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Int J Biol Sci 2014; 10(9):1039-1050. doi:10.7150/ijbs.9737 This issue Cite

Research Paper

Co-Expression Analysis of Fetal Weight-Related Genes in Ovine Skeletal Muscle during Mid and Late Fetal Development Stages

Lingyang Xu^1,4,5#, Fuping Zhao^1#, Hangxing Ren^1,2#, Li Li^1,3#, Jian Lu¹, Jiasen Liu¹, Shifang Zhang¹, George E. Liu⁴, Jiuzhou Song⁵, Li Zhang¹, Caihong Wei^1✉, Lixin Du^1✉

1. National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China;
2. Chongqing Academy of Animal Sciences, Chongqing, 402460, China;
3. College of Animal Science and Technology, Sichuan Agricultural University, Ya′an, Sichuan, 625014, China.
4. Animal Genomics and Improvement Laboratory, U.S. Department of Agriculture-Agricultural Research Services, Beltsville, Maryland 20705, USA;
5. Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland 20742, USA.
^#These authors contributed equally to this work.

✉ Corresponding author: Dr. Lixin Du, E-mail: lxdunet. Tel: (86)1062819997. Or Dr. Caihong Wei, E-mail: weichxxcom.cn Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing, 100193.

Abstract

Background: Muscle development and lipid metabolism play important roles during fetal development stages. The commercial Texel sheep are more muscular than the indigenous Ujumqin sheep.

Results: We performed serial transcriptomics assays and systems biology analyses to investigate the dynamics of gene expression changes associated with fetal longissimus muscles during different fetal stages in two sheep breeds. Totally, we identified 1472 differentially expressed genes during various fetal stages using time-series expression analysis. A systems biology approach, weighted gene co-expression network analysis (WGCNA), was used to detect modules of correlated genes among these 1472 genes. Dramatically different gene modules were identified in four merged datasets, corresponding to the mid fetal stage in Texel and Ujumqin sheep, the late fetal stage in Texel and Ujumqin sheep, respectively. We further detected gene modules significantly correlated with fetal weight, and constructed networks and pathways using genes with high significances. In these gene modules, we identified genes like TADA3, LMNB1, TGF-β3, EEF1A2, FGFR1, MYOZ1, and FBP2 correlated with fetal weight.

Conclusion: Our study revealed the complex network characteristics involved in muscle development and lipid metabolism during fetal development stages. Diverse patterns of the network connections observed between breeds and fetal stages could involve some hub genes, which play central roles in fetal development, correlating with fetal weight. Our findings could provide potential valuable biomarkers for selection of body weight-related traits in sheep and other livestock.

Keywords: Serial expression analysis, WGCNA, fetal development stages, fetal weight.

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