Applications of next-generation sequencing in fisheries research: A review

Kumar, Girish; Kocour, Martin

doi:10.1016/j.fishres.2016.07.021

Cited by 68 publications

(34 citation statements)

References 108 publications

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“…The integration of genetic information into fish stock assessments has been relatively slow, primarily because traditional genetic markers such as microsatellites typically provide limited insight toward recent population genetic change, or local adaptation in marine organisms (Waples, Punt, & Cope, 2008). The advent of high-throughput sequencing methods has significantly increased the amount of data and the resolution of genetic insight for fisheries management in other species (Hauser & Carvalho, 2008;Kumar & Kocour, 2017;Riginos, Crandall, Liggins, Bongaerts, & Treml, 2016;Valenzuela-Quiñonez, 2016). Many studies have attempted to identify neutral and adaptive genetic variation (e.g., Gagnaire et al, 2015;Nielsen, Hemmer-Hansen, Foged Larsen, & Bekkevold, 2009;Ovenden et al, 2015;Valenzuela-Quiñonez, 2016), which has improved the delineation of populations and fish stocks in both migratory species such as Greenland halibut Reinhardtius hippoglossoides (Walbaum, 1792) (Westgaard et al, 2017) and European hake Merluccius merluccius (Linnaeus, 1758) (Milano et al, 2014), and sedentary species such as bluespotted Cornetfish Fistularia commersonii Rüppell, 1838 (Bernardi, Azzurro, Golani, & Miller, 2016).…”

Section: Otolith Shape Has Been Used To Identify and Differentiate Vamentioning

confidence: 99%

Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus)

Vaux

Rasmuson

Kautzi

et al. 2019

Ecology and Evolution

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Little is known about intraspecific variation within the deacon rockfish (Sebastes diaconus), a recently described species found in the northeast Pacific Ocean. We investigated population structure among fish sampled from two nearshore reefs (Siletz Reef and Seal Rock) and one offshore site (Stonewall Bank) within a <50‐km2 area off the Oregon coast. Fish from the three sample sites exhibited small but statistically significant differences based on genetic variation at >15,000 neutral loci, whether analyzed independently or classified into nearshore and offshore groups. Male and females were readily distinguished using genetic data and 92 outlier loci were associated with sex, potentially indicating differential selection between males and females. Morphometric results indicated that there was significant secondary sexual dimorphism in otolith shape, but further sampling is required to disentangle potential confounding influence of age. This study is the first step toward understanding intraspecific variation within the deacon rockfish and the potential management implications. Since differentiation among the three sample sites was small, we consider the results to be suggestive of a single stock. However, future studies should evaluate how the stock is affected by differences in sex, age, and gene flow between the nearshore and offshore environments.

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Section: Otolith Shape Has Been Used To Identify and Differentiate Vamentioning

confidence: 99%

Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus)

Vaux

Rasmuson

Kautzi

et al. 2019

Ecology and Evolution

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“…The smaller scale methods include SSCP and heteroduplex analyses, random shotgun, direct polymerase chain reaction (PCR) product sequencing and expressed sequence tags (ESTs) (Liu and Cordes, 2004). Large scale SNP discovery enabled with high throughput sequencing platforms NGS and whole genome sequencing in fish has been reviewed more recently (Abdelrahman et al, 2017;Kumar and Kocour, 2017). SNP have been used for the identification of brood stocks, traits and strains in aquaculture.…”

Section: Introductionmentioning

confidence: 99%

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Wenne

2017

Aquat. Living Resour.

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-An increase in aquatic animal production can be achieved by extending aquaculture areas geographically, utilizing new species for culture, and using new technologies. Among new technologies useful for the increase of aquaculture production is the application of genetics and genomics. New molecular tools that benefit aquaculture have been developed. There has been a large number of experimental and review papers published concerning molecular markers and the range of their applications, including aquaculture and food product analyses. Analysis of single nucleotide polymorphisms (SNPs) has emerged as genotyping technology with wide and significant applications in aquaculture. SNPs can be used for construction of genetic linkage maps, finding quantitative trait loci (QTL) for useful traits like growth, body weight, grilsing, thermal and low oxygen tolerance, resistance to stress and diseases, mapping sex determination loci and identification of progeny in selection and chromosome manipulation experiments, assessment of genomic selectionand marker assisted selection in aquaculture. Genome-wide association studies (GWAS) facilitate the finding associations between SNPs and a trait in related or unrelated specimens. However, many traits are complex and can be controlled by number of QTL. Genotyping by genome reduction complexity sequencing emerged as an efficient and applicable technology in genomic selection. Identification of genes, sequences and nucleotides (substitutions) directly influencing phenotypic variations opens the possibility of marker-assisted selection for desirable characters in culture. SNP and QTL associations can be enhanced using genome editing technology. Examples of successful applications of SNPs in aquaculture of fish, crustacean and mollusk species, representing most geographic areas, and ecological risks assessment are reviewed.

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“…The polymorphisms are identified by size differences, resulting in varying numbers of repeat units in alleles of a single locus [108]. Mutation rates have been detected as high as 10 There have been many studies of wild fish stocks using microsatellites that allowed the analysis of historical population structures, colonisation histories and connectivity between populations [125]. These population characteristics are generally controlled by environmental effects [126][127][128] or by anthropogenic intervention [129][130][131] that can induce the structuring of fish populations with a reduction in gene flow exchange and genetic variability.…”

Section: Microsatellitesmentioning

confidence: 99%

“…This makes it possible to identify the origin of the fish consumed and avoid commercial fishing in places with threatened stocks. However, the fish traceability test alone is not sufficient to reduce the decline in fish numbers; rather, traceability techniques should be used in conjunction with sustainable fisheries, by-catch reduction and management-based policies [125,154,205]. Despite traceability research in fish populations worldwide to avoid predatory and indiscriminate overfishing, there is still a lack of important studies related to DNA traceability markers in freshwater Neotropical fish species.…”

Section: Traceability Of Neotropical Fishmentioning

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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Applications of next-generation sequencing in fisheries research: A review

Cited by 68 publications

References 108 publications

Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus)

Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus)

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Genetic Applications in the Conservation of Neotropical Freshwater Fish

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