Growth performance and selection signatures revealed by whole-genome resequencing in genetically selected grass carp (Ctenopharyngodon idella)

Grass carp (Ctenopharyngodon idella) is a highly productive freshwater fish species that is widely cultivated worldwide, contributing substantial economic value to the aquaculture industry annually. Recently, a breeding program for grass carp has progressed to the fourth generation (F4) after four consecutive generations of family selection. To further assess the growth performance of the genetically selected grass carp F4, a 90-day consecutive growth comparison experiment was conducted between the selected population and a wild base population. The results showed that the selected grass carp F4 had better growth performance. Whole-genome resequencing of both wild and selected populations of grass carp yielded a total of 4,354,416 high-quality single nucleotide polymorphisms (SNPs). Parameters of genetic diversity including observed heterozygosity (Ho), expected heterozygosity (He), nucleotide diversity (pi), and polymorphic information content (PIC) were slightly decreased in the selected population compared to the wild population. The fixation index (Fst) indicated a low level of genetic differentiation (Fst = 0.021). Selection signatures analysis identified a total of 173 candidate selected regions with a cumulative size of 23.75 Mb, and 912 candidate genes including igf-1r, igfbp-2, igfbp-5 and itga6. This study provides valuable insights into the growth performance and the genetic basis of selection signatures in the process of grass carp selective breeding, and offers guidance for future breeding programs.