Open AccessTranscriptomic profiling in muscle and adipose tissue identifies genes related to growth and lipid deposition
Author(s) -
Xuan Tao,
Yan Liang,
Xuemei Yang,
Jianhui Pang,
Zhijun Zhong,
Xiaohui Chen,
Yuekui Yang,
Kai Zeng,
Runming Kang,
Lei Ye,
Sancheng Ying,
Jing Gong,
Yiren Gu,
Xuebin Lv
Publication year - 2017
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0184120
Subject(s) - biology , transcriptome , adipose tissue , phenotype , gene , candidate gene , genetics , gene expression profiling , quantitative trait locus , computational biology , gene expression , endocrinology
Growth performance and meat quality are important traits for the pig industry and consumers. Adipose tissue is the main site at which fat storage and fatty acid synthesis occur. Therefore, we combined high-throughput transcriptomic sequencing in adipose and muscle tissues with the quantification of corresponding phenotypic features using seven Chinese indigenous pig breeds and one Western commercial breed (Yorkshire). We obtained data on 101 phenotypic traits, from which principal component analysis distinguished two groups: one associated with the Chinese breeds and one with Yorkshire. The numbers of differentially expressed genes between all Chinese breeds and Yorkshire were shown to be 673 and 1056 in adipose and muscle tissues, respectively. Functional enrichment analysis revealed that these genes are associated with biological functions and canonical pathways related to oxidoreductase activity, immune response, and metabolic process. Weighted gene coexpression network analysis found more coexpression modules significantly correlated with the measured phenotypic traits in adipose than in muscle, indicating that adipose regulates meat and carcass quality. Using the combination of differential expression, QTL information, gene significance, and module hub genes, we identified a large number of candidate genes potentially related to economically important traits in pig, which should help us improve meat production and quality.