Abstract
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.
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