Development and evaluation of liquid SNP array for large yellow croaker (Larimichthys crocea)

In order to promote the genetic selective breeding of large yellow croaker, we designed and developed the liquid single nucleotide polymorphism (SNP) array named NingXin-III that based on the genotyping by target sequencing (GBTS) technology and 55 K high-throughput solid chip-based array (NingXin-II SNP array) of large yellow croaker. NingXin-III SNP array contains 98.85% of the loci on the NingXin-II SNP array, and 1535 new loci, totaling 54,990 loci, which are evenly distributed on 24 chromosomes of large yellow croaker. Based on the NingXin-III SNP array, 89 samples from two batches of large yellow croaker were genotyped, and the results showed that the genotyping success rate of NingXin-III SNP array in both batches was over 97.4%, the average genotype concordant rate of individuals in different batches was 99.56%, and the average genotype concordant rate of duplicate individuals in the same batch was 99.7%. A comparison of the genotyping results of the shared loci on NingXin-II and NingXin-III showed that the average genotype concordant rate of common loci between them reached over 96%. In summary, NingXin-III SNP array has a high genotyping accuracy, high reproducibility and no batch effect, which can completely replace NingXin-II SNP array. NingXin-III SNP array will provide important technical support for genetic improvement of important economic traits of large yellow croaker.