Mining candidate genes for abnormal red body color traits of cultured Yellow River Carp(Cyprinus carpio haematopterus) based on BSA whole genome resequencing

To reveal the mechanism of abnormal body color variation in the same family of cultured Yellow River carp. In this study, Yellow River carp with normal body color and abnormal red body color cultured in the same cement pond were used as materials. By bulked segregant analysis (BSA) and whole genome resequencing, individuals displaying extreme phenotypes within the offspring were selected and combined into a composite pool for subsequent sequencing. Following the identification of single nucleotide polymorphism (SNP) and insertion/deletion (InDel) variations in the sequencing data, the linkage location analysis revealed that the linkage region was situated on chromosome 25 of Yellow River carp, specifically at LG25: 15881284-26645798. Subsequently, candidate genes within this region were screened, and the resulting candidate loci were further filtered based on the location of the variation loci.Ultimately, a total of 51 differential genes were obtained. Subsequently, GO and KEGG enrichment analyses were performed on these genes, resulting in the identification of four potential candidate genes, namely opn3, dkk1, vkind, and lyst, which may exert an influence on the abnormal synthesis pathway of red body color in Yellow River carp. The primary functions of these genes primarily involve signal transduction and regulation of molecular functions. The findings of this study offer fundamental insights into the mining and functional analysis of genes associated with the atypical red body coloration in Yellow River carp. Moreover, they establish a theoretical foundation for the development of novel germplasm innovations in Yellow River carp.