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

Evaluation of the efficacy of amendment types and rates in reducing ammonia emissions from broiler litter

Several amendments have been used to reduce ammonia (NH3) emissions from broiler litter (BL); however, a comparative study between amendments and their application rates has not been fully explored. This study evaluated the potential of biochar (B), zeolite (Z), Flue Gas Desulphurization-Gypsum (FGD-G), and sodium bisulfate (S) at four application rates in reducing NH3 emissions from BL. The treatments comprised of amendment types (4) and their application rates (4), and a control with no amendment for a total of 17 treatments replicated twice and arranged in a completely randomized design. The treatments were incubated at 30 °C for 40 days at a moisture content of 40% (w/w), and NH3 emissions were measured every day for the first 10 days and 3 days intervals afterward for 40 days. Results showed that the application of 13 and 17% B (w/w) reduced cumulative NH3 emissions by 41 and 46%, respectively, compared to control over a 40-day period. Zeolite application at 8 and 11% reduced NH3 by 20 and 33%, respectively. There was no significant difference between the different rates of FGD-G, and they were generally less effective; however, a 15% FGD-G rate reduced NH3 by 9.1%. Application of S at rates of 2, 4, 6, and 7% significantly reduced NH3 emissions by 91, 99, 100, and 100 %, respectively. The effectiveness of amendments to reduce ammonia emissions followed the order: S > B > Z > FGD-G. These findings contribute to an ongoing effort to identify non-acidic amendments to minimize NH3 emissions in broiler houses.

Ammonia emissions, impacts, and mitigation strategies for poultry production: A critical review

Confined animal feeding operations (CAFOs) are the main sources of air pollutants such as ammonia (NH₃) and greenhouse gases. Among air pollutants, NH₃ is one of the most concerned gasses in terms of air quality, environmental impacts, and manure nutrient losses. It is recommended that NH₃ concentrations in the poultry house should be controlled below 25 ppm. Otherwise, the poor air quality will impair the health and welfare of animals and their caretakers. After releasing from poultry houses, NH₃ contributes to the form of fine particulate matters in the air and acidify soil and water bodies after deposition. Therefore, understanding the emission influential factors and impacts is critical for developing mitigation strategies to protect animals' welfare and health, environment, and ecosystems. This review paper summarized the primary NH₃ emission influential factors, such as how poultry housing systems, seasonal changes, feed management, bedding materials, animal densities, and animals' activities can impact indoor air quality and emissions. A higher level of NH₃ (e.g., >25 ppm) results in lower production efficiency and poor welfare and health, e.g., respiratory disorder, less feed intake, lower growth rates or egg production, poor feed use efficiency, increased susceptibility to infectious diseases, and mortality. In addition, the egg quality (e.g., albumen height, pH, and condensation) was reduced after laying hens chronically exposed to high NH₃ levels. High NH₃ levels have detrimental effects on farm workers' health as it is a corrosive substance to eyes, skin, and respiratory tract, and thus may cause blindness, irritation (throat, nose, eyes), and lung illness. For controlling poultry house NH₃ levels and emissions, we analyzed various mitigation strategies such as litter additives, biofiltration, acid scrubber, dietary manipulation, and bedding materials. Litter additives were tested with 50% efficiency in broiler houses and 80-90% mitigation efficiency for cage-free hen litter at a higher application rate (0.9 kg m^-2). Filtration systems such as multi-stage acid scrubbers have up to 95% efficiency on NH₃ mitigation. However, cautions should be paid as mitigation strategies could be cost prohibitive for farmers, which needs assistances or subsidies from governments.

Oxidative stress mediated immunosuppression caused by ammonia gas via antioxidant/oxidant imbalance in broilers

1. Ammonia is one of major air pollutants in intensive poultry houses, where it causes immunosuppression in broilers. Although previous studies have focused on a particular organ, data on multiple organs have not been reported.2. In the following work, broilers were exposed to environmental ammonia (0, 10, 20, and 40 mg/m³ from 1-21 d old; and 0, 15, 30, and 60 mg/m³ from 22-42 d old).3. Ammonia exposure reduced bird spleen index at 42 d and thymus index at 14, 28, 35 and 42 d, meaning that ammonia caused immunosuppression in birds. Moreover, high ammonia exposure down-regulated the expression of toll-like receptor 4 (TLR4) in lung tissue at 21 d, as well as TLR4 in lung and tracheal mucosa at 42 d when analysed using qRT-PCR. It increased SIgA in saliva at 42 d when analysed by ELISA. Ammonia increased interleukin-6 (IL-6), IL-1β, interferon-α (IFN-α), and IFN-γ in serum at 28 d from the ELISA assay, which indicated that all of these factors took part in ammonia-immunosuppression in birds.4. Three antioxidants (CAT, SOD, T-AOC) decreased, and one oxidant MDA increased after ammonia exposure in the liver and blood, which indicated that ammonia caused oxidative stress via the imbalance of antioxidants/oxidants in birds.5. Correlation analysis showed that TLR4 and TLR15 in the tracheal mucosa were significantly positively related to IFN-γ and negatively related to IL-6. TLR2 in the lung was significantly positively related to IL-1β, and TLR2 in bird tracheal mucosa was negatively related to IL-6 in serum.6. The results suggested that oxidative stress mediated immunosuppression caused by ammonia gas via antioxidant/oxidant imbalance in broilers.

Assessment of Husbandry Practices That Can Reduce the Negative Effects of Exposure to Low Ammonia Concentrations in Broiler Houses

Simple Summary

We used two commercial breeds, differing in growth rate: Fast-growing breed and slow-growing breed. We stocked these birds in two different densities. The slow-growing birds was stocked at a high density and the fast-growing birds at a high density and low density. These birds were reared under two different environmental conditions: A control room with a low concentration of ammonia and a second room with a higher concentration. We analyzed management practices such as the effect of ventilation, animal density and growth rate as management possibilities to reduce the negative effect of ammonia on production parameters.

Abstract

Ammonia is an important pollutant emitted by broiler litter that can accumulate inside farms, impairing animal health and welfare productivity. An experiment was designed to evaluate of precision husbandry practices such as the effect of ventilation, animal density and growth rate as management options to reduce the adverse effects of ammonia exposure on productive parameters in broiler houses. Two identical experimental rooms were used in this study. They were programmed to differ in ammonia concentration from day 32 of the growing period (10 and 20 ppm in Room 1 and Room 2, respectively). Three treatments were tested in each room: slow growth in high stocking density (SHD), fast growth in low density (FLD) and fast growth in high density (FHD). Animal weight, feed intake and feed conversion ratio were determined weekly. In addition, the immune status of animals was assessed by weighing the organs related to immune response as stress indicators. Increasing ventilation was effective to control ammonia concentrations. Exposure to ammonia caused no significant effect on productive parameters. However, lowering stocking density improved response to higher ammonia concentrations by lowering the feed conversion ratio. No other relevant effects of differential exposure to ammonia were found in fast-growing animals, either at high or low stocking density. The use of slow-growing breeds had no effect on production parameters. Despite having a slower growth rate, their feed conversion ratio was not different from that of fast-growing breeds. The productive performance of slow-growing animals was not affected by the differential exposure to ammonia, but the reduced spleen size would suggest an impairment of the immune system.

Genome-wide association study reveals candidate genes relevant to body weight in female turkeys (Meleagris gallopavo)

The underlying genetic mechanisms affecting turkey growth traits have not been widely investigated. Genome-wide association studies (GWAS) is a powerful approach to identify candidate regions associated with complex phenotypes and diseases in livestock. In the present study, we performed GWAS to identify regions associated with 18-week body weight in a turkey population. The data included body weight observations for 24,989 female turkeys genotyped based on a 65K SNP panel. The analysis was carried out using a univariate mixed linear model with hatch-week-year and the 2 top principal components fitted as fixed effects and the accumulated polygenic effect of all markers captured by the genomic relationship matrix as random. Thirty-three significant markers were observed on 1, 2, 3, 4, 7 and 12 chromosomes, while 26 showed strong linkage disequilibrium extending up to 410 kb. These significant markers were mapped to 37 genes, of which 13 were novel. Interestingly, many of the investigated genes are known to be involved in growth and body weight. For instance, genes AKR1D1, PARP12, BOC, NCOA1, ADCY3 and CHCHD7 regulate growth, body weight, metabolism, digestion, bile acid biosynthetic and development of muscle cells. In summary, the results of our study revealed novel candidate genomic regions and candidate genes that could be managed within a turkey breeding program and adapted in fine mapping of quantitative trait loci to enhance genetic improvement in this species.

Impact of Waste Tea Litter on NH3 and CO2 Emissions during Broiler Rearing

Pollution generated by livestock and poultry rearing is an important environmental issue, and gas emissions during animal production are continuously increasing. A digital rearing chamber inspection system was designed in the present study in order to examine the waste tea litter’s impact on the growth performance and harmful gas emissions, such as ammonia (NH3) and carbon dioxide (CO2), during broiler rearing. Broilers were raised without litter and with waste tea litter. According to the results, broiler growth showed little difference between the two groups during the experimental period, and it was concluded that waste tea litter had no impact on broiler growth. Meanwhile, the gas emissions of the waste tea-litter group were lower than the non-bedding-materials group. In detail, the average concentrations of NH3 and CO2 of the non-bedding-materials group were 9.33 ± 3.65 ppm and 797 ± 107 ppm, respectively; while these concentrations in the waste-tea-litter group were 1.01 ± 0.35 ppm and 713 ± 69 ppm, respectively. According to the analysis of the litter properties, it was suggested that waste tea litter can reduce the moisture content in litter, and affect microbial and urease activity due to its low carbon nitrogen ratio (C/N), weak acid, and porous structure characteristics. In conclusion, this study showed the potential of waste tea litter in NH3 and CO2 emission reduction during broiler rearing.

Transcriptomic profile of leg muscle during early growth and development in Haiyang yellow chicken

Skeletal muscle growth and development from embryo to adult consists of a series of carefully regulated changes in gene expression. This study aimed to identify candidate genes involved in chicken growth and development and to investigate the potential regulatory mechanisms of early growth in Haiyang yellow chicken. RNA sequencing was used to compare the transcriptomes of chicken muscle tissues at four developmental stages. In total, 6150 differentially expressed genes (DEGs) (|fold change| ≥ 2; false discovery rate (FDR) ≤ 0.05) were detected by pairwise comparison in female chickens. Functional analysis showed that the DEGs were mainly involved in the processes of muscle growth and development and cell differentiation. Many of the DEGs, such as MSTN, MYOD1, MYF6, MYF5, and IGF1, were related to chicken growth and development. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the DEGs were significantly enriched in four pathways related to growth and development: extracellular matrix (ECM)–receptor interaction, focal adhesion, tight junction, and insulin signalling pathways. A total of 42 DEGs assigned to these pathways are potential candidate genes for inducing the differences in growth among the four development stages, such as MYH1A, EGF, MYLK2, MYLK4, and LAMB3. This study identified a range of genes and several pathways that may be involved in regulating early growth.

RNA seq analyses of chicken reveals biological pathways involved in acclimation into different geographical locations

Transcriptome expression reflects genetic response in diverse conditions. In this study, RNA sequencing was utilized to profile multiple tissues such as liver, breast, caecum, and gizzard of Korean commercial chicken raised in Korea and Kyrgyzstan. We analyzed ten samples per tissue from each location to identify candidate genes which are involved in the adaptation of Korean commercial chicken to Kyrgyzstan. At false discovery rate (FDR) < 0.05 and fold change (FC) > 2, we found 315, 196, 167 and 198 genes in liver, breast, cecum, and gizzard respectively as differentially expressed between the two locations. GO enrichment analysis showed that these genes were highly enriched for cellular and metabolic processes, catalytic activity, and biological regulations. Similarly, KEGG pathways analysis indicated metabolic, PPAR signaling, FoxO, glycolysis/gluconeogenesis, biosynthesis, MAPK signaling, CAMs, citrate cycles pathways were differentially enriched. Enriched genes like TSKU, VTG1, SGK, CDK2 etc. in these pathways might be involved in acclimation of organisms into diverse climatic conditions. The qRT-PCR result also corroborated the RNA-Seq findings with R² of 0.76, 0.80, 0.81, and 0.93 for liver, breast, caecum, and gizzard respectively. Our findings can improve the understanding of environmental acclimation process in chicken.

Effects of atmospheric ammonia on the production performance, serum biochemical indices, and liver RNA-seq data of laying ducks

1. Ammonia is a toxic gas and an air pollutant of great concern. The effects of ammonia-induced damage in ducks are rarely reported. 2. A total of 176 laying ducks were randomly allocated to one of two groups with four replicates and were exposed to ammonia at 5 ± 5 ppm (low ammonia, LA) or 75 ± 5 ppm (high ammonia, HA), respectively, for 30 days. 3. The results showed that atmospheric ammonia exposure significantly decreased body weight and laying performance (P < 0.05). It significantly changed serum biochemical indices by increasing alanine aminotransferase and aspartate aminotransferase (P < 0.05), and decreasing superoxide dismutase activity (P < 0.05). Haematoxylin and eosin staining of hepatocytes revealed severe fatty degeneration. Results of RNA-seq analyses revealed that eight genes were significantly up-regulated in the HA group, which were involved in catalytic activity, single-organism metabolic processes, oxidation-reduction processes, and carbohydrate metabolic processes. 4. These results indicated that atmospheric ammonia exposure reduced production performance, affected serum biochemical indices, and led to severe fatty degeneration in the liver of laying ducks. Differentially expressed genes in liver indicated that there were effects of ammonia exposure on the metabolism and detoxification capabilities in ducks.

Effects of ammonia exposure on growth performance and cytokines in the serum, trachea, and ileum of broilers

This study investigated the effects of ammonia (NH₃) exposure (0, 15, 25, and 35 ppm) on growth performance and cytokines in the serum, trachea, and ileum of broilers. A total of 288 22-day-old male broiler chickens were assigned to 4 treatment groups with 6 replicates of 12 chickens for a 21-D trial period. Growth performance and cytokines (IL-1β, IL-6, and IL-10) concentrations in the serum, trachea, and ileum were measured in response to 3, 7, 14, or 21 D of exposure to NH₃. Correlations between cytokines in the serum, trachea, and ileum and growth performance, and between tracheal and ileal cytokines, were also analyzed. Results showed that exposure to 15 ppm NH₃ did not influence the growth performance, but exposure to both 25 ppm and 35 ppm NH₃ decreased the growth performance compared to that of the control group. Exposure to 15 ppm NH₃ for 3 D increased IL-6 concentrations and induced an inflammatory response in the trachea and ileum, whereas exposure to 15 ppm NH₃ for 7 D increased IL-10 concentrations and induced an anti-inflammatory response in the ileum. Exposure to 25 ppm NH₃ induced an inflammatory response in the serum, trachea, and ileum after 3 D and induced an anti-inflammatory response in the ileum after 7 D. Exposure to 35 ppm NH₃ for 3 D induced both inflammatory and anti-inflammatory responses in the trachea and ileum. Furthermore, increases in cytokines in the serum, trachea, or ileum were accompanied by a decrease in BW, ADFI, ADG, and an increase of feed/gain (F/G) from 7 D to 21 D. In addition, tracheal cytokine, especially IL-1β, was positively correlated with ileal cytokine IL-1β. These results indicated that the low growth performance associated with NH₃ exposure may be due in part to an increase in cytokines, and the inflammatory response in the trachea and ileum may be related to cross-talk by cytokines such as IL-6, IL-10, and, in particular, IL-1β.

Ammonia regulates chicken tracheal cell necroptosis via the LncRNA-107053293/MiR-148a-3p/FAF1 axis

Ammonia (NH₃) is a known harmful gas that causes injury to the respiratory system. Ammonia also exists in haze, forming secondary organic aerosols. However, the specific damage caused by NH₃ in chicken trachea has not been determined. The regulatory mechanism of ceRNA and its multiple roles have been proposed in many pathomechanisms; therefore, we investigated the functional role of ceRNA in chicken trachea after NH₃ inhalation. Broiler chicken trachea exposed to NH₃ was selected as the research object. The pathological ultrastructure was observed by transmission electron microscopy. Transcriptome analyses were applied and referenced, and lncRNA-107053293 and miR-148a-3p and FAF1 were selected. A dual-luciferase reporter assay verified the target relationship. Real-time quantitative PCR (RT-PCR) and western blotting were performed to examine the expression levels of necroptosis genes, such as RIPK1, RIPK3, MLKL, caspase 8, and FADD. Our results indicated that lncRNA-107053293 regulated necroptosis by acting as a competing endogenous RNA of miR-148a-3p. FAF1, as a gene target of miR-148a-3p, also affects necroptosis.

Transcriptome profile in bursa of Fabricius reveals potential mode for stress-influenced immune function in chicken stress model

BACKGROUND

The molecular mechanisms underlying stress-influenced immune function of chicken (Gallus Gallus) are not clear. The stress models can be established effectively by feeding chickens corticosterone (CORT) hormone. The bursa of Fabricius is a unique central immune organ of birds. RNA-Seq technology was used to investigate differences in the expression profiles of immune-related genes and associated pathways in the bursa of Fabricius to clarify molecular mechanisms. The aim of this study was to broaden the understanding of the stress-influenced immune function in chickens.

RESULTS

Differentially expressed genes (DEGs) in the bursa of Fabricius between experimental group (basal diet with added CORT 30 mg/kg; C_B group) and control group (basal diet; B_B group) were identified by using RNA-seq technology. In total, we found 1434 significant DEGs (SDEGs), which included 199 upregulated and 1235 downregulated genes in the C_B group compared with the B_B group. The immune system process GO term was the top significantly GO term, including MYD88, TLR4, IL15, VEGFA gene and so on. The cytokine-cytokine receptor interaction pathway and the Toll-like receptor signaling pathway were the key pathways affected by stress. The protein-protein interaction (PPI) analysis of the SDEGs showed that VEGFA, MyD88 and IL15 were hub genes and module analysis showed that MYD88, TLR4 and VEGFA play important roles in response to stress.

CONCLUSION

This study showed that the VEGFA and ILs (such as IL15) via the cytokine-cytokine receptor interaction pathway, MYD88 and TLR4 via the Toll-like receptor signaling pathway may play important roles in the regulation of immune function under stress condition with CORT administration. The results of this study provide a reference for further studies of the molecular mechanisms of stress-influenced immune function.

Transcriptome profile analysis of leg muscle tissues between slow- and fast-growing chickens

Chicken is widely favored by consumers because of some unique features. The leg muscles occupy an important position in the market. However, the specific mechanism for regulating muscle growth speed is not clear. In this experiment, we used Jinghai yellow chickens with different body weights at 300 days as research subjects. The chickens were divided into fast- and slow-growing groups, and we collected leg muscles after slaughtering for use in RNA-seq. After comparing the two groups, 87 differentially expressed genes (DEGs) were identified (fold change ≥ 2 and FDR < 0.05). The fast-growing group had 42 up-regulated genes and 45 down-regulated genes among these DEGs compared to the slow-growing group. Six items were significantly enriched in the biological process: embryo development ending in birth or egg hatching, chordate embryonic development, embryonic skeletal system development, and embryo development as well as responses to ketones and the sulfur compound biosynthetic process. Two significantly enriched pathways were found in the KEGG pathway analysis (P-value < 0.05): the insulin signaling pathway and the adipocytokine signaling pathway. This study provides a theoretical basis for the molecular mechanism of chicken growth and for improving the production of Jinghai yellow chicken.

Ammonia production in poultry houses can affect health of humans, birds, and the environment-techniques for its reduction during poultry production

Due to greater consumption of poultry products and an increase in exports, more poultry houses will be needed. Therefore, it is important to investigate ways that poultry facilities can coexist in close proximity to residential areas without odors and environmental challenges. Ammonia (NH₃) is the greatest concern for environmental pollution from poultry production. When birds consume protein, they produce uric acid, ultimately converted to NH₃ under favorable conditions. Factors that increase production include pH, temperature, moisture content, litter type, bird age, manure age, relative humidity, and ventilation rate (VR). NH₃ concentration and emissions in poultry houses depend on VR; seasons also have effects on NH₃ production. Modern ventilation systems can minimize NH₃ in enclosed production spaces quickly but increase its emissions to the environment. NH₃ adversely affects the ecosystem, environment, and health of birds and people. Less than 10 ppm is the ideal limit for exposure, but up to 25 ppm is also not harmful. NH₃ can be minimized by housing type, aerobic and anaerobic conditions, manure handling practices, litter amendment, and diet manipulation without affecting performance and production. Antibiotics can minimize NH₃, but consumers have concerns about health effects. Administration of probiotics seems to be a useful replacement for antibiotics. More studies have been conducted on broilers, necessitating the need to evaluate the effect of probiotics on NH₃ production in conjunction with laying hen performance and egg quality. This comprehensive review focuses on research from 1950 to 2018.

Ovarian transcriptomic analysis of Shan Ma ducks at peak and late stages of egg production

Objective

To assess the differences in ovarian transcriptomes in Shan Ma ducks between their peak and late stages of egg production, and to obtain new transcriptomic data of these egg-producing ducks.

Methods

The Illumina HiSeq 2000 system was used for high throughput sequencing of ovarian transcriptomes from Shan Ma ducks at their peak or late stages of egg production.

Results

Greater than 93% of the sequencing data had a base quality score (Q score) that was not less than 20 (Q20). From ducks at their peak stage of egg production, 42,782,676 reads were obtained, with 4,307,499,083 bp sequenced. From ducks at their late stage of egg production, 45,316,166 reads were obtained, with 4,562,063,363 bp sequenced. A comparison of the two datasets identified 2,002 differentially expressed genes, with 790 upregulated and 1,212 downregulated. Further analysis showed that 1,645 of the 2,002 differentially expressed genes were annotated in the non-redundant (NR) database, with 646 upregulated and 999 downregulated. Among the differentially expressed genes with annotations in the NR database, 696 genes were functionally annotated in the clusters of orthologous groups of proteins database, involving 25 functional categories. One thousand two hundred four of the differentially expressed genes with annotations in the NR database were functionally annotated in the gene ontology (GO) database, and could be divided into three domains and 56 categories. The three domains were cellular component, molecular function, and biological process. Among the genes identified in the GO database, 451 are involved in development and reproduction. Analysis of the differentially expressed genes with annotations in the NR database against the Kyoto encyclopedia of genes and genomes database revealed that 446 of the genes could be assigned to 175 metabolic pathways, of which the peroxisome proliferator-activated receptor signaling pathway, insulin signaling pathway, fructose and mannose metabolic pathways, gonadotropin releasing hormone signaling pathway and transforming growth factor beta signaling pathway were significantly enriched.

Conclusion

The differences in ovarian transcriptomes in Shan Ma ducks between their peak and late stages of egg production were elucidated, which greatly enriched the ovarian transcriptomic information of egg-producing ducks.