Genomic insights into pigeon breeding: GWAS for economic traits and the development of a high-throughput liquid phase array chip

Due to the monogamous mating system and late maturity of pigeons, their breeding cycle is longer compared to that of other poultry species, which has hindered the optimization of growth traits and meat quality. While traditional breeding methods are commonly used, they lack precision and are time-consuming. This study integrates phenotypic data from Tarim pigeons and White King pigeons with genomic information, using genome-wide association analysis (GWAS) to identify genetic markers associated with key economic traits, thereby accelerating the breeding process. The results reveal significant correlations between body type characteristics (e.g., live weight and chest depth) and carcass traits, supporting their use as indirect selection criteria. GWAS identified several candidate genes, including PPARGC1A and ADGRA3, linked to muscle development and metabolic regulation. To enhance breeding efficiency, this study developed a Liquid Phase Chip (LPC), designed to use high-throughput technology for identifying genetic markers related to carcass traits. Although the LPC is not yet commercially available, the 50 K pigeon LPC from this study could provide crucial theoretical support for its future application. Ultimately, the LPC will serve as an important tool for precision and efficiency in pigeon breeding, driving the development and optimization of the pigeon industry.