Development and application of a low-density 10 K liquid SNP array for genetic improvement in large yellow croaker (Larimichthys crocea)

Developing cost-effective and scalable genotyping platforms is essential for expanding germplasm identification and genomic breeding in aquaculture. However, the high cost of genotyping remains a major constraint on the large-scale application of these approaches in large yellow croaker. To address this limitation, we developed a low-density 10 K liquid SNP array, “NingXin-IV”, based on the previously established “NingXin-III” 55 K array. Representative SNPs were selected from haplotype blocks and supplemented with trait-associated loci. The array was further evaluated for germplasm identification, pedigree analysis, sex identification, and genomic selection. The 10 K panel showed excellent genotyping performance, with detection rate and genotype concordance both exceeding 99% and SNPs evenly distributed across the 24 chromosomes, indicating excellent genome-wide representativeness. Population genetic analyses showed that the panel effectively distinguished different populations. Machine learning models based on the 10 K dataset achieved an accuracy of > 0.99 for germplasm identification, with results highly consistent with the 55 K panel. In addition, the array achieved 100% accuracy in parentage assignment, pedigree reconstruction, and sex prediction. After genotype imputation, the 10 K panel retained genomic prediction performance close to that of the 55 K panel, although the absolute predictive ability of both datasets was moderate. Imputation accuracy ranged from 0.817 to 0.964, with an 86.21%–87.93% overlap with the 55 K panel among the top 10% of GEBV-ranked individuals. Overall, “NingXin-IV” provides an efficient and cost-effective tool for germplasm evaluation, parentage verification, breeding strain management, and large-scale genomic selection breeding in large yellow croaker, and serves as a useful reference for the development of low-density genotyping platforms in other aquaculture species.