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Development and evaluation of a 50 K SNP array for blotched snakehead ( Channa maculata)

文献类型： 外文期刊

作者： Cui, Tongxin 1 ; Liu, Haiyang 1 ; Zhang, Jin 1 ; Luo, Qing 1 ; Fei, Shuzhan 1 ; Chen, Kunci 1 ; Zhao, Jian 1 ; Ou, Mi 1 ;

作者机构： 1.Chinese Acad Fishery Sci, Pearl River Fisheries Res Inst, Key Lab Trop & Subtrop Fishery Resources Applicat, Minist Agr & Rural Affairs, Guangzhou 510380, Peoples R China

2.Zhejiang Ocean Univ, Sch Fishery, Zhoushan 316022, Peoples R China

3.Shanghai Ocean Univ, Coll Fisheries & Life Sci, Shanghai 201306, Peoples R China

关键词： Channa maculata; SNP array; Lixin-I; GWAS; Population genetic

期刊名称：AQUACULTURE （ 影响因子：3.9； 五年影响因子：4.4 ）

ISSN： 0044-8486

年卷期： 2025 年 598 卷

页码：

收录情况： SCI

摘要： SNP arrays are potent tools for genetic typing, offering several advantages such as high throughput, costeffectiveness, and accuracy. They play a pivotal role in genetic studies, including genome selection and population genetics. The blotched snakehead ( Channa maculata) holds significant economic importance in China as a freshwater fish species. To facilitate genetic breeding research on this species, we developed a 50 K SNP array named "Lixin-I" for genetic typing. We performed whole-genome resequencing on 748 blotched snakeheads from 18 populations, yielding 2,307,294 high-quality SNPs after quality control. From these data, we selected 50,000 SNPs evenly distributed throughout the genome, including SNPs previously associated with growth and sex traits from prior studies. Evaluation of the "Lixin-I" SNP array on 150 blotched snakeheads showed a 96.00 % consistency rate with whole-genome resequencing and a 97.94 % call rate. Using this array, we genotyped 464 cultured blotched snakeheads and performed a genome-wide association analysis (GWAS) for weight trait. We successfully identified 13 SNPs associated with weight, located on three chromosomes. These results indicate that weight in blotched snakeheads is a complex trait regulated by multiple genes, providing valuable insights for the genetic analysis of growth traits. Furthermore, we conducted population genetic structure and genetic diversity analyses on seven wild blotched snakehead populations. These findings provide critical insights for the rational utilization and germplasm innovation of blotched snakehead genetic resources. In summary, the developed "Lixin-I" SNP array is a high-quality genetic typing tool that effectively supports genetic breeding efforts in blotched snakeheads.

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