College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, People's Republic of China.
Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
Genes Genomics. 2019 Oct;41(10):1147-1163. doi: 10.1007/s13258-019-00844-4. Epub 2019 Jun 29.
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.
In this study, the phenotypic quality traits and its associations with DNA methylation levels of the longissimus muscle in two cattle breeds were studied.
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.
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.
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.
牛是最重要的肉类生产家畜之一，因此控制肌肉发育的质量是一个重要的研究重点。
本研究旨在研究两个牛品种的背最长肌的表型质量性状及其与 DNA 甲基化水平的关系。
对三个牛肉品种的背最长肌进行 pH 值、失水率、脂肪和蛋白质及脂肪酸含量的测定；采用 MethylRAD-seq 和 RNA-seq 对背最长肌进行分析。对差异甲基化和差异表达相关基因进行 BSP 分析。
通过 MethylRAD-seq 分析背最长肌的甲基化状态。与西门塔尔牛相比，云岭牛肌肉中存在 39 个差异甲基化和表达基因，文山牛肌肉中存在 123 个差异甲基化和表达基因。MethylRAD-seq 和 RNA-seq 结果的综合分析显示，西门塔尔牛和文山牛之间有 18 个基因存在差异甲基化和表达水平，西门塔尔牛和云岭牛之间有 14 个基因存在差异甲基化和表达水平。此外，文山牛和云岭牛之间有 28 个基因存在差异甲基化。ACAD11、FADS6 和 FASN 启动子甲基化分析结果表明，FADS6 和 FASN 的整体 DNA 甲基化程度与它们的表达水平呈负相关。西门塔尔牛的 FASN 甲基化程度大于云岭牛和文山牛。西门塔尔牛 FADS6 第 CpG4 位的甲基化程度明显高于云岭牛。西门塔尔牛和云岭牛的 FADS6 第 CpG7 位的甲基化水平大于文山牛。FASN 的 CpG1、CpG2、CpG3、CpG5、CpG7 和 CpG10 的甲基化水平与表达呈负相关。
从遗传和表观遗传调控方面，系统揭示了与肉质相关基因的功能和分子调控机制。这些研究将有助于进一步探讨调控不同牛品种生长和肉质的分子机制和表型差异。
