Whole genome resequencing reveals grass carp candidate sex chromosome and sex determination system

With their dynamic sex chromosome systems, teleosts provide an invaluable model for revealing the deep-time evolutionary patterns of sex determination pathways in vertebrates. Grass carp ( Ctenopharyngodon idella ) is the first among China's "four major domestic fishes" and the single species with the highest freshwater aquaculture output in the world. This study provides insights into the sex chromosomes and sex determination system of grass carp via whole-genome resequencing. After strict quality filtering, a total of 6736,499 SNPs and 1927,252 indels were obtained through variation detection and analysis. The functional annotation of SNPs and indels revealed that variations in noncoding regions are abundant, whereas there is a mild enrichment of nonsynonymous mutations in coding regions. PCA and phylogenetic trees revealed that the overall genetic structure of the male and female populations overlapped. The sex association analysis revealed that Chr3 as the candidate sex chromosome of grass carp, with a sex-determining region located at Chr3: 11.00–11.30 Mb. The molecular markers developed for this region further verified that grass carp adopt the XX/XY (male heterogametic) sex determination system. This study provides key markers and a theoretical basis for the monosex breeding of grass carp and the evolution of sex chromosomes in Cyprinidae fishes. • Grass carp candidate sex chromosome is identified as Chr3 with a 0.3 Mb SDR. • Molecular markers confirm an XX/XY sex determination system in grass carp. • Provides key resources for monosex breeding and sex chromosome evolution studies.