Dataset Information

Transcriptome changes provide genetic insights into the effects of rearing systems on chicken welfare and product quality.

ABSTRACT: Farm animals raised under free-range (FR) systems are assumed to have improved welfare and higher-quality products that are better to eat than intensively reared animals. However, the modulations are limited in scientific investigations. In this study, we compared 2 rearing systems (FR and cage) and their effects on chickens, including production performance, product quality, body condition, physiological indicators, and gene expression. By using a match-mismatch design in which each treatment was transferred to the other treatment during the last period of the experiment, we aimed to understand the influence of current and former rearing conditions and the ability of individuals to adapt to the current environment. The results indicated that the FR system led to better chicken welfare (e.g., gait score, feather condition, and physiological indicators, P < 0.05) and contributed to higher product quality (P < 0.05), although it resulted in poorer production performance (P < 0.05) and foot pad condition (P < 0.05) than that of the cage rearing system. Additionally, the FR system triggered a series of inner changes and genetic responses in chickens, such as the upregulation of calcium and GnRH signaling, actin and cytoskeleton regulations, immune functions, and developmental processes, and the downregulation of pathological regulations (q-value < 0.05 for all gene ontology terms and P < 0.05 for all Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways). In conclusion, rearing systems alter chicken gene expression patterns, which provide a genetic basis for the adaptability to rearing environments and ultimately affects chicken welfare and products.

SUBMITTER: Xiang H

PROVIDER: S-EPMC6247852 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Transcriptome changes provide genetic insights into the effects of rearing systems on chicken welfare and product quality.

Xiang Hai H Chen Siyu S Zhang Hui H Zhu Xu X Wang Dan D Liu Huagui H Wang Jikun J Yin Tao T Liu Langqing L Kong Minghua M Zhang Jian J Li Hua H Zhao Xingbo X

Journal of animal science 20181101 11

Farm animals raised under free-range (FR) systems are assumed to have improved welfare and higher-quality products that are better to eat than intensively reared animals. However, the modulations are limited in scientific investigations. In this study, we compared 2 rearing systems (FR and cage) and their effects on chickens, including production performance, product quality, body condition, physiological indicators, and gene expression. By using a match-mismatch design in which each treatment w ...[more]

PMID: 30169713

Similar Datasets

Project description:The quality of poultry products depends on genotype, rearing system, and environment. The aim of this study was to investigate the effects of different rearing systems on meat quality, amino acid composition, and breast muscle transcriptome from Lueyang black-bone chickens. Lueyang black-bone chickens (n = 900) were randomly divided into three groups (cage, flat-net, and free-range groups), with three replicates per group (100 chickens per replicate). At 16 weeks, a total of 36 healthy chickens (six males and six females per group) were collected, and their breast muscles were sampled to detect meat quality parameters, amino acid composition, and fatty acid contents. Furthermore, breast muscles from six random hens in each group were used for RNA-seq analysis. The results revealed that the values of pH, shear force, inosine monophosphate (IMP), palmitic acid, and linoleic acid in the free-range group were significantly higher than those in the caged group (p < 0.05). Fat content in the free-range group was significantly lower than in the caged and flat-net groups (p < 0.05). Glutamate (Glu) levels, the amino acid crucial for the umami taste, was significantly higher in the free-range group than in the caged group (p < 0.05). Meanwhile, there was no significant difference between the free-range and flat-net groups (p > 0.05). The breast muscle transcriptome results showed that there were 291, 131, and 387 differently expressed genes (DEGs) among the three comparison groups (caged vs. free-range, flat-net vs. caged, and flat-net vs. free-range, respectively) that were mainly related to muscle development and amino acid metabolism pathways. To validate the accuracy of the transcriptome data, eight genes (GOS2, ASNS, NMRK2, GADL1, SMTNL2, SLC7A5, AMPD1, and GLUL) which relate to fat deposition, skeletal muscle function, and flavor formation were selected for Real-time Quantitative PCR (RT-qPCR) verification. In conclusion, these results suggested that rearing systems significantly influenced the meat quality and gene expression of Lueyang black-bone chickens. All the data proved that free-range and flat-net systems may provide better flavor to consumers by affecting the deposition of flavor substances and the expression of related genes. These findings will provide a valuable theoretical basis for the rearing system selection in the poultry industry.

Project description:The most reared species of farm animal around the world is the chicken. However, the intensification of livestock systems has led to a gradual increase in the concentration of a limited number of breeds, resulting in substantial erosion to the genetic pool. The initial step of an 'animal conservation program' entails establishing the actual conservation statuses of the breeds concerned in a defined area; in this case, in Italy. To this end, a survey of breeds was performed by means of a census questionnaire divided into two parts. The first part collected information on breeds, breeders, housing facilities, and management aspects, the results of which are presented here. The second part of the questionnaire regarded chicken products and their markets, and these data will be reported in a second paper. The breed status of six chicken breeds was shown to be exceptionally worrying, with total numbers ranging from just 18 to 186 birds. Population sizes exceeding 1000 birds was identified for just four breeds, the maximum being 3400. Some improvements in status were noted in relation to breeds which had been the subject of conservation efforts in the past. The two most common breeds reported are the Bionda Piemontese, a double-purpose breed, and the Livorno egg-laying hen. Collo Nudo Italiano, Millefiori Piemontese, Pollo Trentino, and Tirolese chicken breeds and the Castano Precoce turkey breed were not listed by breeders at all. The most reported turkey breeds are the Bronzato Comune and the Ermellinato di Rovigo. The population sizes of native Italian poultry breeds were shown to be generally poor. Italian poultry farmers and the population at large are largely ignorant about indigenous poultry breeds. Thus, promoting the virtues of Italian breeds would help their conservation by encouraging breeders to rear these birds and consumers to buy their products. The identification of strategies to facilitate access to pure breed birds is essential, and will require the collaboration of university research centers, public entities, and breeders. The results presented in this paper constitute the initial part of a more complex conservation program.

Project description:Eriocheir sinensis, an extremely invasive alien crab species, has important economic value in China. It encounters different salinities during its life cycle, and at the megalopal stage it faces a turning point regarding the salinity in its environment. We applied RNA sequencing to E. sinensis megalopae before (MB) and after (MA) desalination, resulting in the discovery of 21,042 unigenes and 908 differentially expressed genes (DEGs, 4.32% of the unigenes). The DEGs primarily belonged to the Gene Ontology groups "Energy metabolism," "Oxidoreductase activity," "Translation," "Transport," "Metabolism," and "Stress response." In total, 33 DEGs related to transport processes were found, including 12 proton pump genes, three ATP-binding cassettes (ABCs), 13 solute carrier (SLC) family members, two sweet sugar transporter (ST) family members and three other substance transporters. Mitochondrial genes as well as genes involved in the tricarboxylic acid cycle, glycolytic pathway, or β-oxidation pathway, which can generate energy in the form of ATP, were typically up-regulated in MA. 11 unigenes related to amino acid metabolism and a large number of genes related to protein synthesis were differentially expressed in MB and MA, indicating that E. sinensis possibly adjusts its concentration of free amino acid osmolytes for hyper-osmoregulation. Additionally, 33 salinity and oxidative stress induced genes were found to be differentially expressed, such as the LEA2, HSPs, GST and coagulation factor genes. Notably, LEA2 is an extremely hydrophilic protein that responds to desiccation and reported for the first time in crabs. Therefore, we suppose that when the environment is hypo-osmotic, the megalopae might compensate for ion loss via hyper-osmoregulation by consuming more energy, accompanied by a series of stress induced adaptions. This study provides the first genome-wide transcriptome analysis of E. sinensis megalopae for studying its osmoregulation and stress adaption mechanisms.

Project description:Background: Earlobe color is a typical external trait in chicken. There are some previous studies showing that the chicken white/red earlobe color is a polygenic and sex-linked trait in some breeds, but its molecular genetic and histological mechanisms still remain unclear. Methods: We herein utilized histological section, genome-wide association study (GWAS) and RNA-seq, further to investigate the potential histological and molecular genetic mechanisms of white/red earlobe formation in Qiangyuan Partridge chicken (QYP). Results: through histological section analysis, we found the dermal papillary layer of red earlobes had many more blood vessels than that of white earlobes. And we identified a total of 44 SNPs from Chromosome 1, 2, 3, 4, 9, 10, 11, 13, 19, 20, 23 and Z, that was significantly associated with the chicken white/red earlobe color from GWAS, along with 73 significantly associated genes obtained (e.g., PIK3CB, B4GALT1 and TP63), supporting the fact that the white/red earlobe color was also polygenic and sex-linked in QYP. Importantly, PIK3CB and B4GALT1 are both involved in the biological process of angiogenesis, which may directly give rise to the chicken white earlobe formation through regulating blood vessel density in chicken earlobe. Additionally, through contrast of RNA-seq profiles between white earlobe skins and red earlobe skins, we further identified TP63 and CDH1 differentially expressed. Combined with the existing knowledge of TP63 in epithelial development and tumor angiogenesis, we propose that down-regulated TP63 in white earlobes may play roles in thickening the skin and decreasing the vessel numbers in dermal papillary layer, thereby contributing to the white earlobe formation via paling the redness of the skin in QYP, but the specific mechanism remains further clarified. Conclusion: our findings advance the existing understanding of the white earlobe formation, as well as provide new clues to understand the molecular mechanism of chicken white/red earlobe color formation.

Dataset Information

Transcriptome changes provide genetic insights into the effects of rearing systems on chicken welfare and product quality.

Publications

Transcriptome changes provide genetic insights into the effects of rearing systems on chicken welfare and product quality.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets