Specific pathogen free (SPF) chickens are crucial biological resources for fundamental research and industrial development in biomedicine, pharmaceutical sciences, and disease prevention and control. China achieved a significant milestone in 2000 by establishing its first independently developed SPF BWEL chicken population with proprietary intellectual property rights. During SPF chicken population development, rigorous quality control of microorganism, genetics, and environment are crucial for maintaining research-grade standards. In this study, we implemented regular monitoring of 20 specified avian pathogens and established comprehensive surveillance strategies to maintain pathogen-free status. Simultaneously, nine critical isolation environment parameters were systematically monitored to maintain optimal containment conditions. Furthermore, we performed SNP genotyping using chicken breeding chip on 262 F28 generation SPF BWEL chickens, followed by population structure analysis through kinship evaluation and clustering to reconstruct family lineages. Runs of homozygosity (ROH) were statistically analyzed to calculate individual and population-level inbreeding coefficients. The results showed that successful exclusion of 20 specific pathogens exceeding the National Standard of the People's Republic of China requirements, confirming excellent microbial quality. Meanwhile, all isolation parameters also complied with the provisions of the National Standard, ensuring environmental stability. Genetic analyses revealed the population could be clustered into five distinct families and the average inbreeding coefficient based on ROH (FROH) was 0.28, reflecting prolonged selective breeding history. This study provides critical guidelines for sustainable SPF chicken breeding and supports developments in biomedical and vaccine research application.

Keywords: Group family; Inbreeding coefficient; Microbial quality; SNP; SPF chicken.