Development of a genetic method to assess bleaching tolerance in corals (MTSRF Project 2.5i.2c)

Next generation DNA sequencing was used to scan a large proportion of the transcribed coding DNA in Acropora millepora for polymorphisms. Transcribed coding DNA (messenger RNA - mRNA) was extracted from 8 colonies sampled at three thermally distinct habitats along the GBR (Wilke Island Reef in Princess Charlotte Bay, Nelly Bay at Magnetic Island, and Miall Island in the Keppel Islands). The mRNA extractions from each population were pooled and translated back to the complementary DNA (cDNA), which was sequenced using 454 pyrosequencing by the Australian Genome Research Facility. This transcriptome consists of over 500 000 DNA sequences that are assembled into 55 000 contigs, of which over 11 000 aligned to known genes (8 000 unique genes). A database was generated consisting of almost 90 000 SNPs (Single Nucleotide Polymorphisms/gene variants).

26 SNPs from 16 genes were investigated, from which one SNP from each of 15 genes were deemed suitable for large scale genotyping and a genotyping assay was developed.

20 individuals from 17 reefs throughout the Great Barrier Reef were genotyped. Four from the 15 show a geographic pattern.

The relative frequency of each of the nucleotides was measured in each SNP (A, T, C, G).