Development and characterization of 14 microsatellite loci in the Neotropical fish <i>Geophagus brasiliensis</i> (Perciformes, Cichlidae)

Ferreira, Dhiego G.; Galindo, Bruno A.; Alves, A. N.; Almeida, Fernanda Simões de; Ruas, Claudete de Fátima; Sofia, Silvia Helena

doi:10.1111/jfb.12227

Cited by 12 publications

(12 citation statements)

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“…Cross-amplification tests were conducted from seven loci described for Geophagus brasiliensis (Gbra6, Gbra16, Gbra17, Gbra62, Gbra63, Gbra80, and Gbra96) ( Ferreira et al, 2013 ). Reagent concentrations and PCR conditions were performed according to Ferreira et al (2015) , using the modifications proposed by Schuelke (2000) .…”

Section: Methodsmentioning

confidence: 99%

Genetic Diversity of the Endangered Neotropical Cichlid Fish (Gymnogeophagus setequedas) in Brazil

et al. 2018

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Gymnogeophagus setequedas is a rare and rheophilic species of tribe Geophagini, considered endangered in Brazilian red lists. Its previously known geographical distribution range was the Paraná River basin, in Paraguay, and a tributary of the Itaipu Reservoir in Brazil. Since its description no specimens have been collected in the original known distribution area. However, recent records of G. setequedas in the lower Iguaçu River, in a region considered highly endemic for the ichthyofauna, extended the known geographical distribution and may represent one of the last remnants of the species. The aim of this study was to estimate the genetic diversity and population structure of G. setequedas, using microsatellite markers and mitochondrial haplotypes, in order to test the hypothesis of low genetic diversity in this restricted population. Muscular tissue samples of 86 specimens were obtained from nine locations in the Lower Iguaçu River basin, between upstream of the Iguaçu Falls and downstream of the Salto Caxias Reservoir. Seven microsatellites loci were examined and a total of 120 different alleles were obtained. The number of alleles per locus (NA) was 17.429, effective alleles (NE) 6.644, expected heterozygosity (HE) 0.675, observed (HO) heterozygosity 0.592, and inbreeding coefficient (FIS) 0.128. Twelve haplotypes in the D-Loop region were revealed, with values of h (0.7642) and π (0.00729), suggesting a large and stable population with a long evolutionary history. Thus, both molecular markers revealed high levels of genetic diversity and indicated the occurrence of a single G. setequedas population distributed along a stretch of approximately 200 km. The pattern of mismatch distribution was multimodal, which is usually ascribed to populations in demographic equilibrium. Nevertheless, the construction of a new hydroelectric power plant, already underway between the Salto Caxias Reservoir and Iguaçu Falls, could fragment this population, causing loss of genetic diversity and population decline, and for this reason it is necessary to maintain the Iguaçu River tributaries and downstream area from the Lower Iguaçu Reservoir free of additional dams, to guarantee the survival of this species.

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Section: Methodsmentioning

confidence: 99%

Genetic Diversity of the Endangered Neotropical Cichlid Fish (Gymnogeophagus setequedas) in Brazil

et al. 2018

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“…A total of 100 SSR primers were designed for PCR amplification and the results showed that 28 primer pairs could successfully amplify the polymorphic fragments. The polymorphic percentage was 28%, which was lower than Ichthyoelephas longirostris (60%) (Landinez-Garcia RM, 2016) Lateolabrax japonicus (42%) (Li BB, 2016) and Geophagus brasiliensishigh (36%) (Ferreira DG, 2013), but higher than Clarias batrachus (17%) [18], hybrid giant tiger grouper (20%) (Huang YS, 2015) and Girella elevate (22%) (McWilliam RA, 2016).…”

Section: Development Of Polymorphic Microsatellite Markersmentioning

confidence: 99%

Research Article Development and characterization of twenty-eight polymorphic microsatellite for rice field eel (Monopterus albus) using RAD tag sequencing

Zhang¹,

Wang²,

Xu³

et al. 2018

Genet. Mol. Res.

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Monopterus albus is a special economic aquatic animal in China. Most of cultured M. albus are wild species captured from different areas, and this makes the wild resources of M. albus are under great threat. Microsatellite markers can help us understand the genetic resources of M. albus in different areas. In this study, using RAD-seq (restriction site associated DNA sequencing) protocol, a total of 9,897 microsatellites were identified in the genome with average frequency of 195 microsatellites per megabase of genomic sequences. Among these SSRs, the dinucleotide repeat motif was the most abundant type representing 61.77% of the total microsatellite loci, followed by pentanucleotides (13.91%), trinucleotides (12.08%), tetranucleotides (9.30%) and hexanucleotides (2.94%). A total of 100 SSR primers were designed for PCR amplification. The polymorphism analysis showed that 28 primer pairs could successfully amplify the polymorphic fragments and the number of alleles per polymorphic locus ranged from 2 to 13, with an average of 5.70 alleles/locus. The values of observed and expected heterozygosity are ranged from 0.0333 to 0.8000 and 0.0333 to 0.8887, respectively. This microsatellite locus will be useful to understand the structure, genetic diversity, and genetic difference of this species.

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“…In previous studies, microsatellites loci in closely related species have been identified. These include species belonging to the Anostomidae [163], Characidae [164,165], Cichlidae [166], Pimelodidae [167], Prochilodontidae [168][169][170] and Serrasalmidae [171] families.…”

Section: Next Generation Sequencing (Ngs) In Molecular Marker Discoverymentioning

confidence: 99%

Genetic Applications in the Conservation of Neotropical Freshwater Fish

Mastrochirico-Filho¹,

Freitas²,

Ariede³

et al. 2018

Biological Resources of Water

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Neotropical fish correspond to approximately 30% of all fish species worldwide. The diversity of fish species found in Neotropical basins reflects variations in life-history strategies and exhibition of particular morphological, physiological and ecological attributes. These attributes are mainly related to different forms of feeding, life maintenance and reproduction. Today, fish populations are being threatened by anthropogenic actions that are having a visible impact on the natural state of continental aquatic ecosystems. The main causes are overfishing, non-native species introduction, reservoir-dam systems, mining, pollution and deforestation. The biology and population dynamics of the species are still unclear due to lack of research. Genetic tools can be useful resources for the conservation of Neotropical fish species in several ways. Molecular genetic markers are considered powerful tools to identify cryptic and hybrid fish and also allow the evaluation of the genetic variability and structure of populations of Neotropical ichthyofauna. Several analyses of molecular markers have been performed on Neotropical fish, including allozyme analysis, restriction fragment length polymorphisms in regions of DNA (RFLP), randomly amplified polymorphic DNA (AFLP), randomly amplified polymorphic DNA (RAPD), microsatellites, single nucleotide polymorphisms (SNPs) and mitochondrial DNA (mtDNA) markers. In order to analyse a high number of markers, next generation sequencing has allowed researchers to generate a large amount of genomic information that can be applied to the conservation of Neotropical fish.Keywords: molecular markers, genetic conservation, Neotropical ichthyofauna, overfishing, dam © 2018 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Rivers of the Neotropical regionThe distribution of freshwater fish around the world was mediated by historical climatic and geological events at different time points. Today, each global region has distinct patterns of distribution due to physical barriers obstructing species dispersion, representing different tolerances to environmental variables [1]. The tropics of the American continent are well known for their high biodiversity. This is due to habitat heterogeneity and a complex geological history. The Neotropical region is a biogeographic region that comprises Central America (including the southern part of Mexico and the peninsula of Baja California), the south of Florida, the Caribbean and South America. The origin and evolution of the Neotropical region arose through a process of synergism between its fauna that experienced local rainfall variations and gradual climate change resulting in a mosaic of habitats controlled by river migrations, sea-level fluctuations, local dryness and local uplifts [2,3].Regional geo...

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Development and characterization of 14 microsatellite loci in the Neotropical fish Geophagus brasiliensis (Perciformes, Cichlidae)

Cited by 12 publications

References 35 publications

Genetic Diversity of the Endangered Neotropical Cichlid Fish (Gymnogeophagus setequedas) in Brazil

Genetic Diversity of the Endangered Neotropical Cichlid Fish (Gymnogeophagus setequedas) in Brazil

Research Article Development and characterization of twenty-eight polymorphic microsatellite for rice field eel (Monopterus albus) using RAD tag sequencing

Genetic Applications in the Conservation of Neotropical Freshwater Fish

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