Weighted gene co-expression network analysis identifies important modules and hub genes involved in the regulation of breast muscle yield in broilers.

OBJECTIVE: Increasing breast meat production is one of the primary goals of the broiler industry. Over the past few decades, tremendous progress has been made in genetic selection and the identification of candidate genes for improving the breast muscle mass. However, the molecular network contributing to muscle production traits in chickens still needs to be further illuminated. METHODS: A total of 150 1-day-old male 817 broilers were reared in a floor litter system. At the market age of 50 d, eighteen healthy 817 broilers were slaughtered and the left pectoralis major muscle sample from each bird was collected for RNA-seq sequencing. The birds were then plucked and eviscerated and the whole breast muscle was removed and weighed. Breast muscle yield was calculated as the ratio of the breast muscle weight to the eviscerated weight. To identify the co-expression networks and hub genes contributing to breast muscle yield in chickens, we performed weighted gene co-expression network analysis (WGCNA) based on the 18 transcriptome datasets of pectoralis major muscle from eighteen 817 broilers. RESULTS: The WGCNA analysis classified all co-expressed genes in the pectoral muscle of 817 broilers into 44 modules. Among these modules, the turquoise and skyblue3 modules were found to be most significantly positively (r = 0.78, p = 1e-04) and negatively (r = -0.57, p = 0.01) associated with breast meat yield, respectively. Further analysis identified several hub genes (e.g., DLX3, SH3RF2, TPM1, CAV3, MYF6, and CFL2) that involved in muscle structure and muscle development were identified as potential regulators of breast meat production. CONCLUSION: The present study has advanced our understanding of the molecular regulatory networks contributing to muscle growth and breast muscle production and will contribute to the molecular breeding of chickens in the future.

Identification of Key Modules and Hub Genes Involved in Regulating the Color of Chicken Breast Meat Using WGCNA.

Meat color is one of the most important economic traits in chickens. However, the gene network and regulatory mechanisms contributing to meat color traits in chickens remain largely unknown. In the present study, we performed weighted gene co-expression network analysis (WGCNA) based on RNA-Seq datasets of 16 pectoralis major muscle samples from two yellow-feather chicken breeds to identify the modules and hub genes related to meat color in chickens. A total of 18,821 genes were used to construct the weighted gene co-expression network, and 29 co-expression gene modules were identified. Among these modules, five modules including blue, brown, steel blue, paleturquoise and orange modules were found to be significantly correlated with meat color traits. Furthermore, several genes within the association module involved in the regulation of mitochondrial activity (e.g., ATP5L, UQCR10 and COX7C) and lipid oxidation (e.g., CAV3, RBP4A and APOH) were identified as hub genes that may play a crucial role in the regulation of meat color. These results provide valuable information to improve our understanding of gene expression and regulation in relation to meat color traits and contribute to future molecular breeding for improving meat color in chickens.

Genome-wide scan for selection signatures and genes related to heat tolerance in domestic chickens in the tropical and temperate regions in Asia.

Heat stress is one of the major environmental stressors challenging the global poultry industry. Identifying the genes responsible for heat tolerance is fundamentally important for direct breeding programs. To uncover the genetic basis underlying the ambient temperature adaptation of chickens, we analyzed a total of 59 whole genomes from indigenous chickens that inhabit South Asian tropical regions and temperate regions from Northern China. We applied FST and π-ratio to scan selective sweeps and identified 34 genes with a signature of positive selection in chickens from tropical regions. Several of these genes are functionally implicated in metabolism (FABP2, RAMP3, SUGCT, and TSHR) and vascular smooth muscle contractility (CAMK2), and they may be associated with adaptation to tropical regions. In particular, we found a missense mutation in thyroid-stimulating hormone receptor (41020238:G>A) that shows significant differences in allele frequency between the chicken populations of the two regions. To evaluate whether the missense mutation in TSHR could enhance the heat tolerance of chickens, we constructed segregated chicken populations and conducted heat stress experiments using homozygous mutations (AA) and wild-type (GG) chickens. We found that GG chickens exhibited significantly higher concentrations of alanine aminotransferase, lactate dehydrogenase, and creatine kinase than AA chickens under heat stress (35 ± 1°C) conditions (P < 0.05). These results suggest that TSHR (41020238:G>A) can facilitate heat tolerance and adaptation to higher ambient temperature conditions in tropical climates. Overall, our results provide potential candidate genes for molecular breeding of heat-tolerant chickens.

Exercise profile and effect on growth traits, carcass yield, meat quality, and tibial strength in Chinese Wannan chickens.

The aim of the study was to understand the dynamic changes in daily step counts (DSC) during the development of chickens and to further explore the effects of exercise on the growth performance, carcass yield, meat quality, and tibial strength of cocks. A total of 600 (half male and half female) 1-day-old Wannan chickens with similar hatching weights were raised under the same rearing conditions. All birds were wing banded and housed in identical cages for from 1 to 8 wk in the experimental poultry house. The dimensions of the cages were 70 × 70 × 40 cm (length × width × height). At the age of 9 to 16 wk, these birds were reared in indoor pens (2 m × 2 m, 1,000 cm2 per bird). In addition, they also had a free-range grass paddock (20 m × 30 m, 1 m2 per bird). The DSC of male and female Wannan chicks were recorded from 70 to 112 d by using a pedometer. At 112 d of age, based on the average DSC, birds were divided into groups representing the highest (HS), medium, and lowest (LS) number of step groups. Fifteen cocks from each group were selected for subsequent experiments. Compared with the LS group, the HS group displayed higher tibial strength (P = 0.025) and lower BW, cooking loss (P = 0.014), shear force (P = 0.023), and drip loss (P = 0.008). The DSC had no effects on the female BW or male carcass parameters. There was no significant change in the DSC of all birds from 70 to 112 d. However, male chickens took more steps than females at 15 (P = 0.025) and 16 (P = 0.012) week of age. In conclusion, the effects of the DSC on the BW of Wannan chickens depend on sex, and enhanced exercise could improve the meat quality and tibial strength of cocks.

Revisiting the evolutionary history of domestic and wild ducks based on genomic analyses.

Although domestic ducks have been important poultry species throughout human history, their origin remains enigmatic, with mallards and/or Chinese spot-billed ducks being proposed as the direct wild ancestor(s) of domestic ducks. Here, we analyzed 118 whole genomes from mallard, Chinese spot-billed, and domestic ducks to reconstruct their evolutionary history. We found pervasive introgression patterns among these duck populations. Furthermore, we showed that domestic ducks separated from mallard and Chinese spot-billed ducks nearly 38 thousand years ago (kya) and 54 kya, respectively, which is considerably outside the time period of presumed duck domestication. Thus, our results suggest that domestic ducks may have originated from another wild duck population that is currently undefined or unsampled, rather than from present-day mallard and/or Chinese spot-billed ducks, as previously thought. Overall, this study provides new insight into the complex evolution of ducks.