First development of a 100 K SNP array for small yellow croaker and its application in genomic selection for growth and disease resistance

Small yellow croaker, Larimichthys polyactis, is a marine fish species of significant commercial importance in China and Korea, yet it suffers from various challenges including genetic degradation and disease problem. Strains with good performance traits such as fast growth and strong disease resistance are needed in aquaculture. In the present study, a 100 K SNP array with exceptional genotyping quality was developed based on genomic resequencing, achieving a remarkable detection rate of 98.75% and concordance rate of 98.49%. A total of 946 individuals were genotyped for body weight, body length, and disease resistance (quantified by the survival time of fish injected with pathogen Pseudomonas plecoglossicida) using the SNP array. Genomic selection (GS) was conducted using the restricted maximum likelihood (REML) and genomic best linear unbiased prediction (GBLUP) methods. The heritability estimates for body weight, body length, and survival time were 0.47 ± 0.05, 0.43 ± 0.05, and 0.33 ± 0.05, respectively. Notably, Ten-fold cross-validation using genomic BLUP gave a genomic prediction accuracy of 0.70 ± 0.04 for body length, and 0.43 ± 0.09 for body weight, exceeding that for disease resistance trait (0.40 ± 0.13). Evaluation results further indicated that implementing a 30% selection ratio translated into a relative genetic gain (ΔG′) of 17.62% for body weight and 4.28% for disease resistance per generation. This study demonstrates the effectiveness and efficiency of the SNP arrays for applications in GS and breeding. The array and accompanying GS pipeline provide a practical for accelerating genetic improvement in small yellow croaker and can serve as a template for other aquaculture species.