Genome-wide association analysis reveals the genetic basis of ionomic variation in duck breast muscle

Abstract Mineral elements are crucial for biological functions, with meat serving as a key dietary source. Despite advances in ionome analysis, the genetic mechanisms regulating mineral accumulation in meat remain poorly understood. Here, we analyze the ionome of 376 breast muscles from the large gradient consanguinity segregating population generated by Pekin duck × Liancheng white duck crosses, quantifying 7 essential mineral elements (potassium (K), phosphorus (P), sodium (Na), magnesium (Mg), calcium (Ca), iron (Fe), and zinc (Zn)). Notably, Ca exhibited the most pronounced variation between Pekin duck and Liancheng white duck (fold change = 1.83, P < 0.01). Correlation analysis demonstrated significant positive relationships between Zn and Ca (r = 0.49), Na (r = 0.41), and (all P < 0.001), while negative correlations were observed between Na and K (r = −0.29) (P < 0.001). We then analyzed correlations between the ionomic profiles and growth and meat quality traits. Importantly, Ca concentrations showed strong negative correlations with both breast muscle thickness (r = −0.72) and body weight (r = −0.76) (both P < 0.01), but positively correlated with meat lightness (r = 0.54, P < 0.01). To elucidate the genetic architecture underlying the duck pectoralis muscle ionome, we first estimated its narrow-sense heritability, which ranged from 0.19 to 0.58 across different mineral elements. Through comprehensive genetic analyses incorporating genome-wide association studies, linkage disequilibrium mapping, gene annotation, and expression profiling, we identified 2 key genes (SLC25A25 and ATP2B2) on chromosomes 18 and 13 that collectively regulated Ca content. These lead single nucleotide polymorphisms in these loci explained 39.91% and 11.07% of the phenotypic variance, respectively. Notably, the lead SNP on Chr18 also demonstrated pleiotropic effects, contributing to both meat lightness (PVE = 14.79%) and breast muscle thickness (PVE = 1.79%). Furthermore, on chromosome 2, we discovered a significant SNP associated with both Na and Ca concentrations, accounting for 12.6% and 4.35% of phenotypic variation, respectively. Further analysis pinpointed gene SLC25A32 as the most promising candidate within this genomic region. These findings enhance our comprehension of the genetic basis underlying ion content in meat and offer valuable insights for refining breeding programs, while also providing a new direction for the combat hidden hunger through meat biofortification.