Development and validation of a 20 K genome-wide liquid SNP array for Chinese mitten crab (Eriocheir sinensis) breeding and germplasm identification

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. • This is the first study to develop the 20 K liquid SNP array in Chinese mitten crab. • HeXieXin-I SNP array includes 21,285 high-quality loci and has significant advantages in genotyping consistency and cost. • HeXieXin-I SNP array demonstrated effectiveness in genome-wide association and population genetics analysis.