Nine novel, polymorphic microsatellite loci were developed for the scleractinian coral Acropora millepora (Acroporidae) from the Great Barrier Reef. The specificity and polymorphism of 5 microsatellite loci previously developed for a Caribbean congener, and one locus developed for an Indo-Pacific congener were also assessed - only one of those 6 loci produced reliable results: yielding a total of 10 polymorphic microsatellite loci for Acropora millepora.
To construct a microsatellite library, genomic DNA was isolated from sperm (which lacks algal symbionts) of an Acropora millepora colony collected in December 1998 at Magnetic Island, an inshore island in the central Great Barrier Reef. The partial genomic library was constructed using hybridization capture for enrichment of microsatellites using the following probes: dimers (AC) 13 and (AG) 12, trimers (AAC) 6 and (ATC) 8, and tetramers (AATG) 6 and (ACAG) 6. Of 397 clones sequenced, 110 contained microsatellite repeats (excluding a small percentage of repeated clones) after only one round of enrichment. Polymerase chain reaction (PCR) primers were designed from 31 of those clone sequences.
53 Acropora millepora individuals (colonies) were tested, 10 from each of 3 locations (Magnetic Island, Davies Reef and the Keppel Islands), and 23 from Great Palm Island. 31 loci were tested: 20 were abandoned due to the lack or non-specificity of the amplification, one was abandoned because only 2 alleles were observed among the 53 individuals; 3 of 5 Mendelian loci developed for the Caribbean Acropora palmata were initially found to amplify reasonably well and highly polymorphic in Acropora millepora, but nonspecific products were visible when analysed on a capillary sequencer for 2 of the 3 loci making an objective interpretation of allelic patterns impossible. The microsatellite marker developed for Acropora formosa yielded specific and polymorphic products in Acropora millepora, but was discarded as a relatively large fraction of non-amplifying individuals suggested a high frequency of null alleles for this locus.
Nine novel and polymorphic microsatellite loci for Acropora millepora were presented. An additional microsatellite locus previously developed for the Caribbean congener Acropora palmata produced specific and polymorphic products. There was no evidence of linkage disequilibrium among these 10 loci as tested in the online software package genepop; of the 45 pairwise comparisons, one pair of loci showed significant linkage, but this statistical significance was lost after sequential Bonferroni correction.
GenBank Accession numbers for the 9 novel loci: EF014480, EF014481, EF014482, EF014483, EF014484, EF014485, EF014486, EF014487, EF014488.
