Selection Signatures of Pacific White Shrimp Litopenaeus vannamei Revealed by Whole-Genome Resequencing Analysis

• DOI: 10.3389/fmars.2022.844597
• Publication Date: 2022-03-29T05:34:47Z
• Authors: Hao Wang; Mingxuan Teng; Pingping Liu; Mingyang Zhao; Shi Wang; Jingjie Hu; Zhenmin Bao; Qifan Zeng
• Keywords: Litopenaeus; Linkage Disequilibrium; Nucleotide diversity

The Pacific white shrimp Litopenaeus vannamei is among the top aquatic species of commercial importance around world. Over last four decades, breeding works L. have been carried out intensively and generated multiple strains with improved production performance traits. However, signatures domestication artificial selection across genome remain largely unexplored. In present study, we conducted whole genomic resequencing 180 shrimps from two artificially selective breeds market-leading companies. A total 37 million single nucleotide polymorphisms (SNPs) were identified an average density 22.5 SNPs/Kb genome. Ancestry estimation, principal component analysis, phylogenetic inference all revealed obvious stratifications six breeds. We evaluated linkage disequilibrium (LD) decay in each breed genetic variations driven by selection. Pairwise comparison fixation index ( F st ) diversity (θ π has allowed for mining regions under sweep breed. functional enrichment analysis that genes within these are mainly involved cellular macromolecule metabolic process, proteolysis, structural molecule activity, structure constituent ribosome, responses to stimulus. genome-wide SNP datasets provide valuable information germplasm resources assessment genome-assisted shrimps, also shed light on effects breeding.