Abstract：It is speculated that there should be specific selection signatures in the genetic improvement population of Yellow River common carp Cyprinus carpio haematopterus arising from long-term artificial selection after domestication. Understanding and improvement of the signatures at a genetic level is important to inform future efforts to further improve a fish which is one of the most important commercial species in freshwater culture with a long period of artificial selection. In this study, two genetically modified populations: 12 whole sibling families (10) of the new strain of Yellow River common carp (F5) and the culture population of Furui carp No. 2 (FFRC No.2)and one unselected population were resequenced whole-genome, and a total of 8 665 728 high-quality SNP sites were obtained by typing data of SNP sites, and the selected genomic regions were detected by the fixation index (Fst), nucleotide diversity (π ratio)and cross-population composite likelihood ratio test (XP-CLR). Top 5% of values was used as the threshold signature of artificial selection where were annotated to further identify potential candidate genes. To further control the false positive rates of the detection of selection signatures, genes identified by three methods were used in further enrichment analyses. In total, compared with the reference population, 1434 and 1333 genes were potentially selected between two genetic improvement populations, respectively. These candidate genes were enriched in cell development, heart contraction, cell differentiation and protein glycosylation in new strain of Yellow River common carp. The candidate genes were enriched in embryonic skeletal joint development, membrane fusion and neurotransmitter secretion in C. carpio FFRC No.2 strain. Mixing two genetic improvement populations, compared with the reference population, 2037 genes were annotated, including Fabp2, Acaca, Acsl and Cpt1. These candidate genes were significantly enriched in several fatty acid metabolism-related pathways, including glycerophospholipid metabolism, fatty acid biosynthesis, fatty acid degradation and peroxisome proliferators activate receptors (PPAR) signaling pathway, which may partly explain the difference between the genetic improvement population and reference population in terms of growth traits. In the current study, a number of regions with signatures of positive selection were identified, and further functional analyses on these regions identified a list of genes involved in fatty acid metabolism. The findings provide a new insight into the mechanism of genetic improvement of growth traits in common carp and contribute to promote the application of genomic selection in breeding of common carp.
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