RNA-Seq Reveals Pathways Responsible for Meat Quality Characteristic Differences between Two Yunnan Indigenous Chicken Breeds and Commercial Broilers

Author:

Liu Yong123ORCID,Zhang Xia24,Wang Kun2,Li Qihua2,Yan Shixiong12,Shi Hongmei12ORCID,Liu Lixian25,Liang Shuangmin6,Yang Min2,Su Zhengchang7,Ge Changrong2,Jia Junjing2,Xu Zhiqiang6,Dou Tengfei2ORCID

Affiliation:

1. Yunnan Rural Revitalization Education Institute, Yunnan Open University, Kunming 650101, China

2. College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China

3. Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Guangxi Bufialo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China

4. School of Biological and Food Engineering, Lvliang University, Lvliang 033000, China

5. Institute of Science and Technology, Chuxiong Normal University, Chuxiong 675000, China

6. College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China

7. Department of Bioinformatics and Genomics, College of Computing and Informatics, the University of North Carolina at Charlotte, Charlotte, NC 28223, USA

Abstract

Poultry is a source of meat that is in great demand in the world. The quality of meat is an imperative point for shoppers. To explore the genes controlling meat quality characteristics, the growth and meat quality traits and muscle transcriptome of two indigenous Yunnan chicken breeds, Wuding chickens (WDs) and Daweishan mini chickens (MCs), were compared with Cobb broilers (CBs). The growth and meat quality characteristics of these two indigenous breeds were found to differ from CB. In particular, the crude fat (CF), inosine monophosphate content, amino acid (AA), and total fatty acid (TFA) content of WDs were significantly higher than those of CBs and MCs. In addition, it was found that MC pectoralis had 420 differentially expressed genes (DEGs) relative to CBs, and WDs had 217 DEGs relative to CBs. Among them, 105 DEGs were shared. The results of 10 selected genes were also confirmed by qPCR. The differentially expressed genes were six enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathways including lysosomes, phagosomes, PPAR signaling pathways, cell adhesion molecules, cytokine–cytokine receptor interaction, and phagosome sphingolipid metabolism. Interestingly, four genes (LPL, GK, SCD, and FABP7) in the PPAR signal pathway related to fatty acid (FA) metabolism were elevated in WD muscles, which may account for higher CF, inosine monophosphate content, and AA and FA contents, key factors affecting meat quality. This work laid the foundation for improving the meat quality of Yunnan indigenous chickens, especially WD. In future molecular breeding, the genes in this study can be used as molecular screening markers and applied to the molecular breeding of chicken quality characteristics.

Funder

National Natural Science Foundation of China

Natural Science Foundation of Yunnan Province

Yunnan Xichou Black Bone Chicken Industry Science and Technology Mission

Scientific Research Fund Project of Yunnan Provincial Education Department

Publisher

MDPI AG

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