eng Rovedar Journal of World’s Poultry Science 2980-7999 2025-09-01 4 3 50 62 10.58803/jwps.v4i3.80 82 Abdul Rehman 0 https://orcid.org/0009-0009-3221-2984 Nauman Khan 1 https://orcid.org/0009-0008-1289-6859 M Khuzema Niaz 2 https://orcid.org/0009-0009-2039-3570 Ali Mujtaba Shah 3 https://orcid.org/0000-0003-3698-6775 Javed Zafar 4 https://orcid.org/0009-0005-3299-1800 Fasih Ur Rehman 5 https://orcid.org/0000-0002-7750-3453 Naseer Ahmad 1 https://orcid.org/0009-0005-8967-6203 Kassahun Bekana 6 https://orcid.org/0000-0001-9393-2912 Muhammad Mushahid 7 https://orcid.org/0000-0001-8670-3011 Muhammad Talal 4 https://orcid.org/0009-0009-7272-9355 Umar Aziz 1 https://orcid.org/0009-0009-6266-4340 Department of Animal Sciences, Faculty of Animal Production and Technology, Cholistan University of Veterinary and Animal Sciences, Punjab, Pakistan Department of Animal Breeding, Genetics and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling, China Key Laboratory of Animal Breeding, Reproduction, and Molecular Design for Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, Guangzhou, China Department of Livestock and Poultry Production, Faculty of Veterinary Sciences, Bahauddin Zakariya University, Multan, Pakistan Department of Parasitology, University of Veterinary and Animal Sciences, Lahore, Pakistan Department of Animal Science, Ambo University, Guder Mamo Mezemir Campus, Ethiopia Institute of Animal and Dairy Sciences, University of Agriculture Faisalabad, Constituent College, Toba Tek Singh, Pakistan Introduction: The Australorp chicken, known for its exceptional egg production and adaptability, is a valuable genetic resource for the poultry industry. However, the molecular basis underlying their distinctive traits remains poorly understood. The present study aimed to identify novel genes and genetic variants associated with key production traits in Australorp chickens by performing a comprehensive comparative genomic analysis combined with an in silico genome-wide association study (GWAS). Materials and methods: Whole-genome sequencing data from 12 Australorp chickens were compared with data from four other breeds, including ten Rhode Island Red, eight Leghorn, ten Plymouth Rock, and six Red Jungle Fowl. Quality control and preprocessing were applied to ensure high-quality genomic data for downstream analyses. Comparative genomic analysis revealed several breed-specific genetic variants in Australorp chickens, affecting 50 genes functionally involved in metabolic and reproductive pathways, and 30 genes with reduced or altered functional annotations compared to other breeds. Principal component analysis revealed clear genetic differentiation among Australorp chickens, confirming their distinct genetic structure. Results: In silico GWAS identified significant associations between novel candidate genes (GENE 42, GENE 89) and key production traits, including egg production, egg weight, and disease resistance. Functional annotation revealed that these genes, identified in Australorp chickens (Gallus gallus), are mainly involved in metabolic processes, immune response, and reproductive pathways. Notably, several previously unreported genes were discovered that may contribute to the Australorp's superior egg-laying ability and disease resistance in chickens. Conclusion: The present findings offered new insights into the genetic basis of economically important traits in poultry and laid a foundation for marker-assisted selection in breeding programs. The novel genes identified in the present study served as potential targets for improving production traits in commercial chicken breeds and helped advance understanding of avian genomics and evolution. https://jwps.rovedar.com/index.php/JWPS/article/view/80 Australorp chicken Comparative genomic analysis Disease resistance Egg production Novel gene