Fat phenomics reveals shared genetic architecture of abdominal fat and yolk lipids: Insight into the potential for divergent selection.

Excessive abdominal fat deposition reduces production efficiency and metabolic health, whereas yolk lipid content is directly linked to egg quality and reproductive output. These two fat-related traits are often in conflict from a breeding perspective, yet whether they share common genetic and molecular determinants-and whether such sharing could inform divergent selection for lean abdomen with lipid‑rich yolk-remains unclear. Here, we analyzed 22 fat deposition-related traits in a population of 248 laying hens, together with genome-wide genotyping data, transcriptomic data from 10 tissues. Our results showed marked heterogeneity in the genetic architecture of fat deposition-related traits, with a higher degree of signal sharing among biologically related traits but limited overlap across different trait categories. Multi-trait association and trait-trait colocalization analyses further identified multiple shared loci between abdominal fat-related (AF) and egg yolk-related (EY) traits, including several shared candidate signals on chromosomes 2, 10, and 11. Integrative analyses incorporating multi-tissue cis-eQTL data further prioritized shared candidate regulatory genes, including MYO10, GPT2, VPS35, ADAM10, ALDH1A2, and MYO1E. Representative AF-EY shared loci, including 2__74614272, rs318039150, and rs741038415, showed opposite effect tendencies between abdominal fat- and yolk-related traits, whereas loci involving ADAM10, ALDH1A2, and MYO1E showed more directionally consistent associations, indicating both potential antagonistic and coordinated regulatory relationships. Together, these findings reveal a complex shared molecular basis linking abdominal fat deposition and yolk lipid deposition during the extended laying period and provide a framework for dissecting coordinated regulatory mechanisms and informing molecular breeding in laying hens.