Elucidating the genetic basis of earlobe color in Qingyuan partridge chickens through genomics and metabolomics.

The earlobe color trait is a significant characteristic in chickens, exhibiting notable genetic diversity. Elucidating the mechanism of inheritance of the earlobe color trait would be beneficial in promoting genetic improvement with this phenotypic trait and would help in breed identification. Current research mainly hypothesizes that pigment deposition may underlie the phenotypic differences in earlobe color, with few studies exploring the molecular genetic mechanisms from the perspective of metabolomic differences. In this study, we selected Qingyuan Partridge chicken exhibiting both red and white earlobe traits as our subjects. By combining histological, metabolomic, and genomic approaches, we aim to identify the primary factors governing the formation of these two earlobe colorations. Histological analysis of frozen sections from two types of earlobe tissue revealed that red earlobe formation is correlated with capillary density. Untargeted metabolomic sequencing analysis identified 61 high-abundance differential metabolites, Whole-genome FST Study and Case-Control Genome-Wide Association Study, identified 93 significant overlapping SNPs and annotated to 70 relevant candidate genes. It is particularly noteworthy that the differentially expressed metabolites and candidate genes were both significantly enriched in the sphingolipid metabolism pathway. Among them, C16-ceramide in the sphingolipid metabolic pathway is a key metabolite affecting the formation of white earlobes, the genes SGMS1, SGPP2, and SMPD4 contribute to the formation of white earlobes by regulating the metabolism and deposition of relevant lipids in the sphingolipid metabolic pathway. Our research provides new insights into the molecular mechanisms behind poultry earlobe color traits and holds significant implications for the selective breeding of characteristic traits in Qingyuan Partridge chickens, and its application to production can accelerate the efficiency of earlobe color improvement.