Development of a 50K liquid-phase SNP genotyping array to accelerate genetic breeding in Litopenaeus vannamei

Abstract

The high cost of genotyping remains a significant limitation to the widespread adoption of molecular breeding in aquaculture. This study aimed to develop a 50K liquid-phase Single Nucleotide Polymorphism (SNP) array for the economically important shrimp Litopenaeus vannamei, and to comprehensively evaluate its potential for application in genetic breeding programs. Based on whole-genome resequencing (WGS) data from 547 individuals from five commercial populations, we selected 50,031 uniformly distributed SNPs as background loci. These were combined with 951 previously identified functional SNPs related to key economic traits to construct the final 50K SNP array. We validated its technical performance by genotyping 417 offspring and assessed its practical applications through principal component analysis (PCA), genome-wide association study (GWAS) and genomic selection (GS) for body weight. The SNP array exhibited excellent performance, with a 98.21% average call rate, 98.82% average genotype concordance, and high polymorphism (97.44% of SNPs with MAF $>$ 0.05). Application validation through PCA effectively discerned population structure. GWAS using two models identified seven significant SNPs associated with body weight, implicating candidate genes with putative roles in growth and development. Most importantly, GS using the array data improved prediction accuracy for body weight by 11.24% over traditional pedigree-based methods. We also found that a marker density as low as 5 K was sufficient for achieving near-maximum prediction accuracy. This SNP array provides a powerful and cost-effective tool to accelerate genetic improvement in modern shrimp breeding programs.