Development of high throughput SNP genotyping approach using target sequencing in Pacific white shrimp and its application for genetic study

The Pacific white shrimp Litopeneaus vannamei (L. vannamei) is a worldwide aquaculture species and selection of high performance germplasm is urgently needed. Application of molecular breeding method, such as marker assisted selection (MAS) or genomic selection (GS), is an efficient approach to accelerate the breeding program for high-quality germplasm. However, lack of cost-effective genotyping method is the main obstacle for their applications in shrimp breeding program. In this study, we developed a high throughput SNP genotyping method based on AmpliSeq target sequencing. A total of 581 amplicons including the genome-wide distributed markers, immune-related genes, WSSV resistance related SNPs, growth and sex related SNPs were selected and could be genotyped simultaneously. Totally 10 samples were used for genotyping and 2130 high quality SNPs were genotyped. Through analyzing the genotyped SNPs, the genetic relationship of samples could be accurately reconstructed. Besides, the pooling genotyping method using SNP panel was evaluated. It illustrated that the pooling genotyping method was reliable with read depth at >200. Based on the read depth of each amplicons, the panel was further optimized to 508 amplicons, which will enhance the sequencing uniformity and improve the efficiency of the panel. This study provided a useful genetic tool and a new method for genetic study. It will accelerate the application of MAS and GS in shrimp breeding program.