Identification of a large dataset of SNPs in hair‐fin anchovy (<i>Setipinna tenuifilis</i>) based on RAD‐seq

Peng, Ying; Li, J S; Zhang, K; Liu, Y F; Li, X P; Zhang, H; Gong, Li; Liu, L Q; Lü, Zhen-Ming; Liu, B J

doi:10.1111/age.13062

Cited by 3 publications

(3 citation statements)

References 15 publications

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“…In Figure 1c, the QD and ZS populations were grouped into one cluster and the ZJ population was independently grouped into another cluster, which was consistent with previous studies, showing a discontinuity between northern and southern populations (Peng et al, 2021). Our results showed that the newly polymorphic SSR markers developed in this study could assess the different population structures of this species across its distribution range.…”

Section: Re Sults and Discussionsupporting

confidence: 90%

“…Mitochondrial DNA (mtDNA) sequences and single nucleotide polymorphisms (SNPs) have been used in population genetic studies of S. tenuifilis (Peng et al, 2021; Xu et al, 2014). Maternal inheritance and absence of recombination make mtDNA an important role as a genetic marker in population and evolutionary biology (Harrison, 1989), but it is limited to uncovering the fine population structure of marine fish compared to nuclear genes (Hellberg et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

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Development and characterization of seventeen novel microsatellite markers in common hairfin anchovy ( Setipinna tenuifilis ) using third‐generation sequencing technology

Liu

Chen

et al. 2022

J Appl Ichthyol

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Setipinna tenuifilis (Clupeiformes: Engraulidae), commonly known as common hairfin anchovy, is widely distributed in the Western Pacific and Indian Oceans. In the 1970s, China's annual production of S. tenuifilis exceeded 100,000 tons and sequentially increased in the 1980s (Liu et al., 2006). Besides, S. tenuifilis serves as a major prey source for numerous predators in coastal ecosystems, playing

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Section: Re Sults and Discussionsupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

Development and characterization of seventeen novel microsatellite markers in common hairfin anchovy ( Setipinna tenuifilis ) using third‐generation sequencing technology

Liu

Chen

et al. 2022

J Appl Ichthyol

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“…Simple library construction, short duration of the experiment, and well-developed data processing and analysis pipelines have made the RAD-seq technology popular in SNP identification and population genetics studies (Eaton and Ree 2013 ; McCormack et al 2013 ). Furthermore, RAD-seq technology has been successfully applied to detect SNPs in the whole genome of numerous marine species, such as Mugil cephalus (Krück et al 2013 ), Carcinus maenas (Jeffery et al 2017 ) and Setipinna tenuifilis (Peng et al 2021 ), to provide more reliable evidence for studying their genetic structure and adaptive evolution (Miller et al 2007 ). However, no population genetics study has been conducted to detect genome-wide SNPs of K. punctatus based on RAD-seq.…”

Section: Introductionmentioning

confidence: 99%

New perspectives on the genetic structure of dotted gizzard shad (Konosirus punctatus) based on RAD-seq

Peng,

Liu,

et al. 2024

Mar Life Sci Technol

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To maintain, develop and rationally utilize marine organisms, understanding their genetic structure and habitat adaptation pattern is necessary. Konosirus punctatus, which is a commercial fish species inhabiting the Indo-west Pacific Ocean, has shown an obvious annual global capture and aquaculture production decline due to climate changes and human activities. In the present study, restriction-site associated DNA sequencing (RAD-seq) was used to describe its genome-wide single nucleotide polymorphisms panel (SNPs). Among 146 individuals collected at nine locations scattered in China, Korea and Japan, a set of 632,090 SNPs were identified. Population genetic analysis showed that K. punctatus individuals were divided into two significant genetic clusters. Meanwhile, potential genetic differentiation between northern and southern population of K. punctatus was found. Treemix results indicated that gene flow existed among sampling locations of K. punctatus, especially from southern Japan to others. Moreover, candidate genes associated with habitat adaptations of K. punctatus were identified, which are involved in diverse physiological processes of K. punctatus including growth and development (e.g., KIDINS220, PAN3), substance metabolism (e.g., PGM5) and immune response (e.g., VAV3, CCT7, HSPA12B). Our findings may aid in understanding the possible mechanisms for the population genetic structure and local adaptation of K. punctatus, which is beneficial to establish the management and conservation units of K. punctatus, guiding the rational use of resources, with reference significance for a profound understanding of the adaptative mechanisms of other marine organisms to the environment.

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Population structure and genetic diversity in wild dotted gizzard shad (Konosirus punctatus) revealed by microsatellite markers

Liu

Zhang

et al. 2022

Front. Mar. Sci.

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Uncovering the fine-scale genetic structure has been long recognized as a key component in policymaking for the management of marine fisheries. Many species of Clupeiformes have suffered declines owing to overexploitation and habitat destruction. In this study, twenty polymorphic microsatellite markers were used to evaluate the genetic diversity and population structure of Konosirus punctatus, a pelagic fish of economic and ecological importance in the Northwestern Pacific Ocean. Although most of the variance occurred within individuals, significant differentiation (FST = 0.00384~0.19346) was shown in wild K. punctatus populations. Population structure analyses revealed five genetically divergent clades in K. punctatus in the Northwestern Pacific. Significant isolation by distance and one potentially outlier locus were revealed in K. punctatus, suggesting that interactions between historical climate shifts and environmental factors may contribute to the present-day genetic architecture. In summary, these results provided new perspectives on the population genetic structure of K. punctatus, facilitating the development of effective management strategies for this species.

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Identification of a large dataset of SNPs in hair‐fin anchovy (Setipinna tenuifilis) based on RAD‐seq

Cited by 3 publications

References 15 publications

Development and characterization of seventeen novel microsatellite markers in common hairfin anchovy ( Setipinna tenuifilis ) using third‐generation sequencing technology

Development and characterization of seventeen novel microsatellite markers in common hairfin anchovy ( Setipinna tenuifilis ) using third‐generation sequencing technology

New perspectives on the genetic structure of dotted gizzard shad (Konosirus punctatus) based on RAD-seq

Population structure and genetic diversity in wild dotted gizzard shad (Konosirus punctatus) revealed by microsatellite markers

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