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

doi:10.3390/biology9090277

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

Biology (Basel). 2020 Sep 7;9(9):277. doi: 10.3390/biology9090277.

Authors

Li Lian Wong¹, Zulaikha Mat Deris¹, Yoji Igarashi², Songqian Huang³, Shuichi Asakawa³, Qasim Ayub⁴, Shu Yong Lim⁴, Mhd Ikhwanuddin⁵, Shumpei Iehata⁶, Kazutoshi Okamoto⁷, Mariom⁸, Md Asaduzzaman^{3

9}

Affiliations

¹ Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Kuala-Terengganu 21030, Terengganu, Malaysia.
² Graduate School of Bioresources, Mie University, Kurimamachiya 1577, Tsu, Mie 514-8507, Japan.
³ Department of Aquatic Bioscience, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
⁴ School of Science, Monash University Malaysia Genomics Facility, Bandar Sunway 47500, Selangor, Malaysia.
⁵ Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala-Terengganu 21030, Terengganu, Malaysia.
⁶ Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, Kuala-Terengganu 21030, Terengganu, Malaysia.
⁷ Shizuoka Prefectural Research Institute of Fishery and Ocean, Yaizu-shi, Shizuoka 425-0032, Japan.
⁸ Department of Fisheries Biology and Genetics, Faculty of Fisheries, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh.
⁹ Department of Marine Bioresource Science, Faculty of Fisheries, Chattogram Veterinary and Animal Sciences University, Khulshi 4225, Chattogram, Bangladesh.

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 F_ST 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.

Keywords: Penaeus monodon; domesticated population; genetic improvement; low coverage sequencing; outlier approach; population structure.

Abstract

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