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.