Development and evaluation of a 40 K liquid SNP array for kuruma shrimp (Penaeus japonicus)

The kuruma shrimp ( Penaeus japonicus ) is an economically important species in global aquaculture. However, its genetic improvement has been limited by the lack of efficient genotyping tools. Here, we developed the first high‑throughput 40 K liquid SNP array for P. japonicus , named “Lujiangxin‑I”. This SNP array was designed based on whole‑genome resequencing (WGS) of 394 samples using genotyping by target sequencing (GBTS) technology. The “Lujiangxin‑I” comprises 41,340 uniformly distributed SNPs, of which 78.98% showed minor allele frequency (MAF) > 0.1. Performance evaluation demonstrated high genotyping quality, with an average call rate of 98.24%, a reproducibility rate of 99.36%, and 93.67 concordance with WGS data. Population genetic analysis across six P. japonicus populations revealed clear genetic differentiation between a Chinese‑selected line (DongShan) and Japanese cultured stocks. The Dongshan population exhibited lower genetic diversity and slower linkage disequilibrium (LD) decay. In contrast, the Japanese cultured stocks (J1-J4) maintained higher genetic diversity. The “Lujiangxin‑I” offers a reliable, cost-efficient, and high‑throughput tool for genetic research in P. japonicus aquaculture.