Abstract <p>The study of quantitative and qualitative traits from a genetic perspective is impossible without considering diseases or characteristics linked to sex. Currently, genomic selection based on sex chromosomes, conducted through genome-wide association studies (GWAS), has not been a key factor in developing specialized code and functional gene annotation, taking into account GO and KEGG libraries, as well as the analysis of previously identified genes. The aim of this research was to develop a software code for conducting GWAS on pig sex chromosomes and to identify functionally significant genes to explain the “phenotype–sex genetics” relationship. This will further refine the selection process for pigs in the population nucleus and enable the prediction of hereditary diseases in animals. In this article, we performed, for the first time, a GWAS analysis of genomic estimated breeding values for the feed conversion trait, focusing solely on sex chromosomes (sGWAS). Structural annotation identified 21 genes located on the X chromosome and 8 genes on the Y chromosome, including the homologous XY region. Cluster analysis of the identified genes revealed a significant association with the feed conversion ratio in eight of them: <i>STS</i>, <i>DDX3X</i>, <i>PUDP</i>, <i>PNPLA4</i>, <i>DHRSX</i>, <i>GPR143</i>, <i>SHROOM2</i>, and <i>PRKX.</i> Functional annotation of these genes highlighted their significant contribution to biological processes, including hereditary diseases and sex-linked specificity.</p>