Breeding history and candidate genes responsible for black skin of Xichuan black-bone chicken

Li, Donghua; Sun, Guirong; Zhang, Meng; Cao, Yanfang; Zhang, Chenxi; Fu, Yawei; Li, Fang; Li, Guoxi; Jiang, Ruirui; Han, Ruili; Li, Zhuanjian; Wang, Yanbin; Tian, Yadong; Liu, Xiaojun; Li, Wenting; Kang, Xin

doi:10.1186/s12864-020-06900-8

Cited by 46 publications

(45 citation statements)

References 89 publications

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“…This method can aid in identifying many novel SNPs and QTLs associated with phenotypes of interest. In previous GWAS, imputation from low-density SNP chip genotypes to the WGS level was implemented in chickens ( Huang et al, 2018 ; Li D. et al, 2020 ), pigs ( Yan et al, 2018 ), and cattle ( Höglund et al, 2015 ). Imputed genotypes with sufficiently high imputation accuracy are necessary to obtain reliable results in follow-up analyses, such as GWAS.…”

Section: Discussionmentioning

confidence: 99%

“…The weight traits and carcass composition traits were measured in line B as follows: body weight at 42 day of age (BW42), carcass weight (CW), eviscerated weight (EW), whole thigh weight (WThW, weight including feet, and single), thigh weight (ThW, weight with bone, and single), thigh muscle weight (ThMW, single), and the WThW, ThW, and ThMW as percentages of BW42 (WThP, ThP, and ThMP). In addition, the same method ( Li D. et al, 2020 ) was used to calculate the feed intake from 28 to 42 days of age (FI).…”

Section: Methodsmentioning

confidence: 99%

“…Whole-genome sequences (WGS) of 230 broilers (101 males and 129 females) from the same line in G7 were used for the reference panel ( Li D. et al, 2020 ). Briefly, an average depth of 10× was acquired, and variant calling and SNP filtering were performed according to a standardized bioinformatics pipeline.…”

Section: Methodsmentioning

confidence: 99%

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Identification of Major Loci and Candidate Genes for Meat Production-Related Traits in Broilers

et al. 2021

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BackgroundCarcass traits are crucial characteristics of broilers. However, the underlying genetic mechanisms are not well understood. In the current study, significant loci and major-effect candidate genes affecting nine carcass traits related to meat production were analyzed in 873 purebred broilers using an imputation-based genome-wide association study.ResultsThe heritability estimates of nine carcass traits, including carcass weight, thigh muscle weight, and thigh muscle percentage, were moderate to high and ranged from 0.21 to 0.39. Twelve genome-wide significant SNPs and 118 suggestively significant SNPs of 546,656 autosomal variants were associated with carcass traits. All SNPs for six weight traits (body weight at 42 days of age, carcass weight, eviscerated weight, whole thigh weight, thigh weight, and thigh muscle weight) were clustered around the 24.08 Kb region (GGA24: 5.73–5.75 Mb) and contained only one candidate gene (DRD2). The most significant SNP, rs15226023, accounted for 4.85–7.71% of the estimated genetic variance of the six weight traits. The remaining SNPs for carcass composition traits (whole thigh percentage and thigh percentage) were clustered around the 42.52 Kb region (GGA3: 53.03–53.08 Mb) and contained only one candidate gene (ADGRG6). The most significant SNP in this region, rs13571431, accounted for 11.89–13.56% of the estimated genetic variance of two carcass composition traits. Some degree of genetic differentiation in ADGRG6 between large and small breeds was observed.ConclusionWe identified one 24.08 Kb region for weight traits and one 42.52 Kb region for thigh-related carcass traits. DRD2 was the major-effect candidate gene for weight traits, and ADGRG6 was the major-effect candidate gene for carcass composition traits. Our results supply essential information for causative mutation identification of carcass traits in broilers.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Identification of Major Loci and Candidate Genes for Meat Production-Related Traits in Broilers

et al. 2021

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“…The expression of two other genes, SLMO2, and TUBB1 were also significantly increased in expression in both skin and muscle tissue from adult fibromelanosis chickens might contribute to the dermal hyperpigmentation phenotype [23] . Analysis of RNA-seq suggested that SLMO2, ATP5e, and EDN3 were differentially expressed between the black and yellow skin groups, combined analysis of genomic data found that EDN3 might interact with the upstream ncRNA LOC101747896 to generate black skin color during melanogenesis [24] . Wang et al study indicated that a T2270C mutation in GNAS gene promoter in chicken is correlated strongly with the skin color traits [25] .…”

Section: Discussionmentioning

confidence: 99%

Whole genome sequencing revealed genetic diversity and selection of Guangxi indigenous chickens

Sun¹,

Chen

M³

et al. 2021

Preprint

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Guangxi chickens play an important role in promoting the high-quality development of the broiler industry in China, but their value and potential are yet to be discovered. To determine the genetic diversity and population structure of Guangxi indigenous chicken, we analyzed the whole genomes of 185 chicken from 8 phenotypically and geographically representative Guangxi chicken breeds, together with 12 RJFt, 12 BRA and 12 WL genomes available from previous studies. Calculation of heterozygosity (Hp), nucleotide diversity (π), and LD level indicated that Guangxi populations were characterized by higher genetic diversity and lower differentiation than RJFt and commercial breeds except HGFC. Population structure analysis also confirmed the introgression from commercial broiler breeds. Each population clustered together while the overall differentiation was small, MA has the richest genetic diversity among all varieties. Selective sweep analysis revealed BCO2, EDN3 and other candidate genes have received strong selection in local breeds, these also provided novel breeding visual and data basis for future breeding.

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“…The same animals as for transcriptome and metabolome analyses were used. Total RNAs were extracted from breast muscle, leg muscle and skin tissue of one day aged chickens [30]. Additional le 1: Table S1 describes the gene primers (Invitrogen Biotechnology Co., Ltd., Shanghai, China).…”

Section: Transcriptome Analysismentioning

confidence: 99%

Integrative Analysis of Transcriptomics and Metabolomics to Reveal the Melanogenesis Pathway of Muscle and Related Meat Characters in Wuliangshan Black-Boned Chickens

Dou¹,

Yan²,

Liu³

et al. 2021

Preprint

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Background: Melanin is an important antioxidant in food, and has been used in medicine and cosmetology. Chicken meat with high melanin content from black-boned chickens have been considered a high nutritious food with potential medicinal properties. The molecular mechanism of melanogenesis of skeletal muscle in black-boned chickens remain poorly understood. This study investigated the biological gene-metabolite associations regulating the muscle melanogenesis pathways in Wuliangshan black-boned chickens with two normal boned chicken breeds as control.Results: We identified 25 differentially expressed genes and 11 transcription factors in the melanogenesis pathways. High levels of the meat flavor compounds inosine monophosphate, hypoxanthine, lysophospholipid, hydroxyoctadecadienoic acid, and nicotinamide mononucleotide were found in Wuliangshan black-boned chickens.Conclusion: Integrative analysis of transcriptomics and metabolomics revealed the dual physiological functions of the PDZK1 gene, involved in pigmentation and/or melanogenesis and regulating the phospholipid signaling processes in muscle of black boned chickens.

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Breeding history and candidate genes responsible for black skin of Xichuan black-bone chicken

Cited by 46 publications

References 89 publications

Identification of Major Loci and Candidate Genes for Meat Production-Related Traits in Broilers

Identification of Major Loci and Candidate Genes for Meat Production-Related Traits in Broilers

Whole genome sequencing revealed genetic diversity and selection of Guangxi indigenous chickens

Integrative Analysis of Transcriptomics and Metabolomics to Reveal the Melanogenesis Pathway of Muscle and Related Meat Characters in Wuliangshan Black-Boned Chickens

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