Responses of Cobb×Cobb 500 slow feathering broilers to feeding programs with increasing amino acid densities

RNA-Seq-based discovery of genetic variants and allele-specific expression of two layer lines and broiler chicken

Recent advances in the selective breeding of broilers and layers have made poultry production one of the fastest-growing industries. In this study, a transcriptome variant calling approach from RNA-seq data was used to determine population diversity between broilers and layers. In total, 200 individuals were analyzed from three different chicken populations (Lohmann Brown (LB), n = 90), Lohmann Selected Leghorn (LSL, n = 89), and Broiler (BR, n = 21). The raw RNA-sequencing reads were pre-processed, quality control checked, mapped to the reference genome, and made compatible with Genome Analysis ToolKit for variant detection. Subsequently, pairwise fixation index (F ST) analysis was performed between broilers and layers. Numerous candidate genes were identified, that were associated with growth, development, metabolism, immunity, and other economically significant traits. Finally, allele-specific expression (ASE) analysis was performed in the gut mucosa of LB and LSL strains at 10, 16, 24, 30, and 60 weeks of age. At different ages, the two-layer strains showed significantly different allele-specific expressions in the gut mucosa, and changes in allelic imbalance were observed across the entire lifespan. Most ASE genes are involved in energy metabolism, including sirtuin signaling pathways, oxidative phosphorylation, and mitochondrial dysfunction. A high number of ASE genes were found during the peak of laying, which were particularly enriched in cholesterol biosynthesis. These findings indicate that genetic architecture as well as biological processes driving particular demands relate to metabolic and nutritional requirements during the laying period shape allelic heterogeneity. These processes are considerably affected by breeding and management, whereby elucidating allele-specific gene regulation is an essential step towards deciphering the genotype to phenotype map or functional diversity between the chicken populations. Additionally, we observed that several genes showing significant allelic imbalance also colocalized with the top 1% of genes identified by the FST approach, suggesting a fixation of genes in cis-regulatory elements.

Improvement in broiler performance by feeding a nutrient-dense diet after a mild feed restriction

Background: The use of early nutrient-restriction programs in broilers can prevent complications such as increased body fat deposition and its consequences. However, feed restriction not always gives the expected results. Objective: To assess the effect of two levels of feed restriction followed by a re-alimentation period with five increasing nutrient levels on growth performance and immune response of broiler chickens. Methods: A total of 330 animals were used. The treatments were: 25 (T25) and 35% (T35) quantitative feed restriction during the starting period, and 0, 2.5, 5, 7.5, 10, and 15% increased energy and protein contents during the growing and finishing periods. Results: For all the T25 treatments, except for T25-0, feed intake (FI) and body weight gain (BWG) were higher, and feed conversion rate (FCR) was lower (p<0.05) compared to the control treatment. In that group, the response of FI and BWG to the increased nutrient density was mostly quadratic (p<0.001), whereas that of FCR was linear (p<0.001). The FI and BWG results were less homogeneous in the T35 treatments, but FCR was lower compared to the control treatment (p<0.05) in all of them. The FCR showed no differences (p>0.05) between treatments during the finishing period. Conclusion: Feeding a nutrient-dense diet after a period of mild feed restriction gives the best results, while increasing nutrient density after a more severe feed restriction does not improve productive results compared to a standard diet. Carcass traits and immune function were not affected by restriction level or nutrient density.