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

Li Lian Wong,Mariom Mariom,Mhd Ikhwanuddin,Shumpei Iehata,Shuichi Asakawa,Qasim Ayub,Yoji Igarashi,Songqian Huang,Kazutoshi Okamoto,Md Asaduzzaman,Shu Yong Lim,Zulaikha Mat Deris

doi:10.3390/biology9090277

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.

Highlights

The world production of inland aquaculture reached 51.3 million tonnes in 2018, with their dominant production of 97.2% comprising of finfish, while mariculture produced 30.8 million tonnes, with 56.2% represented by mollusc [1]
We suggested that similar founder populations, artificial selection regimes of desired commercial traits and local adaptive process to similar aquaculture practices have dramatically reduced the genetic heterogeneity of the domesticated stocks
We denote that the patterns of genetic homogeneity in wild populations maybe strongly influenced by hydrographic conditions and ecological niches which are expected to increase the adaptive processes of the populations towards their natural habitats

Summary

Introduction

The world production of inland aquaculture reached 51.3 million tonnes in 2018, with their dominant production of 97.2% comprising of finfish, while mariculture produced 30.8 million tonnes, with 56.2% represented by mollusc [1]. While disease outbreak and price fluctuations in the global trade have highly impacted the production and socio-economic development in many countries, the surging prices and shortage of good quality shrimp broodstocks have further impeded the shrimp industry [1,3]. Population structure is the organization of genetic diversity, and it is influenced by multiple evolutionary process, such as genetic drift, mutation, gene flow, natural selection and demographic history [8,9]. It is estimated by parameters like genetic differentiation, variant alleles frequencies, population size and population dynamic [10,11,12,13]. Low number of breeders and inadvertent or mass selection of prospective shrimp broodstocks can result in rapid reduction of genetic diversity [14,15,16,17,18,19]

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