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

Abstract

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

Genome-wide detection of positive and balancing selection signatures shared by four domesticated rainbow trout populations (Oncorhynchus mykiss)

“…This gene is detected under positive selection in a Scottish farmed population of Atlantic salmon (López et al, 2018). In addition, the gene scap (sterol regulatory element-binding protein cleavage-activating protein) was already identified under positive selection in six farmed Pacific white Shrimp populations (Wang et al, 2022).…”

Recent advances in crustacean genomics and their potential application in aquaculture

“…However, the role of these genes in agronomic traits still needs explored. 13,146 As mentioned previously, the sex of an organism is an important economic trait because females and males generally exhibit different growth rates, particularly in shrimp, crayfish and crabs. 147,148 For example, Gammarus duebeni males tend to reach larger sizes than females.…”

“…13,115,[141][142][143][144][145] Genome resequencing and selection signature analysis has also confirmed that genes related to growth and disease resistance are indeed selected during the artificial breeding process. 13,146 After resequencing the genomes of wild and selectively bred broodstocks, a previous study elucidated that the nucleotide diversity of the genes encoding anti-lipopolysaccharide factor-like protein (ALF), A-kinase anchor protein 13 (AKAP13), and lactosylceramide 4-alpha-galactosyltransferase (A4GALT) were significantly lower in the selectively bred broodstocks. These findings demonstrated that these genes were selected during the artificial selection process and may be associated with growth and disease-resistance traits.…”

“…Based on the genome reference, genome‐wide association studies (GWAS) have been conducted to identify genes associated with various economically relevant traits, including sex, growth, disease resistance and environmental adaptation, in shrimp 13,115,141–145 . Genome resequencing and selection signature analysis has also confirmed that genes related to growth and disease resistance are indeed selected during the artificial breeding process 13,146 . After resequencing the genomes of wild and selectively bred broodstocks, a previous study elucidated that the nucleotide diversity of the genes encoding anti‐lipopolysaccharide factor‐like protein (ALF), A‐kinase anchor protein 13 (AKAP13), and lactosylceramide 4‐alpha‐galactosyltransferase (A4GALT) were significantly lower in the selectively bred broodstocks.…”

Whiteleg shrimp Litopenaeus vennamei: Current status, future prospects and opportunities for Bangladesh Aquaculture

“…This great success of L. vannamei aquaculture is consequently due to favourable culture attributes and sustainable modern aquaculture technologies. These are included disease resistance and genetically improve specific pathogen free (SPF) brood stock, higher adaptability to culture conditions and eating various pelleted and live feeds and even small particles, as well as intensive and super-intensive modern culture systems like earthen/concrete ponds culture, recirculating aquaculture system, raceways and microbial/biofloc based systems (Wang et al, 2022).…”