Identification of candidate genes associated with breast muscle of broilers exposed to atmospheric ammonia using RNA sequencing

Abstract: Ammonia is one of the most prominent air pollutants in poultry houses. High levels of ammonia have adverse effects on respiratory health, growth performance, meat production of broilers, and breast meat growth and yield are critical important in the broiler industry. To date, studies focus on the negative relationship of ammonia exposure and breast muscle tissue are still very limited, and the underlying molecular mechanisms remain poorly understood. In this study, high concentrations of atmospheric ammonia were found to lower slaughter rate and broiler breast meat yield significantly (P < 0.05). To explore the candidate genes that ammonia regulates breast meat yield of broilers, high throughout RNA-Seq was used to compare the transcriptome of breast muscle with different ammonia exposure (50 ppm vs 3 ppm). In total, 129 differentially expressed genes (DEGs) were identified (P-value < 0.05; fold-change = 2), among which 87 genes were significantly down-regulated and 42 were up-regulated. Bioinformatics analysis suggested that DEGs (such as PDK4, ACSL1, GLUL, FBXO32) were involved in fatty acid degradation/metabolism, nitrogen metabolism, PPAR signaling and adipocytokine signaling pathways. Functional annotation showed that DEGs were mainly enriched in reactive oxygen species metabolic process and muscle contraction. It can be concluded that decreased meat yield was due to the DEGs participating in above biological processes and pathways. This study provides novel insights into transcriptional differences in breast meat between high- and low-ammonia exposed broiler chickens. Overall design: Breast muscle mRNA profiles of 42-day old Arbor Acres male broilers exposed to 50 ppm (treatment) concentrations of atmospheric ammonia were generated by RNA sequencing, in triplicate, using Illumina HiSeq2000.

摘要：氨气是家禽舍中最主要的空气污染物之一。高浓度氨气会对肉鸡的呼吸系统健康、生长性能及肉品生产造成不良影响，而胸肉的生长与产量均为肉鸡产业的核心指标。迄今为止，针对氨气暴露与胸肌组织之间负相关关系的研究仍十分有限，其潜在的分子机制尚不明晰。本研究发现，大气中高浓度氨气会显著降低肉鸡的屠宰率与胸肉产量（P < 0.05）。为探究氨气调控肉鸡胸肉产量的候选基因，本研究采用高通量RNA测序（RNA-Seq）对比了不同氨气暴露浓度（50 ppm vs 3 ppm）下肉鸡胸肌的转录组。最终共鉴定出129个差异表达基因（differentially expressed genes，DEGs）（P值 < 0.05；倍数变化=2），其中87个基因显著下调，42个基因显著上调。生物信息学分析显示，这些差异表达基因（如PDK4、ACSL1、GLUL、FBXO32）参与了脂肪酸降解/代谢、氮代谢、PPAR信号通路以及脂肪细胞因子信号通路。功能注释结果表明，差异表达基因主要富集于活性氧代谢过程与肌肉收缩相关生物学过程。综上可推断，胸肉产量下降是由参与上述生物学过程与信号通路的差异表达基因所导致的。本研究为高、低氨气暴露条件下肉鸡胸肌的转录组差异提供了新的研究视角。整体实验设计：采用Illumina HiSeq2000测序平台，对暴露于50 ppm（处理组）大气氨气浓度的42日龄爱拔益加（Arbor Acres）雄性肉鸡的胸肌mRNA进行转录组测序，设置3个生物学重复。