Integrative analysis of transcriptomics and metabolomics to reveal the melanogenesis pathway of muscle and related meat characters in Wuliangshan black-boned chickens

Tengfei Dou; Shixiong Yan; Lixian Liu; Kun Wang; Zonghui Jian; Zhiqiang Xu; Jingying Zhao; Qiuting Wang; Shuai Sun; Mir Zulqarnain Talpur; Xiaohua Duan; Dahai Gu; Yang He; Yanli Du; Alsoufi Mohammed Abdulwahid; Qihua Li; Hua Rong; Weina Cao; Zhengchang Su; Guiping Zhao; Ranran Liu; Sumei Zhao; Ying Huang; Marinus F.W. te Pas; Changrong Ge; Junjing Jia

doi:10.1186/s12864-022-08388-w

Integrative analysis of transcriptomics and metabolomics to reveal the melanogenesis pathway of muscle and related meat characters in Wuliangshan black-boned chickens

Tengfei Dou, Shixiong Yan, Lixian Liu, Kun Wang, Zonghui Jian, Zhiqiang Xu, Jingying Zhao, Qiuting Wang, Shuai Sun, Mir Zulqarnain Talpur, Xiaohua Duan, Dahai Gu, Yang He, Yanli Du, Alsoufi Mohammed Abdulwahid, Qihua Li, Hua Rong, Weina Cao, Zhengchang Su, Guiping ZhaoRanran Liu, Sumei Zhao, Ying Huang, Marinus F.W. te Pas^*, Changrong Ge^*, Junjing Jia^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

20 Citations (Scopus)

Abstract

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.

Original language	English
Article number	173
Journal	BMC Genomics
Volume	23
Issue number	1
DOIs	https://doi.org/10.1186/s12864-022-08388-w
Publication status	Published - 2 Mar 2022

Keywords

Lysophospholipid
Melanogenesis
Metabolomics
Muscle metabolite
Transcriptomics
Wuliangshang black-boned chickens

Access to Document

10.1186/s12864-022-08388-wLicence: CC BY

https://edepot.wur.nl/566704Licence: CC BY

RNA-Seq data for Wuliangshan black-boned chickens
Dou, T. (Creator), Yan, S. (Creator), Liu, L. (Creator), Wang, K. (Creator), Jian, Z. (Creator), Xu, Z. (Creator), Zhao, J. (Creator), Wang, Q. (Creator), Sun, S. (Creator), Talpur, M. Z. (Creator), Duan, X. (Creator), Gu, D. (Creator), He, Y. (Creator), Du, Y. (Creator), Abdulwahid, A. M. (Creator), Li, Q. (Creator), Rong, H. (Creator), Cao, W. (Creator), Su, Z. (Creator), Zhao, G. (Creator), Liu, R. (Creator), Zhao, S. (Creator), Huang, Y. (Creator), te Pas, M. (Creator), Ge, C. (Creator) & Jia, J. (Creator), 31 Dec 2022
https://ngdc.cncb.ac.cn/gsa/browse/CRA004775
Dataset
Integrative analysis of transcriptomics and metabolomics to reveal the melanogenesis pathway of muscle and related meat characters in Wuliangshan black-boned chickens
Dou, T. (Creator), Yan, S. (Creator), Liu, L. (Creator), Wang, K. (Creator), Jian, Z. (Creator), Xu, Z. (Creator), Zhao, J. (Creator), Wang, Q. (Creator), Sun, S. (Creator), Talpur, M. Z. (Creator), Duan, X. (Creator), Gu, D. (Creator), He, Y. (Creator), Du, Y. (Creator), Abdulwahid, A. M. (Creator), Li, Q. (Creator), Rong, H. (Creator), Cao, W. (Creator), Su, Z. (Creator), Zhao, G. (Creator), Liu, R. (Creator), Zhao, S. (Creator), Huang, Y. (Creator), te Pas, M. (Creator), Ge, C. (Creator) & Jia, J. (Creator), 3 Mar 2022
DOI: 10.6084/m9.figshare.c.5873123
Dataset

Cite this

Dou, T., Yan, S., Liu, L., Wang, K., Jian, Z., Xu, Z., Zhao, J., Wang, Q., Sun, S., Talpur, M. Z., Duan, X., Gu, D., He, Y., Du, Y., Abdulwahid, A. M., Li, Q., Rong, H., Cao, W., Su, Z., ... Jia, J. (2022). Integrative analysis of transcriptomics and metabolomics to reveal the melanogenesis pathway of muscle and related meat characters in Wuliangshan black-boned chickens. BMC Genomics, 23(1), Article 173. https://doi.org/10.1186/s12864-022-08388-w

@article{24b868b1ad594826ad9fc99bcd2463d4,

title = "Integrative analysis of transcriptomics and metabolomics to reveal the melanogenesis pathway of muscle and related meat characters in Wuliangshan black-boned chickens",

abstract = "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.",

keywords = "Lysophospholipid, Melanogenesis, Metabolomics, Muscle metabolite, Transcriptomics, Wuliangshang black-boned chickens",

author = "Tengfei Dou and Shixiong Yan and Lixian Liu and Kun Wang and Zonghui Jian and Zhiqiang Xu and Jingying Zhao and Qiuting Wang and Shuai Sun and Talpur, {Mir Zulqarnain} and Xiaohua Duan and Dahai Gu and Yang He and Yanli Du and Abdulwahid, {Alsoufi Mohammed} and Qihua Li and Hua Rong and Weina Cao and Zhengchang Su and Guiping Zhao and Ranran Liu and Sumei Zhao and Ying Huang and {te Pas}, {Marinus F.W.} and Changrong Ge and Junjing Jia",

year = "2022",

month = mar,

day = "2",

doi = "10.1186/s12864-022-08388-w",

language = "English",

volume = "23",

journal = "BMC Genomics",

issn = "1471-2164",

publisher = "BioMed Central",

number = "1",

}

Dou, T, Yan, S, Liu, L, Wang, K, Jian, Z, Xu, Z, Zhao, J, Wang, Q, Sun, S, Talpur, MZ, Duan, X, Gu, D, He, Y, Du, Y, Abdulwahid, AM, Li, Q, Rong, H, Cao, W, Su, Z, Zhao, G, Liu, R, Zhao, S, Huang, Y, te Pas, MFW, Ge, C & Jia, J 2022, 'Integrative analysis of transcriptomics and metabolomics to reveal the melanogenesis pathway of muscle and related meat characters in Wuliangshan black-boned chickens', BMC Genomics, vol. 23, no. 1, 173. https://doi.org/10.1186/s12864-022-08388-w

TY - JOUR

T1 - Integrative analysis of transcriptomics and metabolomics to reveal the melanogenesis pathway of muscle and related meat characters in Wuliangshan black-boned chickens

AU - Dou, Tengfei

AU - Yan, Shixiong

AU - Liu, Lixian

AU - Wang, Kun

AU - Jian, Zonghui

AU - Xu, Zhiqiang

AU - Zhao, Jingying

AU - Wang, Qiuting

AU - Sun, Shuai

AU - Talpur, Mir Zulqarnain

AU - Duan, Xiaohua

AU - Gu, Dahai

AU - He, Yang

AU - Du, Yanli

AU - Abdulwahid, Alsoufi Mohammed

AU - Li, Qihua

AU - Rong, Hua

AU - Cao, Weina

AU - Su, Zhengchang

AU - Zhao, Guiping

AU - Liu, Ranran

AU - Zhao, Sumei

AU - Huang, Ying

AU - te Pas, Marinus F.W.

AU - Ge, Changrong

AU - Jia, Junjing

PY - 2022/3/2

Y1 - 2022/3/2

N2 - 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.

AB - 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.

KW - Lysophospholipid

KW - Melanogenesis

KW - Metabolomics

KW - Muscle metabolite

KW - Transcriptomics

KW - Wuliangshang black-boned chickens

U2 - 10.1186/s12864-022-08388-w

DO - 10.1186/s12864-022-08388-w

M3 - Article

C2 - 35236293

AN - SCOPUS:85125568604

SN - 1471-2164

VL - 23

JO - BMC Genomics

JF - BMC Genomics

IS - 1

M1 - 173

ER -

Integrative analysis of transcriptomics and metabolomics to reveal the melanogenesis pathway of muscle and related meat characters in Wuliangshan black-boned chickens

Abstract

Keywords

Access to Document

Fingerprint

Datasets

RNA-Seq data for Wuliangshan black-boned chickens

Integrative analysis of transcriptomics and metabolomics to reveal the melanogenesis pathway of muscle and related meat characters in Wuliangshan black-boned chickens

Cite this