Microsatellite assessment of the genetic diversity in indigenous populations of curimba (Prochilodus argenteus) in the São Francisco river (Brazil)

Coimbra, Maria Raquel Moura; Lima, Ana Paula de; Oliveira, Karine Kelly Cavalcanti; Severi, William

doi:10.1007/s10592-017-0947-5

Cited by 12 publications

(9 citation statements)

References 30 publications

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“…Here we tested eight loci per individual. Nevertheless, our pipeline has the potential to provide analysis of a significantly larger number of loci and recent publications with neotropical migratory fish revealed a minimum of seven and a maximum of 13 loci for up to 30 individuals ( Rueda et al, 2011 ; Berdugo and Narvaez Barandica, 2014 ; Coimbra et al, 2017 ).…”

Section: Discussionmentioning

confidence: 99%

High-Throughput Sequencing Strategy for Microsatellite Genotyping Using Neotropical Fish as a Model

et al. 2018

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Genetic diversity and population studies are essential for conservation and wildlife management programs. However, monitoring requires the analysis of multiple loci from many samples. These processes can be laborious and expensive. The choice of microsatellites and PCR calibration for genotyping are particularly daunting. Here we optimized a low-cost genotyping method using multiple microsatellite loci for simultaneous genotyping of up to 384 samples using next-generation sequencing (NGS). We designed primers with adapters to the combinatorial barcoding amplicon library and sequenced samples by MiSeq. Next, we adapted a bioinformatics pipeline for genotyping microsatellites based on read-length and sequence content. Using primer pairs for eight microsatellite loci from the fish Prochilodus costatus, we amplified, sequenced, and analyzed the DNA of 96, 288, or 384 individuals for allele detection. The most cost-effective methodology was a pseudo-multiplex reaction using a low-throughput kit of 1 M reads (Nano) for 384 DNA samples. We observed an average of 325 reads per individual per locus when genotyping eight loci. Assuming a minimum requirement of 10 reads per loci, two to four times more loci could be tested in each run, depending on the quality of the PCR reaction of each locus. In conclusion, we present a novel method for microsatellite genotyping using Illumina combinatorial barcoding that dispenses exhaustive PCR calibrations, since non-specific amplicons can be eliminated by bioinformatics analyses. This methodology rapidly provides genotyping data and is therefore a promising development for large-scale conservation-genetics studies.

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Section: Discussionmentioning

confidence: 99%

High-Throughput Sequencing Strategy for Microsatellite Genotyping Using Neotropical Fish as a Model

et al. 2018

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Section: Biological Resources Of Water 264mentioning

confidence: 99%

“…However, lack of knowledge about the genetics of local species can have the opposite effect. Analyses of restocking programmes for P. argenteus indicate differences between stock populations and wild populations, and this differentiation represents a risk and interrupts the diversity of local genes [190].In addition to hydroelectric dams and inappropriate programmes for genetic restocking, the inadequate management of cultivated populations may also interfere with the genetic variability of species. Fish escaping from aquaculture facilities may influence the level of genetic diversity in natural populations living in the vicinity of fish farms.…”

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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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“…O coeficiente de dispersão que apresentava uma maior estabilidade (0,07) antes da construção da barragem e teve um grande aumento (0,49) após a construção, perdendo precisão. Essa alteração interrompe a desova de peixe com ovos pelágicos, porque a atividade de desova de muitos peixes é desencadeada pela elevação da água e pelo aumento da temperatura na primavera [33][34][35]. Além disso, o uso de reservatórios modifica o acesso dos peixes as zonas de desova [36] mesmo quando há escada de peixes pois o fluxo de peixes jovens ou adultos é mínima [37].…”

Section: Figura 4 Medianas Mensais Da Vazão Nos Períodos Pré-impactounclassified

Avaliação das alterações hidrológicas da bacia do rio São Francisco causadas pela construção da usina hidrelétrica de Sobradinho

et al. 2017

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Um ecossistema equilibrado é a base da vida e desenvolvimento de milhares de espécies de seres vivos. Os rios fazem um papel muito importante nesse equilíbrio. Um dos mais importantes rios do Brasil é o Rio São Francisco que contém, ao longo do seu percurso, cinco usinas hidrelétricas. As hidrelétricas são uma das fontes de energia mais baratas entre as disponíveis, por isso é a mais usada, porém a construção de hidrelétricas causa vários impactos ao meio ambiente. Para avaliar este impacto, fornecendo base para uma avaliação mais criteriosa na escolha do método de obtenção de energia e um melhor planejamento nas futuras construções de hidrelétricas, foi usado o método de Indicadores de Alteração Hidrológica (IAH) para estudar a variabilidade das características hidrológicas da vazão observada diariamente abaixo da represa de Sobradinho. Foram retirados da análise anos com chuva muito abaixo ou muito acima do normal. A partir desses dados, o método IAH gera 33 indicadores hidrológicos de relevância ecológica. Todos os indicadores de alteração hidrológica foram avaliados e os resultados mostraram que, quando comparamos o período anterior à construção da barragem com o período posterior, houve alteração hidrológica em todos os indicadores hidrológicos fornecidos pelo método de IAH.

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Microsatellite assessment of the genetic diversity in indigenous populations of curimba (Prochilodus argenteus) in the São Francisco river (Brazil)

Cited by 12 publications

References 30 publications

High-Throughput Sequencing Strategy for Microsatellite Genotyping Using Neotropical Fish as a Model

High-Throughput Sequencing Strategy for Microsatellite Genotyping Using Neotropical Fish as a Model

Genetic Applications in the Conservation of Neotropical Freshwater Fish

Avaliação das alterações hidrológicas da bacia do rio São Francisco causadas pela construção da usina hidrelétrica de Sobradinho

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