"黄海芯1号"10K SNP面板在凡纳对虾基因组选择中的应用评估OA

Penaeus vannamei represents one of the most economically vital aquaculture species in China,where the implementation of genomic selection(GS)has emerged as a promising strategy to enhance breeding efficiency and accelerate the pace of genetic improvement.Nevertheless,the prohibitive genotyping cost associated with currently available medium-and high-density single nucleotide polymorphism(SNP)chips has severely restricted their large-scale deployment in shrimp breeding programs.To systematically evaluate the practical applicability of low-density SNP panels in commercial breeding scenarios,the present study assessed the genomic prediction performance of the newly developed"Yellow Sea Array No.1"10K SNP panel using harvest weight phenotypic data collected from two successive generations of P.vannamei.Two representative models,the pedigree-based PBLUP-GG model and the genomic information-integrated ssGBLUP-MF model,were constructed and comparatively analyzed,while two independent validation strategies,namely cross-validation and progeny testing,were adopted to quantify prediction accuracy across different SNP density gradients.The cross-validation results demonstrated that the prediction accuracy of the ssGBLUP-MF model using the 10K panel reached 0.43,which was marginally lower than that of the 55K panel(0.46)but substantially superior to that of the conventional PBLUP-GG model(0.27).Notably,under progeny testing,the 10K and 55K panels yielded identical prediction accuracy values of 0.45,both of which outperformed the PBLUP-GG model(0.42).Further validation using actual genotyping data generated from the 10K SNP panel showed that the ssGBLUP model achieved a prediction accuracy of 0.38 under routine genotyping and quality control workflows,significantly higher than the 0.28 obtained from the PBLUP model.Collectively,this study validates the reliability of the self-developed"Yellow Sea Array No.1"10K low-density SNP panel in P.vannamei breeding through combined cross-validation and progeny testing,providing a solid technical reference for the industrial-scale application of low-cost genomic selection in shrimp breeding.