Pedigree reconstruction based on target sequencing in Pacific white shrimp Litopeneaus vannamei

Litopenaeus vannamei is one of the most economically productive species in aquaculture. It accounts for about 80% of the world's mariculture production of shrimp. Genetic selection of shrimp is mainly based on family selection. Therefore, accurate pedigree information is essential to ensure the reliability of estimated genetic parameters and the selection of the best broodstock. Recent advances in molecular breeding have facilitated molecular pedigree reconstruction based on SNPs and improved the accuracy of selection. However, breeding populations of aquatic species tend to be large. Therefore, a high-throughput and cost-effective method was needed for the commercial application of parentage assignment. In this study, we developed a low-density SNP panel based on target sequencing. A total of 200 amplicons, evenly distributed across the genome, were captured by multiplex PCR and sequenced by next-generation sequencing. Genotyping of 320 individuals in four ponds including multiple families identified 1,169 SNPs. Based on these SNPs, two softwares including Sequoia and PaternityT were used to reconstruct the sibling information. Consequently, a total of 39 families were accurately identified, and the results of the two software programs were highly consistent. Analysis based on different numbers of amplicons showed that at least 50 amplicons were required for accurate assignment. The identification result was also validated by principal component analysis and phylogenetic analysis. With the development of NGS technology, thousands of individuals could be genotyped with high throughput and low cost, making the method developed in this study affordable for parentage assignment in commercial breeding program. Meanwhile, the low-density SNP panel also has high value and prospects for application in shrimp genetic research.