数字农科院2.0

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

文献类型： 外文期刊

作者： 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

作者机构：

关键词： Aquaculture breeding;Genomic prediction;GWAS;Penaeus vannamei;STR

期刊名称： Scientific Reports

ISSN：

年卷期： 2025 年 15 卷 1 期

页码：

收录情况： SCIE（2025版）

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.

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