Multi-marker GWAS and variant-specific genomic prediction for growth traits in Pacific white shrimp

The genome of Penaeus vannamei is rich in short tandem repeats (STRs), occupying 18.96% of the genome, with 68.6% of loci showing high polymorphic information content, highlighting their potential as molecular markers. Accordingly, we performed an integrative GWAS leveraging STR, SNP, and InDel markers to identify 78 growth-associated loci, including 17 additional STRs compared with single-marker GWAS and six high-linkage regions containing metabolic, molting, and other growth-related genes. Four markers were validated in an independent population. In genomic prediction, STRs outperformed SNPs under the GBLUP model at low marker densities (20-50 loci), with accuracy gains up to 183%. GWAS-informed marker selection improved cross-population prediction performance, with STR-Top sets enhancing accuracy by 0.6%-3.0% under the GBLUP model, while SNP-Top sets achieved greater and more consistent gains under the KRR model. These results demonstrate the utility of STRs and support multi-marker integration for trait dissection and breeding in aquatic animals.