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Copy Number Variations in Short Tandem Repeats Modulate Growth Traits in Penaeid Shrimp Through Neighboring Gene Regulation

文献类型： 外文期刊

作者： Zhou, Hao 1 ; Qiang, Guangfeng 1 ; Xia, Yan 1 ; Tan, Jian 1 ; Fu, Qiang 1 ; Luo, Kun 1 ; Meng, Xianhong 1 ; Chen, Baolong 1 ; Chen, Meijia 1 ; Sui, Juan 1 ; Dai, Ping 1 ; Li, Xupeng 1 ; Liu, Mianyu 1 ; Xing, Qun 3 ; Kong, Jie 1 ; Luan, Sheng 1 ;

作者机构： 1.Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, State Key Lab Mariculture Biobreeding & Sustainabl, Qingdao 266071, Peoples R China

2.Qingdao Marine Sci & Technol Ctr, Lab Marine Fisheries Sci & Food Prod Proc, Qingdao 266237, Peoples R China

3.BLUP Aquabreed Co Ltd, Weifang 261311, Peoples R China

关键词： short tandem repeats; STR; growth trait; penaeid shrimp; molecular breeding

期刊名称：ANIMALS （ 影响因子：2.7； 五年影响因子：3.2 ）

ISSN： 2076-2615

年卷期： 2025 年 15 卷 2 期

页码：

收录情况： SCI

摘要： Penaeid shrimp, with its genomes enriched in short tandem repeats (STRs), presents an ideal model for studying the distribution and biological functions of STRs. In this study, we systematically identified and compared STRs across multiple species, confirming a significantly higher prevalence of STRs (26-32%) in penaeid shrimp, which is markedly higher than that observed in other species, such as mammals (1.3-2.1%) and plants (0.21-0.73%). Further analysis utilizing a cohort of 326 Pacific white shrimp revealed a total of 672,507 high-quality STRs evenly distributed across the genome, with a notably lower frequency of SNPs within these STR regions. Focusing on growth traits as a case study, we conducted a genome-wide association study (GWAS) and correlation analyses to identify the regulatory relationship of STRs on complex traits. We discovered 84 STRs that showed a significant association with body weight. Interestingly, eleven of these STRs, with 81% being composed of an A/T base, showed a significant linear correlation with body weight, revealing the key role of A/T-related STRs in shrimp weight regulation. For instance, a significant association and a negative correlation were found between the copy number of the STR [(A)n] at NW_020872788.1:580574 and body weight. The cytokinesis protein 7-like (LOC113800912) gene, which contains this STR in its splice region, exhibits differential expression associated with body weight variation. These findings introduce a model for STR copy number regulation in non-human species, illuminating the influence of STRs on growth traits. It offers a valuable framework for investigating complex traits and the biological functions of STRs in agricultural animals.

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