Whole-genome resequencing of Russian sturgeon (Acipenser gueldenstaedtii) reveals selection signatures associated with caviar color

Russian sturgeon, Acipenser gueldenstaedtii, a primitive freshwater fish, holds high economic value as the source of caviar. Remarkably, the economic significance of gold caviar surpasses that of its black counterpart. However, the genetic basis underlying the color variations in caviar remains unexplored. In this study, we conducted whole-genome resequencing of 62 individuals from gold caviar (G) and black caviar (B) populations, achieving an average sequencing depth of approximately 12.21×, and each individual produced approximately 32.47 million high-quality single nucleotide polymorphisms (SNPs). By combining FST and XPEHH methods, we identified 1138 candidate selection regions spanning 26.7 Mb, encompassing 771 genes. Furthermore, significantly enriched GO terms and KEGG pathways were related to pigmentation (e.g., Protein digestion and absorption and Retinol metabolism, etc.) and immunity (e.g., Purine metabolism, Phagosome and Vibrio cholerae infection). Based on the findings, 12 genes (ACTA1, ADCY3, ADCY5, ATP6V1C1, ATP6V1H, CHST11, COL6A3, GART, KCNJ13, RDH10, KCNN4 and XDH) were identified as candidate genes that may affect caviar color. Furthermore, four genes (ATP6V1H, GART, RDH10 and KCNN4) detected simultaneously by FST and XPEHH methods were validated using KASP. This study lays the groundwork for unraveling the molecular mechanisms underlying caviar color and provides insights for the selective breeding of sturgeons with the desired gold caviar trait.