Identification of candidate genes affecting the tibia quality in Nonghua duck

The skeleton is a vital organ providing structural support in poultry. Weakness in bone structure can lead to deformities, osteoporosis, cage fatigue, and fractures, resulting in economic losses. Research has substantiated that genetic factors play a significant role in influencing bone quality. The discovery of genetic markers associated with bone quality holds paramount importance for enhancing genetic traits related to the skeletal system in poultry. This study analyzed nine phenotypic indicators of tibia quality in 120-day-old ducks. The phenotypic correlation revealed a high correlation among diameter, Perimeter, and weight (0.69-0.78), and a strong correlation was observed between toughness and breaking strength (0.62). Then, we conducted a genome-wide association analysis of the phenotypic indicators to elucidate the genetic basis of tibial quality in Nonghua ducks. Among the 11 candidate genes that were annotated, TAPT1, BST1, and STIM2 were related to the diameter indicator, ZNF652, IGF2BP1, CASK, and GREB1L were associated with the weight and toughness indicators. RFX8, GLP1R, and DNAAF5 were identified for ash, calcium, and phosphorus content, respectively. Finally, KEGG and GO analysis for annotated genes were performed. STIM2 and BST1 were enriched into the Calcium signalling pathway and Niacin and nicotinamide metabolic pathway, which may be key candidate genes affecting bone quality phenotypes. Gene expression analysis of the candidate genes, such as STIM2, BST1, TAPT1, and CASK showed higher expression levels in bones compared to other tissues. The obtained results can contribute to new insights into tibial quality and provide new genetic biomarkers that can be employed in duck breeding.