Transcriptomic and Metabolomic Analysis of the Uterine Tissue of Yaoshan Chicken and Its Crossbreeds to Reveal the Molecular Mechanism Influencing Eggshell Quality

<b>Background/Objectives:</b> Eggshell quality is a critical factor influencing consumer preference and the economic benefits of poultry enterprises, and the uterus is the key site for eggshell synthesis. Yaoshan chicken (YS), an indigenous chicken breed in China, is renowned for its flavorful meat and high-quality eggs. However, its egg production is lower compared to specialized strains. Therefore, the GYR crossbreed was developed by three-line hybridization for YS chicken, which can produce green-shelled eggs with better eggshell thickness and strength than YS chicken (<i>p</i> < 0.01). To explore the molecular mechanisms underlying the differences in eggshell quality between GYR and YS chickens, we conducted an integrated transcriptomic and metabolomic analysis. <b>Methods:</b> Twelve uterus samples (six from GYR and six from YS chickens) were collected during the period of eggshell calcification at 260 days of age. RNA sequencing (RNA-seq) and liquid chromatography-mass spectrometry (LC-MS/MS) were performed to identify differentially expressed genes (DEGs) and differential metabolites (DMs), respectively. <b>Results:</b> A total of 877 DEGs were identified in the GYR group, including 196 upregulated and 681 downregulated genes (|log₂ (fold change)| > 1, <i>p</i>-value < 0.05). Additionally, 79 DMs were detected, comprising 50 upregulated and 29 downregulated metabolites (|log₂ (fold change)| > 1, VIP > 1). Notably, the key DEGs (<i>SLCO1B3</i>, <i>SLCO1B1</i>, <i>PTGR1</i>, <i>LGR6</i>, <i>MELTF</i>, <i>CRISP2</i>, <i>GVINP1</i>, and <i>OVSTL</i>), important DMs (prostaglandin-related DMs and biliverdin) and signaling pathways (calcium signaling, neuroactive ligand-receptor interaction, arachidonic acid metabolism, bile secretion, and primary bile acid biosynthesis) were major regulators of the eggshell quality. Furthermore, an integrated transcriptomic and metabolomic analysis revealed two significant gene-metabolite pairs associated with eggshell quality: <i>PTGDS-</i>prostaglandin E2 and <i>PTGS1-</i>prostaglandin E2. <b>Conclusions:</b> This study provides a theoretical foundation for the improved eggshell quality of Yaoshan chicken.