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<p>The genome of <i>Penaeus vannamei</i> 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.</p>

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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年11月26日

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  • Tianzan Lv,
  • Yan Xia,
  • Jian Tan,
  • Qiang Fu,
  • Kun Luo,
  • Xianhong Meng,
  • Baolong Chen,
  • Meijia Chen,
  • Juan Sui,
  • Ping Dai,
  • Xupeng Li,
  • Junyu Liu,
  • Mianyu Liu,
  • Jiawang Cao,
  • Qun Xing,
  • Guangfeng Qiang,
  • Jie Kong,
  • Hao Zhou,
  • Sheng Luan

摘要

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.