Development of twelve novel polymorphic microsatellite DNA markers for the Boeseman’s rainbowfish (Melanotaenia boesemani) and tests for their cross-utility in 21 rainbowfish species from West Papua (Indonesia)

Abstract

We developed 12 microsatellite markers for the endangered Boeseman's rainbowfish (Melanotaenia boesemani). Twenty-eight individuals from the type locality at Ayamaru Lake were examined, and all loci were polymorphic with a number of alleles per locus varying from 3 to 18. Average observed and expected heterozygosities were 0.681 and 0.678, respectively. Cross-species amplification was successfully obtained for 21 Melanotaenia species, with a number of alleles per locus ranging between 1 and 20. Average observed and expected heterozygosities varied between 0.105 and 0.708 and 0.118-0.755, respectively. Only 21 inbreeding coefficient (Fis) values presented a significant homozygote excess among the 264 locus-by-locus calculated values. Tests for genotyping errors revealed that four of these 21 significant Fis values could be explained by the presence of null alleles. These new microsatellite markers appear highly reliable for further conservation purposes or population genetic studies of the many rainbowfish endangered species.

Genetic Diversity of Boeseman's Rainbowfish (Melanotaenia Boesemani) Reared in Indonesian Farms Compared to Endangered Natural Populations

“…Individual samples were genotyped with 12 nuclear microsatellite markers that were recently developed [9]. DNA was extracted from a small fragment (10 mg) of anal fin clip with the NucleoSpin® 96 Tissue kit (Macherey-Nagel), according to the manufacturer's instructions, using a Janus automated Workstation (Perkin Elmer).…”

“…Cycling conditions were as follows: initial denaturation at 95°C for 4 min, followed by 30 cycles of 95°C for 20 s, 56°C for 20 s, and 72 °C for 30 s, and a final elongation step of 7 min at 72°C. Amplicon size was analyzed by capillary electrophoresis as previously described [9], in the technical facilities of the labex "Centre Méditerranéen de l'Environnement et de la Biodiversité" (Montpellier). Allele sizing and genotyping were achieved with the Peak Scanner v1.0 and GeneMapper® v5.0 software (Applied Biosystems).…”

“…Twelve nuclear DNA microsatellite markers were recently developed in this species [9] for conservation purposes. We used these microsatellite markers to assess the genetic variability of six different strains of Boeseman's Rainbowfish reared in six Javanese farms.…”

Rapid development of novel microsatellite markers from Mauremys reevesii (Testudines: Geoemydidae) using next-generation DNA sequencing technology

“…The eight microsatellite core motifs were AC/GT, these microsatellites consisted of five dinucleotides and three compound motifs were unitary. In order to isolate more types of microsatellite for analyzing the genetic diversity, we reported the development of novel microsatellite primers (including di-to pentanucleotide motifs) for M. reevesii using RADseq technology (Castoe et al 2012;Brandt et al 2014;Nugraha et al 2014).…”

Genetic diversity in Radix species from the middle and south of Iraq based on simple sequence repeats

“…Although no cross-transferability between families/within order of freshwater snail has been reported, successful transferability of SSR marker has been demonstrated in many studies (Iyengar et al, 2000;Gaur et al, 2003;Dawson et al, 2004). In addition, SSRs have also been widely used in population genetics and phylogenetic studies in insects (Daly-Engel et al, 2012), birds (Parine et al, 2013), fish (Nugraha et al, 2014) and snails (Stoeckle et al, 2014). This study therefore aimed to develop species specific SSR markers for genetic diversity study of rom Radix sp.…”