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Analysis of longissimus muscle quality characteristics and associations with DNA methylation status in cattle

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Abstract

Background

As cattle represent one of the most important livestock species for meat production, control of muscle development in regards to quality is an important research focus.

Objectives

In this study, the phenotypic quality traits and its associations with DNA methylation levels of the longissimus muscle in two cattle breeds were studied.

Methods

The pH value, water loss rate, fat and protein and fatty acid content were measured in three beef cattle breeds of longissimus mucle; The longissimus mucle was analyzed by MethylRAD-seq and RNA-seq. The differentially methylated and differentially expressed related genes were subjected to BSP.

Results

Methylation status of longissimus mucle was analyzed by MethylRAD-seq. Compared with Simmental, there were 39 differentially methylated and expressed genes in muscle of Yunling cattle, and 123 differentially methylated and expressed genes in Wenshan muscle. A combined analysis of MethylRAD-seq and RNA-seq results revealed differential methylation and expression level of 18 genes between Simmental and Wenshan cattle, and 14 genes between Simmental and Yunling cattle. In addition, 28 genes were differentially methylated between Wenshan and Yunling cattle. Results of promoter methylation analysis of ACAD11, FADS6 and FASN showed that the overall degree of DNA methylation of FADS6 and FASN was negatively correlated with their expression levels. Methylation level of FASN in Simmental was greater than Yunling and Wenshan. The degree of methylation at the FADS6 CpG4 site was significantly higher in Simmental than that in Yunling. The levels of methylation at the CpG7 locus of the Simmental and Yunling breeds were greater than Wenshan cattle. A negative correlation was detected between the methylation levels and the expression of FASN CpG1, CpG2, CpG3, CpG5, CpG7, and CpG10.

Conclusion

The functional and molecular regulatory mechanism of the genes related to meat quality can be revealed systematically from aspects of the genetic and epigenetic regulation. These studies will help to further explore the molecular mechanisms and phenotypic differences that regulate growth and quality of different breeds of cattle.

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Funding

National Natural Science Foundation of China (31872324,31472067, 31802035), This study was funded by the National High Technology Research and Development Program of China (2013AA102505–5), China Postdoctoral Science Foundation (2017M621841).

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Author notes

  1. Zhi Chen, Shuangfeng Chu and Xin Xu contributed equally to this work.

Authors and Affiliations

  1. College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, People’s Republic of China

    Zhi Chen, Shuangfeng Chu, Xin Xu, Jingyi Jiang, Wenqiang Wang, Mingxun Li, Huimin Zhang, Yongjiang Mao & Zhangping Yang

  2. Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, 225009, China

    Zhi Chen, Shuangfeng Chu, Xin Xu, Jingyi Jiang, Wenqiang Wang, Mingxun Li, Huimin Zhang, Yongjiang Mao & Zhangping Yang

  3. Animal Health Inspection, Suzhou Industrial Park, Suzhou, 215021, China

    Hongliang Shen

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  1. Zhi Chen
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  2. Shuangfeng Chu
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  8. Huimin Zhang
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  10. Zhangping Yang
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Contributions

Zhangping Yang conceived and designed the experiments. Zhi Chen, Xin Xu, Wenqiang Wang and Hongliang Shen performed the experiments. Zhi Chen, Mingxun Li, Huimin Zhang and Yongjiang Mao analyzed the data. Zhi Chen wrote the paper.

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Correspondence to Zhangping Yang.

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Chen, Z., Chu, S., Xu, X. et al. Analysis of longissimus muscle quality characteristics and associations with DNA methylation status in cattle. Genes Genom 41, 1147–1163 (2019). https://doi.org/10.1007/s13258-019-00844-4

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  • DOI: https://doi.org/10.1007/s13258-019-00844-4

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