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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.

Conditions in early life play profound and long-lasting effects on the welfare and adaptability to stress of chickens. This study aimed to explore the hypothesis that the provision of environmental complexity in early life improves birds’ adaptive plasticity and ability to cope with a challenge later in life. It also tried to investigate the effect of the gut-brain axis by measuring behavior, stress hormone, gene expression, and gut microbiota. One-day-old chicks were split into 3 groups: (1) a barren environment (without enrichment items) group (BG, n = 40), (2) a litter materials group (LG, n = 40), and (3) a perches with litter materials group (PLG, n = 40). Then, enrichment items were removed and simulated as an environmental challenge at 31 to 53 d of age. Birds were subjected to a predator test at 42 d of age. In the environmental challenge, when compared with LG, PLG birds were characterized by decreased fearfulness, lower plasma corticosterone, improved gut microbial functions, lower relative mRNA expression of GR, and elevated mRNA expressions of stress-related genes CRH, BDNF, and NR2A in the hypothalamus (all P < 0.05). Unexpectedly, the opposite was true for the LG birds when compared with the BG (P < 0.05). Decreased plasma corticosterone and fearfulness were accompanied by altered hypothalamic gene mRNA expressions of BDNF, NR2A, GR, and CRH through the HPA axis in response to altered gut microbial compositions and functions. The findings suggest that gut microbiota may integrate fearfulness, plasma corticosterone, and gene expression in the hypothalamus to provide an insight into the gut-brain axis in chicks. In conclusion, having access to both perches and litter materials in early life allowed birds to cope better with a future challenge. Birds in perches and litter materials environment may have optimal development and adaptive plasticity through the gut-brain axis.

In recent decades, artificial selection has contributed greatly to meeting the demands for animal meat, eggs, and milk. However, it has also resulted in changes in behavior, metabolic and digestive function, and alterations in tissue development, including the brain and skeleton. Our study aimed to profile the behavioral traits and transcriptome pattern of chickens (broilers, layers, and dual-purpose breeds) in response to artificial selection. Broilers spent less time gathered as a group in a novel arena (P < 0.01), suggesting reduced fearfulness in these birds. Broilers also showed a greater willingness to approach a model predator during a vigilance test but had a greater behavioral response when first exposed to the vocalization of the predator. Genes found to be upregulated and downregulated in previous work on chickens divergently selected for fear responses also showed consistent differences in expression between breeds in our study and indicated a reduction in fearfulness in broilers. Gene ACTB_G1 (actin) was differentially expressed between breeds and is a candidate gene involved with skeletal muscle growth and disease susceptibility in broilers. Furthermore, breed-specific alterations in the chicken domestic phenotype leading to differences in growth and egg production were associated with behavioral changes, which are probably underpinned by alterations in gene expression, gene ontology terms, and Kyoto Encyclopedia of Genes and Genomes pathways. The results highlight the change in behavior and gene expression of the broiler strain relative to the layer and a dual-purpose native breed.

Hens are raised apart from roosters in modern poultry production, a substantial change from their natural social structure. We compared productivity, injuries, behavior, physiology, microbiome and transcriptome of hens housed with (R+) or without (R-) roosters to quantify the effects of this change in social structure. Hens were raised free-range from 70 to 280 days when 30 birds per treatment were assigned to battery cages until Day 315 (R+C vs. R-C), while 30 birds per treatment remained in free-range pens (R+F vs. R-F). Response to a novel environment and object, behavioral time budgets, cecum microbiome, blood composition and transcriptomic sequencing of thigh muscle and spleen were analyzed. Hens housed without roosters showed better survival, consumed less food, produced more eggs and had better feed conversion. R+F hens clustered around the rooster and were less mobile in the novel environment and object tests. R+F hens displayed the richest microbiome, and the presence of roosters resulted in differentially expressed genes related to muscle development, cellular processes, environmental information processing and immune function. Removing roosters from housed hens intensified desirable characteristics favored by domestication probably operating by deprivation of mating behavior and reduced fear, along with altered microbial and genetic function.

The association between mitochondrial DNA haplotype and productive performances has been widely reported in chicken breeds. However, there has not been physiological evidence of this seen previously. In this study, chicken transmitochondrial cells were generated using the nucleus of the DF-1 cell line and mitochondria of primary cell lines derived from two native chicken breeds, Tibetan chicken and Shouguang chicken. Generally, Tibetan chicken primary cells showed a stronger metabolic capacity than Shouguang chicken primary cells. However, the Tibetan chicken cybrids had a dramatic drop in relative mtDNA copies and oxygen consumption. Higher rates of oxygen consumption (OCR) and expression levels of mitochondrial biogenesis and fusion genes were observed in Shouguang chicken cybrids, potentially reflecting that the mitochondrial DNA haplotype of Shouguang chicken had better coordination with the DF-1 nucleus than others. Meanwhile, mitonuclear incompatibility occurred in Tibetan chicken cybrids. The results demonstrate functional differences among mitochondrial DNA haplotypes and may shed light on the interaction between the mitochondria and nucleus in Gallus gallus domesticus.

It has been long demonstrated that cage rearing (CR) deprives the animal of the possibility to express natural behaviors and results in stress. However, the effect of the rearing system on gene expression and the molecular levels of the gut microbiome are unknown. 10-wk-old Beijing You chickens were studied in parallel CR and free-range (FR) systems for 30 wk, to investigate the effect of rearing systems on behavior, microbiota composition, and gene expression. From week 40, a match-mismatch design was conducted for 5 wk. The results indicated that CR deprives the animals of natural behaviors, evidenced by sham dust-bathing behavior. A decreased alpha diversity of gut microbiome composition of CR chickens was seen in FR compared to CR-FR chickens (P < 0.001), and the alpha diversity of gut microbiome composition of FR-CR was decreased as compared to FR chickens (P = 0.045). The heat map and beta-diversity analysis showed that the cluster of gut microbial compositions were similar between the mismatch groups (FR-CR and CR-FR), while those of CR showed the lowest diversity from the 4 groups. The relative abundance of gut microbes at genera and species levels was different between comparisons (P < 0.05). Moreover, the CR (both CR and FR-CR) triggered the downregulation of most Kyoto encyclopedia of genes and genomes pathways, while it was upregulated in 2 genetic information processing pathways, compared to FR hens regardless of long or short term. In conclusion, CR deprived chickens of their normal behavior and resulted in changes in the microbiome diversity and pathways and gene expression of chickens.

TME, true amino acid availability (TAAA), AME, and apparent amino acid availability (AAAA) were determined in Chinese high oil corn (CHOC) and conventional corn (CC). The CC and CHOC contained 4.58 and 8.44% ether extract (DM basis), respectively. A precision-fed rooster assay was used in which each corn sample was tube-fed (50 g) to 16 roosters and excreta were collected for 48 h. A N-free diet and fasting methods were used to evaluate endogenous amino acid (AA) losses. Endogenous losses of 10 AA were different (P0.05) with the N-free and fasting methods; in most cases the mean value for the N-free treatment was greater (P0.05) than for the fasting treatment. The TME value for CHOC was greater than for CC (4,193 vs. 3,961 cal/g DM; P0.05). The true availability of aspartic acid, threonine, isoleucine, and leucine of CC and CHOC was higher (P0.05) for the N-free method than for the fasting method. When compared within the N-free or within the fasting method, the true availabilities of lysine, methionine, and proline were higher (P0.05) in CHOC than in CC, but the true availability of phenylalanine was lower (P0.05) in CHOC than in CC. The AAAA values, although lower, followed similar patterns as the TAAA values. The results of this study indicated that availability of AA in CHOC is equal or superior to that in CC and that the available energy for poultry is higher in CHOC than in CC.