Genetic diversity in coral aquaculture

Full description

Background [Extract from Related publication]

Amidst global reef declines, large-scale coral aquaculture is being developed to support reef intervention. Because genetic diversity underpins population resilience, it is critical that aquaculture methods maintain diversity. Yet, it remains unclear how genetic diversity of coral progeny is shaped by 1) parental genetic composition, 2) winnowing during aquaculture grow-out, and 3) field deployment. We utilised single nucleotide polymorphisms to examine genetic diversity dynamics in two coral progeny cohorts produced from 5 and 14 parents, with standardised gamete input per parent. Cohorts were sampled over one month of aquarium rearing, and for the 14-parent cohort, again after two years of field deployment.

Data Methods [Compiled from Related publication]

Tissue samples (sperm, embryos, larvae, and 2-year-old juveniles) were fixed in absolute ethanol and stored at −20 °C prior to DNA extraction. Genomic DNA extraction and SNP genotyping were performed by Diversity Arrays Technology Pty Ltd (DArT; Canberra, Australia) using DArTseq™, a reduced-representation sequencing method combining restriction enzyme-based genome complexity reduction with Illumina HiSeq 2500 next-generation sequencing.

After quality assurance and quality control (QAQC), sequencing data were returned pre-processed through a proprietary DArT pipeline as scored single nucleotide polymorphisms (SNPs), where 0 = homozygous reference allele, 1 = homozygous alternate allele, and 2 = heterozygous. The initial dataset comprised 34,282 SNP loci prior to filtering.

SNP filtering and downstream analyses were conducted in R. Filtering included locus reproducibility and call-rate thresholds, minor allele frequency filtering, removal of monomorphic loci, and exclusion of low-quality individuals based on call rate. The R code used to manipulate and analyse the data is maintained as a live document available in GitHub.

Full experimental methods describing coral spawning, culture maintenance, and field deployment are provided in the Related publication.

Software/equipment used to create/collect the data: Diversity Arrays Technology (DArT) DArTseq™ platform; Illumina HiSeq 2500 sequencing system.

Software/equipment used to manipulate/analyse the data: R statistical software; custom R scripts (available via GitHub).