Skim-Sequencing Based Genotyping Reveals Genetic Divergence of the Wild and Domesticated Population of Black Tiger Shrimp (Penaeus monodon) in the Indo-Pacific Region

Abstract

The domestication of a wild-caught aquatic animal is an evolutionary process, which results in genetic discrimination at the genomic level in response to strong artificial selection. Although black tiger shrimp (Penaeus monodon) is one of the most commercially important aquaculture species, a systematic assessment of genetic divergence and structure of wild-caught and domesticated broodstock populations of the species is yet to be documented. Therefore, we used skim sequencing (SkimSeq) based genotyping approach to investigate the genetic structure of 50 broodstock individuals of P. monodon species, collected from five sampling sites (n = 10 in each site) across their distribution in Indo-Pacific regions. The wild-caught P. monodon broodstock population were collected from Malaysia (MS) and Japan (MJ), while domesticated broodstock populations were collected from Madagascar (MMD), Hawaii, HI, USA (MMO), and Thailand (MT). After various filtering process, a total of 194,259 single nucleotide polymorphism (SNP) loci were identified, in which 4983 SNP loci were identified as putatively adaptive by the pcadapt approach. In both datasets, pairwise FST estimates high genetic divergence between wild and domesticated broodstock populations. Consistently, different spatial clustering analyses in both datasets categorized divergent genetic structure into two clusters: (1) wild-caught populations (MS and MJ), and (2) domesticated populations (MMD, MMO and MT). Among 4983 putatively adaptive SNP loci, only 50 loci were observed to be in the coding region. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that non-synonymous mutated genes might be associated with the energy production, metabolic functions, respiration regulation and developmental rates, which likely act to promote adaptation to the strong artificial selection during the domestication process. This study has demonstrated the applicability of SkimSeq in a highly duplicated genome of P. monodon specifically, across a range of genetic backgrounds and geographical distributions, and would be useful for future genetic improvement program of this species in aquaculture.

Genomic signatures of artificial selection in the Pacific oyster, Crassostrea gigas

“…So far, it has been extensively applied in a large number of plants and animals, such as maize ( Zea mays ssp. mays L.) (Wang et al, 2020 ), rice ( Oryza sativa L.) (Yano et al, 2016 ), chicken ( Gallus gallus ) (Rubin et al, 2010 ), sheep ( Ovis aries ) (Li et al, 2020 ), Atlantic salmon ( Salmo salar ) (Bertolotti et al, 2020 ), large yellow croaker ( Larimichthys crocea ) (Kon et al, 2021 ), and black tiger shrimp ( Penaeus monodon ) (Wong et al, 2020 ). In the present study, in order to profile genome signatures of selection in Pacific oyster, we performed whole‐genome resequencing of 20 oysters from two fast‐growing strains and 20 oysters from their corresponding wild populations.…”

“…So far, it has been extensively applied in a large number of plants and animals, such as maize (Zea mays ssp. mays L.) (Wang et al, 2020), rice (Oryza sativa L.) (Yano et al, 2016), chicken (Gallus gallus) (Rubin et al, 2010), sheep (Ovis aries) (Li et al, 2020), Atlantic salmon (Salmo salar) (Bertolotti et al, 2020), large yellow croaker (Larimichthys crocea) (Kon et al, 2021), and black tiger shrimp (Penaeus monodon) (Wong et al, 2020).…”

Improved reproductive performance of captive male broodstock of tiger shrimp Penaeus monodon with 17α-methyltestosterone induction

“…Until now, the provision of tiger shrimp broodstock for breeding still relies on mature wild broodstock. However, the availability of wild male broodstock has begun to be limited, depending on the season, and quality decreases (Wong et al, 2020).…”

Genomic signatures of artificial selection in fecundity of Pacific white shrimp, Penaeus vannamei

“…Whole-genome resequencing has become a practical approach for the analysis of genome-wide variations and genomic signatures of domestication or artificial selection ( Stratton, 2008 ; Rubin et al, 2010 ; Xia et al, 2015 ; Zhang et al, 2018 ). The method has been applied to many aquatic animals, such as Atlantic salmon ( Bertolotti et al, 2020 ), Nile tilapia ( Cadiz et al, 2019 ), channel catfish ( Nam et al, 2020 ), large yellow croaker ( Kon et al, 2021 ), and black tiger shrimp ( Wong et al, 2020 ). Such analyses are usually costly because a large number of individuals need to be genotyped individually.…”