Optimal open nucleus breeding system for long-term genetic gain in the Pacific white shrimp using genomic selection

The open nucleus breeding system (ONBS) has been widely employed in livestock breeding and has demonstrated a desirable genetic gain compared to the traditional closed nucleus breeding system (CNBS). However, no related study and application for ONBS exist on aquatic animal breeding. The present investigation simulates the family-based ONBS with different proportions of introduced multiplier individuals used as parents of the nucleus population (NP) and CNBS schemes for the harvest body weight of the Pacific white shrimp (Litopenaeus vannamei). The multiplier population (MP) comprised progenies from eight families with high estimated breeding value (EBV) or genomic EBV (GEBV) of NP of the previous generation. ONBS was assigned three proportions (10%, 30%, and 50%) of the introduced MP individuals. The short-term selection (G0 to G10) and long-term selection (G0 to G20) were performed for CNBS and ONBS schemes using pedigree-based best linear unbiased prediction (PBLUP) with the A relationship matrix from the pedigree or single-step genomic BLUP (ssGBLUP) with the H relationship matrix integrating SNP markers and pedigree. The genetic gain of body weight and inbreeding coefficient of NP for eight breeding schemes with CNBS_PBLUP (CP), CNBS_ssGLUP (CS), ONBS_PBLUP (OP10, OP30, OP50), and ONBS_ssGBLUP (OS10, OS30, OS50) with three proportions of the introduced MP individuals were calculated. Compared to CP, genetic gains for the three OP schemes increased by 7.68 to 11.27% after short-term selection, and by 2.51 to 5.79% after long-term selection. In comparison to CS, genetic gains for the three OS schemes increased by 8.21 to 8.96% after short-term selection, and from 4.46 to 5.87% after long-term selection. The ONBS schemes achieved higher genetic gains than the corresponding CNBS schemes whether using genomic or pedigree information. The advantage of ONBS over CNBS is reduced after long-term selection. Genetic gains for the three OS schemes increased by 9.77 to 14.06% after long-term selection compared with the corresponding OP schemes. Furthermore, no significant difference (P > 0.05) in genetic gain was revealed among the ONBS schemes after either pedigree-based or genomic selection. Inbreeding coefficients for the three OP schemes increased from 59.45 to 70.98% compared with CP, whereas inbreeding coefficients for the three OS schemes increased from 24.72 to 32.22% compared with CS. Besides, after long-term selection, inbreeding coefficients for the three OS schemes decreased from 13.13 to 14.79% compared with the corresponding OP schemes. In a nutshell, ONBS using introduced MP individuals has great promise in the selective breeding program of L. vannamei. Genomic information has more potential to improve selection response and control inbreeding level than pedigree information when applying ONBS.