GWAS and genomic prediction revealed potential for genetic improvement of large yellow croaker adapting to high plant protein diet

Fish meal as an indispensable feed source for aquaculture, seriously affects the development of wild fish resources. As an alternative aquafeed, plant-based diets are very important for healthy and sustainable culture of large yellow croaker. Genomic selection, as a method of genetic improvement of economic traits, has great potential and value in breeding new lines of large yellow croaker that are highly adaptable to plant proteins. In this study, 2048 large yellow croakers were injected with passive integrated transponder (PIT) tags and divided into two groups with the same feeding management. One group (C group) replaced 30% fish meal with plant protein, and the other group (P group) replaced 70% fish meal with plant protein. Body weight and body length of group C and P were measured respectively at 0, 84 and 206 days. To eliminate differences in initial body weight and influence on weight gain, weight gain rate (WGR) was used as the primary analysis trait. Fin clips were collected and were sequenced using Double-digest restriction-associated (ddRAD) approach. A total of 891 individuals and 34,994 SNPs passed the quality control procedure for Genome wide association study (GWAS) and genomic prediction (GP) analyses. The heritability of each trait was also calculated. The result shows that there is no difference in growth performance when 70% fish meal was replaced with plant protein compared with 30% fish meal replaced. The heritability of WGR1 (weight gain rate from 0 to 84 days) in the P group was 0.16. A total of 36 SNPs associated with WGR were identified, and a significant peak was found at 11.9–18.9 Mb on chromosome 18. The predictive ability of GBLUP and BayesB for WGR1 in P group was 0.10 and 0.11, respectively. This study provided reference for genetic improvement of efficient plant protein utilization in large yellow croaker by using genomic selection. • This is the first study on GWAS and genomic prediction of replacement fish meal with plant protein in large yellow croaker. • We were identified 10 SNPs associated with weight gain rate trait in the region of 11.9–18.9 Mb on chromosome 18. • In the experiment group, the heritability of weight gain rate trait of 70% fish meal replacement with plant protein was 0.16.