Association of SNP rs80659072 in the ZRS with polydactyly in Beijing You chickens

Chu, Qing; Yan, Zhixun; Zhang, Jian; Usman, Τahir; Zhang, Yao; Liu, Hui; Wang, Haihong; Geng, Ailian; Liu, Huagui

doi:10.1371/journal.pone.0185953

Cited by 9 publications

(9 citation statements)

References 32 publications

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“…The Beijing You chicken is an ancient breed that originated during the Qing Dynasty in Beijing. Known as “royal chickens”, they are valued for their high-quality meat and eggs, and are uniquely marked by a crest on the head, a beard under the lower jaw, and feathers on both shanks [ 15 – 17 ].…”

Section: Methodsmentioning

confidence: 99%

Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs

et al. 2018

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BackgroundMaintaining maximum genetic diversity and preserving breed viability in conserved populations necessitates the rigorous evaluation of conservation schemes. Three chicken breeds (Baier Yellow Chicken (BEC), Beijing You Chicken (BYC) and Langshan Chicken (LSC)) are currently in conservation programs in China. Changes in genetic diversity were measured by heterozygosity, genomic inbreeding coefficients, and autozygosity, using estimates derived from runs of homozygosity (ROH) that were identified using SNPs.ResultsNinety DNA samples were collected from three generations for each breed. In the most recent generation, the highest genetic diversity was observed in LSC, followed by BEC and BYC. Inbreeding coefficients based on ROH for the three breeds declined slightly between the first and middle generations, and then rapidly increased. No inbreeding coefficients exceeded 0.1. Population structure assessments using neighbor-joining tree analysis, principal components analysis, and STRUCTURE analysis indicated that no genetic differentiation existed within breeds. LD decay and ROH at different cut-off lengths were used to identify traces left by recent or ancient inbreeding. Few long ROH were identified, indicating that inbreeding has been largely avoided with the current conservation strategy. The observed losses in genetic diversity and occurrences of inbreeding might be consequences of sub-optimal effective population sizes.ConclusionsThe conserved Chinese chicken populations have high genomic diversity under the current conservation program (R: F). Furthermore, this study highlights the need to monitor dynamic changes in genetic diversity in conserved breeds over successive generations. Our research provides new insights into genetic diversity dynamics in conserved populations, and lays a solid foundation for improving conservation schemes.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4973-6) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs

et al. 2018

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“…The Beijing You chicken is an ancient breed that originated during the Qing Dynasty in Beijing. Known as -royal chickens‖, they are valued for their high-quality meat and eggs, and are uniquely marked by a crest on the head, a beard under the lower jaw, and feathers on both shanks [15][16][17].…”

Section: Samplingmentioning

confidence: 99%

Genomic Diversity Dynamics in Conserved Chicken Populations are Revealed by Genome-Wide SNPs

Zhang¹,

Wang²,

Tang³

et al. 2019

Prime Archives in Genetics

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Background: Maintaining maximum genetic diversity and preserving breed viability in conserved populations necessitates the rigorous evaluation of conservation schemes. Three chicken breeds (Baier Yellow Chicken (BEC), Beijing You Chicken (BYC) and Langshan Chicken (LSC)) are currently in conservation programs in China. Changes in genetic diversity were measured by heterozygosity, genomic inbreeding coefficients, and autozygosity, using estimates derived from runs of homozygosity (ROH) that were identified using SNPs.

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“…Beijing‐You chicken (BYC) is a typical indigenous breed of China characterized by a slow growth rate, high‐quality traits of meat, and unique appearance (Chu et al., 2017). Recent studies have investigated the nutritional components, muscle fiber characteristics, color, texture, and structure of the meat of BYC, with the objective to characterize their special meat quality properties (Fu et al., 2015; Zhao et al., 2011).…”

Section: Introductionmentioning

confidence: 99%

UHPLC‐QTOF/MS‐based comparative metabolomics in pectoralis major of fast‐ and slow‐growing chickens at market ages

Zhang

Cao

Geng

et al. 2021

Food Science & Nutrition

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The molecular regulatory mechanism underlying meat quality between different chicken genotypes remains elusive. This study aimed to identify the differences in metabolites and pathways in pectoralis major (breast muscle) between a commercial fast‐growing chicken genotype (Cobb500) and a slow‐growing Chinese native chicken genotype (Beijing‐You chickens, BYC) at market ages respectively based on ultra‐high‐performance liquid chromatography‐quadrupole/time of flight mass spectrometry (UHPLC‐QTOF/MS). Eighteen metabolites were identified as potential biomarkers between BYC and Cobb500 at market ages. Among them, L‐cysteine exhibited a higher relative intensity in BYC compared with Cobb500 and was enriched into 10 potential flavor‐associated KEGG pathways. In addition, the glycerophospholipid metabolism pathway was found to be associated with chicken meat flavor and the accumulation of sn‐glycerol 3‐phosphate and acetylcholine was more predominant in BYC than that in Cobb500, which were catalyzed by glycerophosphocholine phosphodiesterase (GPCPD1, EC:3.1.4.2), choline O‐acetyltransferase (CHAT, EC:2.3.1.6), and acetylcholinesterase (ACHE, EC:3.1.1.7). Overall, the present study provided some metabolites and pathways for further investigating the roles of the differences in meat flavor quality in breast muscle between Cobb500 and BYC at market ages.

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Association of SNP rs80659072 in the ZRS with polydactyly in Beijing You chickens

Cited by 9 publications

References 32 publications

Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs

Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs

Genomic Diversity Dynamics in Conserved Chicken Populations are Revealed by Genome-Wide SNPs

UHPLC‐QTOF/MS‐based comparative metabolomics in pectoralis major of fast‐ and slow‐growing chickens at market ages

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