Mitochondrial and nuclear genetic analyses of the tropical black-lip rock oyster (Saccostrea echinata) reveals population subdivision and informs sustainable aquaculture development

BMC Genomics

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[1] 0000 0001 1555 3415, grid.1034.6, Australian Centre for Pacific Islands Research and School of Science and Engineering, University of the Sunshine Coast, 4556, Maroochydore, Queensland, Australia;0000 0004 0394 3004, grid.483876.6, Aquaculture Unit, Department of Primary Industry and Resources, Northern Territory Government, GPO Box 3000, 0801, Darwin, NT, Australia;0000 0001 1555 3415, grid.1034.6, School of Science and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, 4556, Sippy Downs, Queensland, Australia;0000 0001 1555 3415, grid.1034.6, Australian Centre for Pacific Islands Research and School of Science and Engineering, University of the Sunshine Coast, 4556, Maroochydore, Queensland, Australia;0000 0004 0474 1797, grid.1011.1, Centre for Sustainable Tropical Fisheries and Aquaculture, and College of Science and Engineering, James Cook University, 4811, Townsville, Queensland, Australia;

关键词: Population genetics;    Aquaculture;    Black-lip rock oyster;    Genetic management;    Saccostrea;   

DOI  :  10.1186/s12864-019-6052-z

来源: publisher

【 摘 要 】

BackgroundThe black-lip rock oyster (Saccostrea echinata) has considerable potential for aquaculture throughout the tropics. Previous attempts to farm S. echinata failed due to an insufficient supply of wild spat; however, the prospect of hatchery-based aquaculture has stimulated renewed interest, and small-scale farming is underway across northern Australia and in New Caledonia. The absence of knowledge surrounding the population genetic structure of this species has raised concerns about the genetic impacts of this emerging aquaculture industry. This study is the first to examine population genetics of S. echinata and employs both mitochondrial cytochrome c oxidase subunit I gene (COI) and single nucleotide polymorphism (SNP) markers.ResultsThe mitochondrial COI data set included 273 sequences of 594 base pair length, which comprised 74 haplotypes. The SNP data set included 27,887 filtered SNPs for 272 oysters and of these 31 SNPs were identified as candidate adaptive loci. Data from the mitochondrial COI analyses, supports a broad tropical Indo-Pacific distribution of S. echinata, and showed high haplotype and nucleotide diversities (0.887–1.000 and 0.005–0.008, respectively). Mitochondrial COI analyses also revealed a ‘star-like’ haplotype network, and significant and negative neutrality tests (Tajima’s D = − 2.030, Fu’s Fs = − 25.638, P < 0.001) support a recent population expansion after a bottleneck. The SNP analyses showed significant levels of population subdivision and four genetic clusters were identified: (1) the Noumea (New Caledonia) sample location; (2) the Bowen (north Queensland, Australia) sample location, and remaining sample locations in the Northern Territory, Australia (n = 8) were differentiated into two genetic clusters. These occurred at either side of the Wessel Islands and were termed (3) ‘west’ and (4) ‘east’ clusters, and two migrant individuals were detected between them. The SNP data showed a significant positive correlation between genetic and geographic distance (Mantel test, P < 0.001, R2 = 0.798) and supported isolation by distance. Three candidate adaptive SNPs were identified as occurring within known genes and gene ontology was well described for the sex peptide receptor gene.ConclusionsData supports the existence of genetically distinct populations of S. echinata, suggesting that management of wild and farmed stocks should be based upon multiple management units. This research has made information on population genetic structure and connectivity available for a new aquaculture species.

【 授权许可】

CC BY