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.

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Publication Details

Journal
Scientific Reports
Published
2025-11-26
DOI
https://doi.org/10.1038/s41598-025-26048-3
Primary Topic
Genetic and phenotypic traits in livestock
Type
article
Field-Weighted Citation Impact
0.00

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article

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

Qun Xing, Jiawang Cao, Mianyu Liu, Baolong Chen et al.
Scientific Reports
Genetic and phenotypic traits in livestock
article

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

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

Abstract

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.

Scientific ReportsVol. 15(1)
Shenyang Center for Disease Control and Prevention (CN), Weifang People's Hospital (CN), Qingdao National Laboratory for Marine Science and Technology (CN), Chinese Academy of Agricultural Sciences (CN), Chinese Academy of Fishery Sciences (CN)
National Natural Science Foundation of China, Natural Science Foundation of Shandong Province
Openalex Percentile: Top 61%
Genetic and phenotypic traits in livestock
DOIOpen Access PDFOpenAlex
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