Chickens are the world’s most widely used farm animal and have a significant genetic diversity. In the current study, we investigated three strains for their suitability as dual-purpose chickens, with a focus on the fattening ability and welfare of the cockerels: 1. layer cockerels (Lohmann Brown, LB, n = 714); 2. cockerels of a dual-purpose hybrid (Lohmann Dual, LD, n = 844); and 3. cockerels of a native breed (Rhinelander, RL, n = 458). Chicks were raised under identical conditions and marked individually to compare focus and random sampling methods for weighing birds weekly. Because chicks of dual-purpose origins are usually raised mixed-sex, cockerels and pullets were weighed and observed together until sexes the were identifiable at week 10 of their life. During the 10th to 20th week of life, investigations were continued on 100 cockerels per genotype. Key figures for growth performance, such as feed conversion ratio (FCR) and European production efficiency factor (EPEF), were also calculated at weekly intervals. LD cockerels showed considerable growth performance (p < 0.001 compared to LB, RL, 2 kg at 9 weeks), whereas LB reached a live weight of 2 kg at 13 weeks and RL at 15 weeks of age. Genotype-dependent differences were also evident, with favorable FCR and EPEF for LD, intermediate for LB, and unfavorable for RL (all p < 0.001). The results of the FCR and EPEF suggest that cockerels should be slaughtered around week 8 of life, although only the carcass of the LD might be marketable. Thus, the optimal time of slaughter based on production parameters such as FCR and EPEF is different from the time when the animal reaches a marketable 2 kg live weight. Animal-based welfare indicators revealed that the RL are not adapted to production environments, including those that are extensive. Further research aimed at adapted feed management, including better FCR, and animals adapted to the respective production environments is necessary to improve alternative poultry production in the future.

Avian influenza is a severe viral infection that has the potential to cause human pandemics. In particular, chickens are susceptible to many highly pathogenic strains of the virus, resulting in significant losses. In contrast, ducks have been reported to exhibit rapid and effective innate immune responses to most avian influenza virus (AIV) infections. To explore the distinct genetic programs that potentially distinguish the susceptibility/resistance of both species to AIV, the investigation of coincident SNPs (coSNPs) and their differing causal effects on gene functions in both species is important to gain novel insight into the varying immune-related responses of chickens and ducks. By conducting a pairwise genome alignment between these species, we identified coSNPs and their respective effect on AIV-related differentially expressed genes (DEGs) in this study. The examination of these genes (e.g., CD74, RUBCN, and SHTN1 for chickens and ABCA3, MAP2K6, and VIPR2 for ducks) reveals their high relevance to AIV. Further analysis of these genes provides promising effector molecules (such as I$\kappa$B$\alpha$, STAT1/STAT3, GSK-3$\beta$, or p53) and related key signaling pathways (such as NF-$\kappa$B, JAK/STAT, or Wnt) to elucidate the complex mechanisms of immune responses to AIV infections in both chickens and ducks.