Local Enrichment of Multi-SNP Markers Improves Genomic Prediction from Low-Density Genotyping in Pacific White Shrimp

Low-density SNP panels are widely used to reduce genotyping costs in genomic selection (GS) in aquaculture, but sparse marker density can constrain prediction accuracy, particularly in species with rapid linkage disequilibrium decay. In this study, we evaluated a locally enriched multi-SNP (mSNP) strategy derived from a conventional 1K SNP panel in a family-based breeding population of Pacific white shrimp (Penaeus vannamei). Targeted sequencing was used to recover multiple nearby variants surrounding each marker locus, and conventional SNP and mSNP panels were compared for genomic features, imputation performance, and genomic prediction accuracy for body weight. The mSNP panel exhibited higher polymorphism and broader gene-region coverage than the corresponding SNP panel. The original mSNP panel improved prediction accuracy by 11.6% over the original 1K SNP panel. This advantage was maintained or slightly improved when mSNPs were restricted to on-target variants within ±300 bp of the target markers. A locus-matched comparison further showed that enriched mSNPs consistently outperformed conventional SNPs derived from the same target loci, with a 12.0% improvement at the full 961-locus panel. Although imputation improved the 1K SNP panel, the original mSNP panel already outperformed the imputed SNP panel and reached 0.509 after imputation. These findings demonstrate that locally enriched mSNP markers provide an effective and practical strategy for improving low-density GS in aquaculture species with rapid LD decay.