2.5 Selection signature analysis
Cultured F. chinensis shrimps were obtained from Haifeng Aquaculture Co., Ltd, which has undergone continuous, high-intensity artificial selection for growth traits for more than ten generations. Wild F. chinensis were captured from the northeast region of the Huanghai Sea. We used 22 cultured and 22 wild shrimps to collect muscle tissue and extract DNA. The DNA samples were sequenced using the BGISEQ platform (BGI, Wuhan, China). Sequencing data were mapped to the reference genome, and VCFtools (Danecek et al., 2011) was used to calculate the fixation index (F ST) and nucleotide diversity (π) in 40 kb sliding windows with a step size of 20 kb. Windows with the top 5% values of both F ST and π were considered as outliers. Genes in these windows were picked for the subsequent Gene ontology (GO) and KEGG pathway enrichment analysis.