Evaluation of genomic selection for high salinity tolerance trait in Pacific white shrimp Litopeneaus vannamei

The Pacific white shrimp ( Litopeneaus vannamei ) can tolerate wide range of salinity from 0.5 to 40. However, the growth and survival rate of shrimp is relatively low when they are cultured in high salinity seawater (>40). There is a large area of high salinity water which could be utilized for shrimp aquaculture. It is necessary to select new varieties of shrimp with high salinity tolerance, which can be cultured in these areas. In this study, the genetic parameters and genomic prediction accuracy on high salinity tolerance trait of Litopenaeus vannamei were evaluated using genome-wide SNPs. The survival time, lethal salinity and survival status of shrimp during high salinity treatments were recorded as phenotypes for each individual. The heritabilities of three phenotypes including survival time, lethal salinity and survival status were 0.38 ± 0.1, 0.40 ± 0.1, 0.5 ± 0.1, respectively. Among different GS models, GBLUP and BayesB showed similar prediction accuracy. The prediction accuracy of GBLUP for survival time, lethal salinity, and survival state of shrimp were 0.62 ± 0.03, 0.64 ± 0.04, and 0.76 ± 0.01, respectively. Compared with traditional pedigree selection (PBLUP), GS models showed a higher prediction accuracy by up to 12.1%. In addition, the optimal training population size was predicted to be around 1000, in which the prediction accuracy can rise to around 0.9. These results indicate that the heritability of high salinity tolerance trait of shrimp is medium to high heritability, and the genomic selection is superior to traditional selection approach. This study provides important guidance for genomic selection of shrimp tolerant to high salinity. • The estimated heritability of high salinity tolerance traits is middle to high (0.38–0.5) for Litopeneaus vannamei . • GBLUP outperformed PBLUP, and the prediction accuracy increased by up to 12.1% when comparing GBLUP against PBLUP in high salinity tolerance traits. • The optimal size of training population is predicted to be almost 1000 for shrimp high salinity tolerance traits.