RNA-seq of muscle from pigs divergent in feed efficiency and product quality identifies differences in immune response, growth, and macronutrient and connective tissue metabolism.
RNA-seq of muscle from pigs divergent in feed efficiency and product quality identifies differences in immune response, growth, and macronutrient and connective tissue metabolism.
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DOI：
10.1186/s12864-018-5175-y
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发表时间：
2018-11-01
期刊：
影响因子：
4.4
通讯作者：
Hamill RM
中科院分区：
文献类型：
--
作者：
Horodyska J;Wimmers K;Reyer H;Trakooljul N;Mullen AM;Lawlor PG;Hamill RM
饲料效率（FE）是将能量和营养物质从饲料转化为具有重要环境和经济意义的组织的效率指标。导致FE差异的分子机制尚未完全阐明，因此本研究的目的是分析猪胸腰最长肌（LTL）肌肉转录组，检查FE差异猪的产品质量，并研究支撑产品质量与FE之间潜在关系的功能网络。在FE状态不同的猪的LTL中进行RNA-Seq（n = 16）和产品质量（n = 40）分析。共有272个注释基因差异表达，P < 0.01。功能注释揭示了许多与免疫反应、生长、碳水化合物和脂质代谢以及结缔组织相关的生物学事件，表明这些可能是控制FE差异的关键机制。FE组中五个最显著的生物功能改变是“血液系统发育和功能”，“淋巴组织结构和发育”，“组织形态”，“细胞运动”和“免疫细胞运输”。在差异表达基因中最重要的典型途径包括“IL-8信号传导”、“白细胞外渗信号传导”、“1-磷酸鞘氨醇信号传导”、“T淋巴细胞中的PKCθ信号传导”和“嗜中性粒细胞中的fMLP信号传导”。一个轻微的损害的肉的质量，质地和持水能力，高FE猪生产的观察。高FE猪还具有降低的肌内脂肪含量和改善的脂肪酸组成方面的营养概况。本体分析显示，增强的适应性免疫和吞噬细胞的活动，在高FE猪，这表明更有效地保护资源，可用于其他重要的生物过程。碳水化合物转化为葡萄糖的FE-发散肌肉的变化可能会支持的FE-组肉的pH值曲线的发散演变。此外，氨基酸代谢的改变和钙的动员和流动的增加可能会影响FE发散肌肉的生长。此外，FE-发散肌肉中成纤维细胞降解减少可能影响胶原蛋白周转并改变肉的嫩度，而高FE猪中脂质降解增强可能是这些动物中更有效的脂肪代谢的潜在基础。本文的在线版本（10.1186/s12864-018-5175-y）包含补充材料，可供授权用户使用。
Feed efficiency (FE) is an indicator of efficiency in converting energy and nutrients from feed into a tissue that is of major environmental and economic significance. The molecular mechanisms contributing to differences in FE are not fully elucidated, therefore the objective of this study was to profile the porcine Longissimus thoracis et lumborum (LTL) muscle transcriptome, examine the product quality from pigs divergent in FE and investigate the functional networks underpinning the potential relationship between product quality and FE. RNA-Seq (n = 16) and product quality (n = 40) analysis were carried out in the LTL of pigs differing in FE status. A total of 272 annotated genes were differentially expressed with a P < 0.01. Functional annotation revealed a number of biological events related to immune response, growth, carbohydrate & lipid metabolism and connective tissue indicating that these might be the key mechanisms governing differences in FE. Five most significant bio-functions altered in FE groups were ‘haematological system development & function’, ‘lymphoid tissue structure & development’, ‘tissue morphology’, ‘cellular movement’ and ‘immune cell trafficking’. Top significant canonical pathways represented among the differentially expressed genes included ‘IL-8 signalling’, ‘leukocyte extravasation signalling, ‘sphingosine-1-phosphate signalling’, ‘PKCθ signalling in T lymphocytes’ and ‘fMLP signalling in neutrophils’. A minor impairment in the quality of meat, in relation to texture and water-holding capacity, produced by high-FE pigs was observed. High-FE pigs also had reduced intramuscular fat content and improved nutritional profile in terms of fatty acid composition. Ontology analysis revealed enhanced activity of adaptive immunity and phagocytes in high-FE pigs suggesting more efficient conserving of resources, which can be utilised for other important biological processes. Shifts in carbohydrate conversion into glucose in FE-divergent muscle may underpin the divergent evolution of pH profile in meat from the FE-groups. Moreover, altered amino acid metabolism and increased mobilisation & flux of calcium may influence growth in FE-divergent muscle. Furthermore, decreased degradation of fibroblasts in FE-divergent muscle could impact on collagen turnover and alter tenderness of meat, whilst enhanced lipid degradation in high-FE pigs may potentially underlie a more efficient fat metabolism in these animals. The online version of this article (10.1186/s12864-018-5175-y) contains supplementary material, which is available to authorized users.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
4.3
作者：
Morales PE;Bucarey JL;Espinosa A
通讯作者：
Espinosa A
影响因子：
7.1
作者：
Faure, J.;Lefaucheur, L.;Lebret, B.
通讯作者：
Lebret, B.
影响因子：
3.3
作者：
Casas, E;White, SN;Smith, TPL
通讯作者：
Smith, TPL
影响因子：
64.5
作者：
EVAN, GI;WYLLIE, AH;HANCOCK, DC
通讯作者：
HANCOCK, DC