Deciphering Pleiotropic Single‐Nucleotide Polymorphisms Governing Fertility–Milk Yield Trade‐Offs in Dairy Cattle: A Genome‐Wide Chromosomal Landscape Analysis

Fertility and milk production in dairy cattle are economically significant traits, but they exhibit an unfavorable genetic correlation, making simultaneous improvement challenging. Identifying pleiotropic genes that influence both traits can provide valuable insights for genomic selection. This study aimed to identify common significant SNPs (CSSNPs) associated with both fertility and milk production traits and map these SNPs to pleiotropic genes, highlighting genomic regions with potential for simultaneous improvement of these traits. Significant SNPs for fertility (6336 SNPs) and milk production (6353 SNPs) were analyzed to identify 196 CSSNPs. These SNPs were mapped to 160 pleiotropic genes, and their distribution across cattle chromosomes (BTAs) was examined, focusing on key genomic regions. The highest number of CSSNPs (35) and pleiotropic genes (24) was identified on BTA6, while BTA14 harbored 21 pleiotropic genes. Several chromosomes, including BTA24 and BTA29, had no pleiotropic genes. In chromosome X, 4 CSSNPs and 3 pleiotropic genes were identified. This study identified critical genomic regions and pleiotropic genes associated with both fertility and milk production, providing insights into the genetic architecture of these traits. The findings highlight specific regions, particularly BTA6 and BTA14, which are promising targets for genomic selection. These results can inform breeding programs by enabling the development of strategies to simultaneously improve fertility and milk production in dairy cattle, optimizing productivity and sustainability.