Development of a 20 K SNP array for the leopard coral grouper, Plectropomus leopardus

Abstract

Single nucleotide polymorphism (SNP) genotyping array is a powerful tool for providing information on polymorphic variations of species of interest. These genomic variations can be used to investigate the genetic architecture of complex traits, population structures, and genomic selection of breeding programs. The aquaculture of the leopard coral grouper (Plectropomus leopardus), is rapidly developing in South China and Southeast Asia. However, the lack of a high-efficient genotyping platform has hampered the progress of both genetic studies and selective breeding practices of this fish. Here we developed and evaluated a 20 K SNP array namely “DongXin-I” for P. leopardus. Using the genome re-sequencing data of 730 leopard coral groupers, we identified over 3.67 million SNPs, from which 20,737 loci, with even distribution across the genome, were finally involved in the SNP array. Evaluation of the array performance with 232 fish showed a high overall SNP call rates (> 99%) and an average minor allele frequency (MAF) of 0.312. Comparison of genotyping results of 87 fish from both the “DongXin-I” array and genome resequencing demonstrated a high genotyping repeatability and accurate performance of the genotyping array. Furthermore, using the gentyping results generated by the “DongXin-I” array, we revealed the genetic structure of breeding populaitons currently used the in Hainan Province. To summarize, the “DongXin-I” array should be a useful tool for the genetic studies and genomic selection breeding in the aquaculture industry of the coral leopard grouper.