Table7_MicroRNA breed and parent-of-origin effects provide insights into biological pathways differentiating cattle subspecies in fetal liver.XLSX

Introduction: MicroRNAs (miRNAs) play a crucial role in regulating gene expression during key developmental processes, including fetal development. Brahman (Bos taurus indicus) and Angus (Bos taurus taurus) cattle breeds represent two major cattle subspecies with strikingly different phenotypes.
Methods: We analyzed miRNA expression in liver samples of purebred and reciprocal crosses of Angus and Brahman to investigate breed and parent-of-origin effects at the onset of accelerated fetal growth.
Results: We identified eight novel miRNAs in fetal liver samples and 14 differentially expressed miRNAs (DEMs) between purebred samples. Correlation of gene expression modules and miRNAs by breed and parent-of-origin effects revealed an enrichment of genes associated with breed-specific differences in traits such as heat tolerance (Brahman) and fat deposition (Angus). We demonstrate that genes predicted to be targets of DEMs were more likely to be differentially expressed than non-targets (p-value < 0.05). We identified several miRNAs (bta-miR-187, bta-miR-216b, bta-miR-2284c, bta-miR-2285c, bta-miR-2285cp, bta-miR-2419-3p, bta-miR-2419-5p, and bta-miR-11984) that showed similar correlation patterns as bta-miR-2355-3p, which has been associated with the glutamatergic synapse pathway, a key facilitator of heat tolerance. Furthermore, we report Angus-breed-specific miRNAs (bta-miR-2313-5p, btamiR-490, bta-miR-2316, and bta-miR-11990) that may be involved in fat deposition. Finally, we showed that the DEMs identified in fetal liver are involved in Rap1, MAPK, and Ras signalling pathways, which are important for fetal development, muscle development and metabolic traits such as fat metabolism.
Conclusion: Our work sheds light on the miRNA expression patterns that contribute to gene expression differences driving phenotypic differences in indicine and taurine cattle.

引言：微小RNA（microRNAs, miRNAs）在包括胎儿发育在内的关键发育过程中，对基因表达调控发挥着至关重要的作用。婆罗门牛（Bos taurus indicus）与安格斯牛（Bos taurus taurus）是两个主要的牛亚种，二者的表型差异极为显著。
材料与方法：本研究对安格斯牛与婆罗门牛的纯种及正反交后代的肝脏样本进行miRNA表达分析，以探究胎儿生长加速启动阶段的品种效应和亲本来源效应。
结果：本研究在胎儿肝脏样本中鉴定出8种新型miRNA，并在纯种样本间鉴定出14种差异表达miRNA（differentially expressed miRNAs, DEMs）。通过品种和亲本来源效应对基因表达模块与miRNA进行关联分析，结果发现与品种特异性性状差异相关的基因存在富集现象，这些性状包括婆罗门牛的耐热性以及安格斯牛的脂肪沉积能力。本研究证实，相较于非靶标基因，差异表达miRNA的预测靶标基因更易出现差异表达（p值<0.05）。本研究鉴定出多种miRNA（bta-miR-187、bta-miR-216b、bta-miR-2284c、bta-miR-2285c、bta-miR-2285cp、bta-miR-2419-3p、bta-miR-2419-5p及bta-miR-11984），其关联模式与bta-miR-2355-3p相似；而bta-miR-2355-3p已被证实与谷氨酸能突触通路（glutamatergic synapse pathway）相关，该通路是耐热性的关键调控通路。此外，本研究发现安格斯牛特异性miRNA（bta-miR-2313-5p、bta-miR-490、bta-miR-2316及bta-miR-11990）可能参与脂肪沉积过程。最后，本研究证实，胎儿肝脏中鉴定出的差异表达miRNA参与Rap1、丝裂原活化蛋白激酶（Mitogen-Activated Protein Kinase, MAPK）及Ras信号通路，这些通路对胎儿发育、肌肉发育以及脂肪代谢等代谢性状具有重要作用。
结论：本研究阐明了瘤牛与普通牛表型差异背后，驱动基因表达差异的miRNA表达模式。