Development and validation of a 20 K genome-wide liquid SNP array for Chinese mitten crab (Eriocheir sinensis) breeding and germplasm identification
文献类型： 外文期刊
作者： Bai, Yulin 1 ; Jiang, Zhou 1 ; Ma, Junlei 2 ; Liang, Yidong 3 ; Zhang, Ting 3 ; Wang, Anqi 1 ; Hu, Changsui 1 ; Xu, Dongpo 1 ;
作者机构： 1.Chinese Acad Fishery Sci, Freshwater Fisheries Res Ctr, Key Lab Freshwater Fisheries & Germplasm Resources, Minist Agr & Rural Affairs, Wuxi 214081, Peoples R China
2.Nanjing Agr Univ, Wuxi Fisheries Coll, Wuxi 214081, Peoples R China
3.Shanghai Ocean Univ, Natl Demonstrat Ctr Expt Fisheries Sci Educ, Shanghai 201306, Peoples R China
关键词： Eriocheir sinensis; Genome resequencing; Liquid SNP array; GWAS; Phylogenetic analysis
期刊名称：AQUACULTURE REPORTS （ 影响因子：3.7； 五年影响因子：4.0 ）
ISSN： 2352-5134
年卷期： 2025 年 43 卷
页码：
收录情况： SCI
摘要： High-density SNP arrays have proven to be effective tools for assessing thousands of SNPs simultaneously, facilitating genome-scale studies and genomic selection (GS) in aquaculture species. The Chinese mitten crab (Eriocheir sinensis) is an economically significant aquaculture species in China. However, the lack of efficient high-throughput genotyping tools has hindered GS and GWAS, thereby slowing genetic improvement efforts. In this study, we developed and evaluated a novel SNP array based on Genotyping by Targeted Sequencing (GBTS) technology, named HeXieXin-I. The array includes 21,285 SNPs distributed across 70 chromosomes, with 98.66 % of SNPs having a MAF greater than 0.1. Genotyping accuracy and consistency were validated, achieving a genotype concordance of 95.57 % with resequencing data and a 100 % consistency rate across different batches. The GWAS analysis for four growth traits (BW, BH, CL, and CW) identified 46 significant SNPs associated with CL. Among these, the most significant SNP (chr46_1686249) is located within a 100 Kb upstream and downstream region that contains three candidate genes: ptpn11, profilin-1, and lei. Additionally, population genetic analysis based on 240 individuals demonstrated the array's capability to distinguish geographical populations, highlighting its potential for genetic resource management and breeding applications. The HeXieXin-I SNP array provides a robust and cost-effective genotyping tool to accelerate genetic improvement and sustainable aquaculture development for Chinese mitten crab.
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