Whole-genome resequencing reveals selection signatures in China's first rainbow trout (Oncorhynchus mykiss) strain “Shuike No. 1”

Abstract

Rainbow trout (Oncorhynchus mykiss) is a globally significant cold-water farmed fish, first introduced to China in 1959. After 17 years of selective breeding, China ‘s first new rainbow trout strain, “Shuike No. 1” (SK), was developed in 2021. SK exhibits superior growth performance compared to the source populations from which it was bred, but its selection characteristics remain understudied. To investigate genetic changes associated with the selective breeding process of SK, we conducted whole-genome resequencing of 68 individuals from the SK population and its original hybrid population. A total of 19,825,329 single nucleotide polymorphism (SNP) loci were identified, with an average density of 8.88 SNPs/Kb. Significant genetic differentiation and linkage disequilibrium (LD) were observed between the two populations. Combined analysis of genetic differentiation and diversity between populations (using fixation indices F_st and nucleotide diversity θ_π) and genomic selection sweeps within the SK population (using the composite likelihood ratio CLR) identified genomic regions under selection in the SK population. We detected 217 and 59 candidate genes associated with selection, encompassing traits related to growth, early development, reproduction, behavior, immune function, and adaptation to the aquaculture environment. Both analysis methods identified the Rgs12a gene, which encodes a protein involved in cell signal transduction, particularly the G protein-coupled receptor signaling pathway, and is associated with parturition, skeletal muscle development, and tumor suppression. Functional enrichment analysis revealed that genes within the selected regions play crucial roles in intercellular interactions, cell signaling, cell membrane structure and function, regulation of ion homeostasis, energy metabolism, and regulation of the biological clock. These findings provide valuable insights for germplasm resource assessment, genome-assisted breeding of rainbow trout, and understanding the genetic effects and genomic features of selective breeding in this commercially important fish.