Development and Validation of a 20K 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 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, HeXieXin-I based on GBTS technology. 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. GWAS analysis of four growth traits - BW, BH, CL, and CW revealed 46 significant SNPs associated with CL, including a peak region on chromosome 46 harboring 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.