GWAS Enhances Genomic Prediction Accuracy of Caviar Yield, Caviar Color and Body Weight Traits in Sturgeons Using Whole-Genome Sequencing Data

Caviar yield, caviar color, and body weight are crucial economic traits in sturgeon breeding. Understanding the molecular mechanisms behind these traits is essential for their genetic improvement. In this study, we performed whole-genome sequencing on 673 Russian sturgeons, renowned for their high-quality caviar. With an average sequencing depth of 13.69×, we obtained approximately 10.41 million high-quality single nucleotide polymorphisms (SNPs). Using a genome-wide association study (GWAS) with a single-marker regression model, we identified SNPs and genes associated with these traits. Our findings revealed several candidate genes for each trait: caviar yield: <i>TFAP2A</i>, <i>RPS6KA3</i>, <i>CRB3</i>, <i>TUBB</i>, <i>H2AFX</i>, <i>morc3</i>, <i>BAG1</i>, <i>RANBP2</i>, <i>PLA2G1B</i>, and <i>NYAP1</i>; caviar color: <i>NFX1</i>, <i>OTULIN</i>, <i>SRFBP1</i>, <i>PLEK</i>, <i>INHBA</i>, and <i>NARS</i>; body weight: <i>ACVR1</i>, <i>HTR4</i>, <i>fmnl2</i>, <i>INSIG2</i>, <i>GPD2</i>, <i>ACVR1C</i>, <i>TANC1</i>, <i>KCNH7</i>, <i>SLC16A13</i>, <i>XKR4</i>, <i>GALR2</i>, <i>RPL39</i>, <i>ACVR2A</i>, <i>ADCY10</i>, and <i>ZEB2</i>. Additionally, using the genomic feature BLUP (GFBLUP) method, which combines linkage disequilibrium (LD) pruning markers with GWAS prior information, we improved genomic prediction accuracy by 2%, 1.9%, and 3.1% for caviar yield, caviar color, and body weight traits, respectively, compared to the GBLUP method. In conclusion, this study enhances our understanding of the genetic mechanisms underlying caviar yield, caviar color, and body weight traits in sturgeons, providing opportunities for genetic improvement of these traits through genomic selection.