Comparative Genomic Analysis Across Multiple Species to Identify Candidate Genes Associated with Important Traits in Chickens

<b>Background:</b> As one of the most important poultry species worldwide, chickens provide substantial amounts of meat, eggs, and other products for human consumption. With continuous improvements in living standards, consumer demand for high-quality animal products is increasing, making it essential to understand the genetic basis of key traits such as egg production, meat quality, and disease resistance for targeted genetic improvement. <b>Methods:</b> In this study, a number of the candidate genes associated with important traits in chickens were screened by various comparative genomics analysis methods. To further clarify the relationship between these candidate genes and important traits in chickens, they were functionally annotated through the KOG, GO, and KEGG databases. <b>Results:</b> These candidate genes are mainly concentrated in the functional categories of transcription and signal transduction mechanisms and are involved in biological processes such as cyclic nucleotide biosynthesis and intracellular signaling, which involve signaling pathways such as ECM-receptor interactions and calcium signaling. <b>Conclusions:</b> Based on the annotation results from various databases, a functional search of the candidate genes and related literature reports, the following results were obtained: genes such as <i>TBX22</i>, <i>LCORL</i>, and <i>GH</i> were associated with chicken growth traits; genes such as <i>A-FABP</i>, <i>H-FABP</i>, and <i>PRKAB2</i> were associated with chicken meat quality; genes such as <i>IGF-1</i>, <i>SLC25A29</i>, and <i>WDR25</i> were associated with chicken reproductive traits; and genes such as <i>C1QBP</i>, <i>VAV2</i> and <i>IL12B</i> were associated with chicken disease resistance traits. Overall, the findings of this study provide novel insights and candidate genes for genetic improvements in chickens, laying a foundation for future research and breeding strategies targeting key economic traits.