The assessment of population genetic structure is the basis for understanding the genetic information of indigenous breeds and is important for the protection and management of indigenous breeds. However, the population genetic differentiation of many local breeds still remains unclear. Here, we performed a genome-wide comparative analysis of Jinding, Liancheng white, Putian black, and Shanma ducks based on the genomic sequences using RAD sequencing to understand their population structure and genetic diversity. The population parameters showed that there were obvious genetic differences among the four indigenous breeds, which were separated groups. Among them, Liancheng white and Shanma ducks may come from the same ancestor because the phylogenetic tree forms three tree trunks. In addition, during the runs of homozygosity (ROH), we found that the average inbreeding coefficient of Liancheng white and Putian black ducks was the lowest and the highest, respectively. Five genomic regions were considered to be the hotspots of autozygosity among these indigenous duck breeds, and the candidate genes involved a variety of potential variations, such as muscle growth, pigmentation, and neuroregulation. These findings provide insights into the further improvement and conservation of Fujian duck breeds.

Duck Tembusu virus (DTMUV) is an emerging flavivirus that has inflicted significant economic losses on China’s poultry industry. Rapid and accurate detection of DTMUV is crucial for effective prevention and control measures. In this study, we developed a novel, rapid visual detection assay that combines reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) with the CRISPR/Cas12a system for on-site detection of DTMUV. Our results demonstrate that this assay can sensitively and specifically detect the specific DNA plasmids containing the DTMUV NS3 gene within 100 min, with a limit of detection as low as 19.3 copies/μL. We successfully applied the RT-LAMP-CRISPR/Cas12a assay to diagnose DTMUV in eight duck embryos and 11 chicken embryonic fibroblast samples, and the results obtained with direct visualization by the naked eye were consistent with those obtained using real-time RT-PCR. Overall, our RT-LAMP-CRISPR/Cas12a assay is a reliable, sensitive, specific, and user-friendly method that holds great promise for early on-site detection of DTMUV in clinical samples, facilitating timely interventions and improved disease management in the poultry industry.

Duck Tembusu virus (DTMUV), a novel positive-sense RNA virus, has caused significant economic losses in the poultry industry of Eastern and Southeast Asia since its outbreak in 2010. Furthermore, the rapid transmission and potential zoonotic nature of DTMUV pose a threat to public health safety. In this study, a 4D-DIA quantitative proteomics approach was employed to identify differentially expressed cellular proteins in DTMUV-infected DF-1 cells, which are routinely used for virus isolation and identification for DTMUV, as well as the development of vaccines against other poultry viruses. One hundred fifty-seven differentially expressed cellular proteins were identified, including 84 upregulated and 73 downregulated proteins at 48 h post-infection, among which CXCL8, DDX3X, and TRPV2 may play crucial roles in viral propagation. Notably, for the upregulated protein TRPV2, the DTMUV replication was inhibited in TRPV2-low-expressing DF-1 cells. In summary, our research represents the application of 4D-DIA quantitative proteomics to analyze the proteomic landscape of DTMUV-infected poultry cells. These findings may provide valuable insights into understanding the interaction mechanism between DTMUV and poultry cells, as well as the identification of disease-resistant host factors in poultry breeding research.