Fishing for divergence in a sea of connectivity: the utility of ddRADseq genotyping in a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera

Lal, Monal M., Southgate, Paul C., Jerry, Dean R., and Zenger, Kyall R. (2016) Fishing for divergence in a sea of connectivity: the utility of ddRADseq genotyping in a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera. Marine Genomics, 25. pp. 57-68.

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Abstract

Population genomic investigations on highly dispersive marine organisms typically require thousands of genome-wide SNP loci to resolve fine-scale population structure and detect signatures of selection. This information is important for species conservation efforts and stock management in both wild and captive populations, as well as genome mapping and genome wide association studies. Double digest Restriction site-Associated DNA Sequencing (ddRADseq) is a recent tool for delivering genome wide SNPs for non-model organisms. However, its application to marine invertebrate taxa has been limited, particularly given the complex and highly repetitive nature of many of these organisms' genomes. This study develops and evaluates an optimised ddRADseq technique together with associated analyses for generating genome-wide SNP data, and performs population genomic analyses to inform aquaculture and fishery management of a marine bivalve, the black-lip pearl oyster Pinctada margaritifera. A total of 5243 high-quality genome-wide SNP markers were detected, and used to assess population structure, genome diversity, detect Fₛₜ outliers and perform association testing in 156 individuals belonging to three wild and one hatchery produced populations from the Fiji Islands. Shallow but significant population structure was revealed among all wild populations (average pairwise Fₛₜ = 0.046) when visualised with DAPC and an individual network analysis (NetView P), with clear evidence of a genetic bottleneck in the hatchery population (Nₑ(LD) = 6.1), compared to wild populations (Nₑ(LD) > 192.5). Fₛₜ outlier detection revealed 42–62 highly differentiated SNPs (p < 0.02), while case–control association discovered up to 152 SNPs (p < 0.001). Both analyses were able to successfully differentiate individuals between the orange and black tissue colour morphotypes characteristic of this species. BLAST searches revealed that five of these SNPs were associated with a melanin biosynthesis pathway, demonstrating their biological relevance. This study has produced highly informative SNP and population genomic data in P. margaritifera, and using the same approach promises to be of substantial value to a range of other non-model, broadcast-spawning or marine invertebrate taxa.

Item ID: 43167
Item Type: Article (Research - C1)
ISSN: 1876-7478
Keywords: population genomics; aquaculture; SNP; fine-scale differentiation; colour morphotype; Fiji Islands
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A version of this publication was included as Chapter 1 of the following PhD thesis: Lal, Monal M. (2016) Genetic structure, population connectivity and taxonomic identity of the black-lip pearl oyster Pinctada margaritifera (Bivalvia: Pteriidae), across its Indo-Pacific distribution. PhD thesis, James Cook University, which is available Open Access in ResearchOnline@JCU. Please see the Related URLs for access.

Funders: Australian Centre for International Agricultural Research (ACIAR), John Allwright Fellowship (JAF)
Projects and Grants: ACIAR FIS/2009/057
Date Deposited: 10 Mar 2016 01:27
FoR Codes: 07 AGRICULTURAL AND VETERINARY SCIENCES > 0704 Fisheries Sciences > 070405 Fish Physiology and Genetics @ 50%
07 AGRICULTURAL AND VETERINARY SCIENCES > 0704 Fisheries Sciences > 070401 Aquaculture @ 50%
SEO Codes: 83 ANIMAL PRODUCTION AND ANIMAL PRIMARY PRODUCTS > 8301 Fisheries - Aquaculture > 830104 Aquaculture Oysters @ 100%
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