunnan chickens and those from all other provinces. Haplogroups F and G had the highest levels of genetic diversity and were restricted to Southwest China, particularly Yunnan Province. Based on neutrality tests and mismatch distribution analyses, we did not obtain evidence for rapid population expansions and observed similar demographic histories in BBCs and local non-BBCs. Our results suggest that Chinese BBCs have complex breeding histories and may be selected in situ from local domestic chickens. These results improve our understanding of the genetic heritage and breeding histories of these desirable chickens.

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Section: Introductionmentioning

confidence: 99%

Mitochondrial DNA diversity and demographic history of Black-boned chickens in China

Huang

Weng

et al. 2021

Mitochondrial DNA Part B

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“…The lack of data from India and the considerable interest in BBC breeds in Europe, China, and Korea have meant that studies have focused mainly on non-Indian BBCs. Hence, Southern China and Tibet are considered the source of all BBC breeds ( Zhu et al, 2014 ; Zhang et al, 2018 ; Xue et al, 2023 ). However, despite a traditionally restricted geographic distribution, the Kadaknath breed has nucleotide diversity comparable to Chinese BBC breeds and much higher than the Korean BBC.…”

Section: Discussionmentioning

confidence: 99%

Decoding the fibromelanosis locus complex chromosomal rearrangement of black-bone chicken: genetic differentiation, selective sweeps and protein-coding changes in Kadaknath chicken

2023

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Black-bone chicken (BBC) meat is popular for its distinctive taste and texture. A complex chromosomal rearrangement at the fibromelanosis (Fm) locus on the 20th chromosome results in increased endothelin-3 (EDN3) gene expression and is responsible for melanin hyperpigmentation in BBC. We use public long-read sequencing data of the Silkie breed to resolve high-confidence haplotypes at the Fm locus spanning both Dup1 and Dup2 regions and establish that the Fm_2 scenario is correct of the three possible scenarios of the complex chromosomal rearrangement. The relationship between Chinese and Korean BBC breeds with Kadaknath native to India is underexplored. Our data from whole-genome re-sequencing establish that all BBC breeds, including Kadaknath, share the complex chromosomal rearrangement junctions at the fibromelanosis (Fm) locus. We also identify two Fm locus proximal regions (∼70 Kb and ∼300 Kb) with signatures of selection unique to Kadaknath. These regions harbor several genes with protein-coding changes, with the bactericidal/permeability-increasing-protein-like gene having two Kadaknath-specific changes within protein domains. Our results indicate that protein-coding changes in the bactericidal/permeability-increasing-protein-like gene hitchhiked with the Fm locus in Kadaknath due to close physical linkage. Identifying this Fm locus proximal selective sweep sheds light on the genetic distinctiveness of Kadaknath compared to other BBC.

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“…The lack of data from India and the considerable interest in BBC breeds in Europe, China, and Korea has meant that studies have focussed mainly on non-Indian BBC. Hence, Southern China and Tibet are considered the source of all BBC breeds[25, 77]. However, despite a traditionally restricted geographic distribution, the Kadaknath breed has nucleotide diversity comparable to Chinese BBC breeds and much higher than the Korean BBC.…”

Section: Discussionmentioning

confidence: 99%

“…China and Tibet are considered the source of all BBC breeds [25,77]. However, despite a traditionally restricted geographic distribution, the Kadaknath breed has nucleotide diversity comparable to Chinese BBC breeds and much higher than the Korean BBC.…”

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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Genetic Diversity of Mitochondrial DNA of Chinese Black-bone Chicken

Abstract: domestic chicken population, and the two populations are closely related, which are multiple origins from different regions in Asia.

Cited by 6 publications

References 15 publications

Mitochondrial DNA diversity and demographic history of Black-boned chickens in China

Mitochondrial DNA diversity and demographic history of Black-boned chickens in China

Decoding the fibromelanosis locus complex chromosomal rearrangement of black-bone chicken: genetic differentiation, selective sweeps and protein-coding changes in Kadaknath chicken

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

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