Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake.
Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake.
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DOI：
10.1186/s12864-016-2395-x
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发表时间：
2016-01-22
期刊：
影响因子：
4.4
通讯作者：
Tuggle CK
中科院分区：
文献类型：
--
作者：
Liu H;Nguyen YT;Nettleton D;Dekkers JC;Tuggle CK
通过遗传选择提高猪的饲料效率具有重要的经济意义和环境意义。饲料效率的一个越来越被接受的衡量标准是剩余采食量(RFI)。目前，RFI的分子机制在很大程度上尚不清楚。此外，为了将RFI纳入动物育种计划，必须记录每头猪的饲料摄入量，这是昂贵和耗时的。因此，非常需要能够在早期测量的方便和可预测的RFI生物标记物。在这项研究中，我们的目的是探索在生长-育肥阶段被不同地选择用于RFI的两个品系的35到42头极低(更有效)和高RFI(较低效率)的日龄猪外周血的全球基因表达谱是否存在差异，以利用这些信息来探索RFI差异的潜在分子基础，并启动RFI预测生物标志物的开发。我们利用 ≤ 测序技术，在低 = 组(n = 15)和高RFI16组(N RFI16)之间鉴定了1972个差异表达基因(DGs)(Q RFI0.15)。我们通过对同一组猪的31个样本中的24个(每行12个)的联合分析，验证了37个选定的DEG中的24个(每行12个)，并对来自同一组猪的24个(每行12个)新样本进行了RNA-seq加24个新样本的联合分析。仅用对24个新样本的分析，37个选定的DEG中只有9个得到了验证。参与小分子生物合成过程、抗原加工和通过主要组织相容性复合体(MHC)I类递呈多肽抗原以及类固醇生物合成过程的基因在低RFI组和高RFI组高表达的DEG中过度表达。在低RFI组和高RFI组动物中，已知在蛋白酶体复合体或线粒体中起作用的基因也在高表达的基因中显著丰富。或者，在低RFI和高RFI动物中，参与信号转导、骨矿化和磷酸化调节的基因在DEGS中过度表达，而表达较低。DEGS与与疾病相关的基因显著重叠，包括吞噬过多、饮食失调和线粒体疾病(Q <； 1E-05)。加权基因共表达网络分析(WGCNA)确定了四个在低RFI组和高RFI组之间差异表达的共表达模块。涉及脂肪代谢、骨矿化调节、细胞免疫和对刺激反应的基因在两个模块中过度表达，这两个模块在低RFI组和高RFI组之间的表达差异最显著。我们还发现5个DEG和1个共表达模块与个体动物的RFI表型显著相关(Q <； 0.05)。断奶后血液转录组在低RFI组和高RFI组之间有明显差异。尽管断奶后血液基因表达与生长-育肥阶段测得的RFI表型之间的关系不强，但已鉴定的DEGS表明两个RFI组之间在线粒体和蛋白酶体活性、小分子生物合成过程和信号转导方面的潜在差异，并为猪RFI的分子基础提供了潜在的新见解。DEGS和与RFI表型相关的共表达模块中的代表性基因为开发猪RFI的预测性生物标志物提供了初步清单。本文的在线版本(doi：10.1186/s12864-0162395-x)包含补充材料，可供授权用户使用。
Improving feed efficiency (FE) of pigs by genetic selection is of economic and environmental significance. An increasingly accepted measure of feed efficiency is residual feed intake (RFI). Currently, the molecular mechanisms underlying RFI are largely unknown. Additionally, to incorporate RFI into animal breeding programs, feed intake must be recorded on individual pigs, which is costly and time-consuming. Thus, convenient and predictive biomarkers for RFI that can be measured at an early age are greatly desired. In this study, we aimed to explore whether differences exist in the global gene expression profiles of peripheral blood of 35 to 42 day-old pigs with extremely low (more efficient) and high RFI (less efficient) values from two lines that were divergently selected for RFI during the grow-finish phase, to use such information to explore the potential molecular basis of RFI differences, and to initiate development of predictive biomarkers for RFI. We identified 1972 differentially expressed genes (DEGs) (q ≤ 0.15) between the low (n = 15) and high (n = 16) RFI groups of animals by using RNA sequencing technology. We validated 24 of 37 selected DEGs by reverse transcription-quantitative PCR (RT-qPCR) in a joint analysis of 24 (12 per line) of the 31 samples already used for RNA-seq plus 24 (12 per line) novel samples from the same contemporary group of pigs. Using an analysis of the 24 novel samples alone, only nine of the 37 selected DEGs were validated. Genes involved in small molecule biosynthetic process, antigen processing and presentation of peptide antigen via major histocompatibility complex (MHC) class I, and steroid biosynthetic process were overrepresented among DEGs that had higher expression in the low versus high RFI animals. Genes known to function in the proteasome complex or mitochondrion were also significantly enriched among genes with higher expression in the low versus high RFI animals. Alternatively, genes involved in signal transduction, bone mineralization and regulation of phosphorylation were overrepresented among DEGs with lower expression in the low versus high RFI animals. The DEGs significantly overlapped with genes associated with disease, including hyperphagia, eating disorders and mitochondrial diseases (q < 1E-05). A weighted gene co-expression network analysis (WGCNA) identified four co-expression modules that were differentially expressed between the low and high RFI groups. Genes involved in lipid metabolism, regulation of bone mineralization, cellular immunity and response to stimulus were overrepresented within the two modules that were most significantly differentially expressed between the low and high RFI groups. We also found five of the DEGs and one of the co-expression modules were significantly associated with the RFI phenotype of individual animals (q < 0.05). The post-weaning blood transcriptome was clearly different between the low and high RFI groups. The identified DEGs suggested potential differences in mitochondrial and proteasomal activities, small molecule biosynthetic process, and signal transduction between the two RFI groups and provided potential new insights into the molecular basis of RFI in pigs, although the observed relationship between the post-weaning blood gene expression and RFI phenotype measured during the grow-finish phase was not strong. DEGs and representative genes in co-expression modules that were associated with RFI phenotype provide a preliminary list for developing predictive biomarkers for RFI in pigs. The online version of this article (doi:10.1186/s12864-016-2395-x) contains supplementary material, which is available to authorized users.