Transcriptome Profile Analysis of Breast Muscle Tissues from High or Low Levels of Atmospheric Ammonia Exposed Broilers (<i>Gallus gallus</i>)

Atmospheric ammonia is a common problem in poultry industry. High concentrations of aerial ammonia cause great harm to broilers' health and production. For the consideration of human health, the limit exposure concentration of ammonia in houses is set at 25 ppm. Previous reports have shown that 25 ppm is still detrimental to livestock, especially the gastrointestinal tract and respiratory tract, but the negative relationship between ammonia exposure and the tissue of breast muscle of broilers is still unknown. In the present study, 25 ppm ammonia in poultry houses was found to lower slaughter performance and breast yield. Then, high-throughput RNA sequencing was utilized to identify differentially expressed genes in breast muscle of broiler chickens exposed to high (25 ppm) or low (3 ppm) levels of atmospheric ammonia. The transcriptome analysis showed that 163 genes (fold change ≥ 2 or ≤ 0.5; P-value < 0.05) were differentially expressed between Ammonia25 (treatment group) and Ammonia3 (control group), including 96 down-regulated and 67 up-regulated genes. qRT-PCR analysis validated the transcriptomic results of RNA sequencing. Gene Ontology (GO) functional annotation analysis revealed potential genes, processes and pathways with putative involvement in growth and development inhibition of breast muscle in broilers caused by aerial ammonia exposure. This study facilitates understanding of the genetic architecture of the chicken breast muscle transcriptome, and has identified candidate genes for breast muscle response to atmospheric ammonia exposure.大气氨污染是家禽养殖业中的常见问题。高浓度的空气氨会对肉鸡的健康与生产性能造成严重损害。出于保障畜禽养殖场所内人员健康的考量，场所内氨的暴露限值被设定为25 ppm。既往研究表明，25 ppm浓度的氨仍会对畜禽产生危害，尤其会损伤其胃肠道与呼吸道，但氨暴露与肉鸡胸肌组织之间的负面关联仍未明确。本研究发现，家禽养殖环境中25 ppm浓度的氨会降低肉鸡的屠宰性能与胸肌产出率。随后，本研究采用高通量RNA测序技术，对暴露于高浓度（25 ppm）与低浓度（3 ppm）大气氨的肉鸡胸肌组织中的差异表达基因进行了筛选鉴定。转录组分析结果显示，氨25组（处理组）与氨3组（对照组）之间共有163个基因呈现显著差异表达（差异倍数≥2或≤0.5，P值<0.05），其中96个基因表达下调，67个基因表达上调。实时荧光定量PCR（qRT-PCR）验证了RNA测序的转录组分析结果。基因本体（Gene Ontology，GO）功能注释分析揭示了可能参与大气氨暴露诱导肉鸡胸肌生长发育抑制的潜在基因、生物学过程与信号通路。本研究有助于解析肉鸡胸肌转录组的遗传调控机制，并筛选得到了参与肉鸡胸肌对大气氨暴露应答的候选基因。