Development and characterization of novel cross-species tetranucleotide microsatellite markers for sterlet (Acipenser ruthenus) from Chinese sturgeon (Acipenser sinensis)

Sterlet (Acipenser ruthenus) is an important economic fish because of its nourishing caviar, isinglass and flesh. In order to facilitate the recovery of this species, the full understanding of its population genetic structure is necessary for taking appropriate management actions. However, genetic data on the use of nuclear loci in sterlet is still quite poor because microsatellite markers in sterlet that had been developed appeared to be polyploidy which add difficulties in studying the genetic of the sterlet. In this study, 24 tetranucleotide microsatellite markers were developed in sterlet from 160 microsatellite markers of the endangered Chinese sturgeon (Acipenser sinensis). Ten (ZHX76, ZHX64, Z194, Z217, Z184, Z242, Z250, Z258, Z268 and Z269) of the 24 loci showed disomic patterns while the rest loci showed tetrasomic patterns. In this paper, 24 microsatellite markers were characterized in 16 sterlet individuals and all of them were polymorphic with 2 to 7 alleles per locus. The Hardy-Weinberg departure value (d), polymorphic information content (PIC), the observed heterozygosity (HO), the Shannon-Wiener Diversity Indices (H') and the mean expected heterozygosity (HE) of all 24 polymorphic loci ranged from -0.334 to 0.484, 0.367 to 0.725, 0.438 to 1, 0.659 to 1.695, from 0.466 to 0.777, respectively. The markers described here will help in addressing practical problems such as the study of population genetics, conservation genetics and evolution in the polyploidy derivative nature of sterlet.

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Review: Genetic diversity studies using microsatellite markers and their contribution in supporting sustainable sheep breeding programs

Asian Journal of Agriculture ◽

10.13057/asianjagric/g010109 ◽

2017 ◽

Vol 1 (01) ◽

pp. 46-51

Author(s):

OUMER SHERIFF ◽

KEFYALEW ALEMAYEHU

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Polymorphic Information Content ◽

Domestic Sheep ◽

Breeding Programs ◽

Sheep Breeding ◽

Population Structures ◽

The Mean ◽

Tree Building ◽

Diversity Studies

Sheriff O, Alemayehu K. 2017. Review: Genetic diversity studies using microsatellite markers and their contribution in supporting sustainable sheep breeding programs. Asian J Agric 1: 46-51. Microsatellites have been widely accepted and employed as useful molecular markers for measuring genetic diversity and divergence within and among populations. The various parameters developed so far to measure genetic diversity within and among populations are observed and expected heterozygosities (Ho and He), the mean number of alleles per locus (MNA),polymorphic information content (PIC), genetic distance and phylogenetic or tree building approach.The objective of thisreview was therefore to quantifythe genetic diversity studies of domestic sheep populations using microsatellite markersand their contribution in supporting sustainable sheep breeding programs. From the review, it is possible to see that there was high within population genetic variations in all the studied sheep populations, poor level of population differentiations and high levels of inbreeding. On the other hand, low estimates of hetrozygosities and mean number of alleles and employing only few and weak markers were observed in some of the studies. The gaps observed in the previous genetic diversity studies of the sheep populations may demand further works to reveal more information on the population structures andto start appropriate and sustainable breeding programs.

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Microsatellite development via next-generation sequencing in Acacia stenophylla (Fabaceae) and Duma florulenta (Polygonaceae): two ecologically important plant species of Australian dryland floodplains

10.7287/peerj.preprints.27027v1 ◽

2018 ◽

Author(s):

Bruce F Murray ◽

Michael A Reid ◽

Shu-Biao Wu

Keyword(s):

Gene Flow ◽

Next Generation Sequencing ◽

Microsatellite Markers ◽

Information Content ◽

Polymorphic Information Content ◽

Extreme Variability ◽

Polymorphic Microsatellite ◽

Generation Sequencing ◽

Semi Arid

Duma florulenta and Acacia stenophylla are two ecologically important but understudied species that naturally occur on the floodplains and riverbanks of Australia’s arid and semi-arid river systems. This paper describes the discovery and characterization of 12 and 13 polymorphic microsatellite markers for D. florulenta and A. stenophylla respectively. The number of alleles per locus for D. florulenta ranged from 2-12 with an average of 6.1. Across all samples, observed and expected heterozygosities ranged from 0.026 to 0.784 and 0.026 to 0.824 respectively and mean polymorphic information content was equal to 0.453. For A. stenophylla, the number of alleles per locus ranged between 2 and 8 with an overall mean of 4.8. Across all samples, observed and expected heterozygosities ranged from 0.029 to 0.650 and 0.029 to 0.761 respectively and mean polymorphic information content was 0.388. The developed suites of 12 and 13 microsatellite markers for D. florulenta and A. stenophylla respectively provide opportunity for novel research into mechanisms of gene flow, dispersal and breeding system and how they operate under the extreme variability these species are exposed to in the environments in which they live.

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Acoustic Target Strength of the Endangered Chinese Sturgeon (Acipenser sinensis) by Ex Situ Measurements and Theoretical Calculations

Applied Sciences ◽

10.3390/app8122554 ◽

2018 ◽

Vol 8 (12) ◽

pp. 2554 ◽

Cited By ~ 1

Author(s):

Hui Zhang ◽

Junyi Li ◽

Chongrui Wang ◽

Chengyou Wang ◽

Jinming Wu ◽

...

Keyword(s):

Theoretical Calculations ◽

Breeding Population ◽

Ex Situ ◽

Target Strength ◽

Effective Management ◽

Chinese Sturgeon ◽

Acipenser Sinensis ◽

Acoustic Target ◽

The Mean ◽

Db Difference

The Chinese sturgeon, Acipenser sinensis, is a large anadromous and highly endangered protected species. The assessment of its breeding population in the Yangtze River is critically important for effective management and population preservation. Currently, hydroacoustic methods have been widely used to study the adult sturgeons in the river, whereas the acoustic target strength (TS) characteristics of the species have not been studied. In this study, the TS of Chinese sturgeon was carefully evaluated both by ex situ measurements and theoretical calculations. Six Chinese sturgeons (Body Length (BL): 74.0−92.6 cm) were measured by a 199 kHz split echosounder in a 10-m deep net cage. The computed tomography of a Chinese sturgeon (BL: 110.0 cm) was conducted and the Kirchhoff ray mode (KRM) method was used to estimate the theoretical TS. As a result, the mean ex situ TS range of the six specimens was from −26.9 to −31.4 dB, which was very close to the KRM estimation (~1 dB difference). Then, the KRM method was used to predict the TS of Chinese sturgeon as a function of BL in six frequencies commonly used in freshwater environments and to estimate the TS of a representative adult Chinese sturgeon (250 cm) as a function of frequency and tilt angle. This study can provide a good basis for future hydroacoustic studies on the critically endangered Chinese sturgeon.

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Development and characterization of a duplex PCR assay in Chinese sturgeon (Acipenser sinensis) for genetic analysis

Scientific Reports ◽

10.1038/s41598-020-60401-y ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Yacheng Hu ◽

Xueqing Liu ◽

Jing Yang ◽

Kan Xiao ◽

Binzhong Wang ◽

...

Keyword(s):

Genetic Analysis ◽

Duplex Pcr ◽

Chinese Sturgeon ◽

Pcr Assay ◽

Acipenser Sinensis ◽

Duplex Pcr Assay

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Characterization of hydraulic suitability of Chinese sturgeon (Acipenser sinensis) spawning habitat in the Yangtze River

Hydrological Processes ◽

10.1002/hyp.8407 ◽

2012 ◽

Vol 26 (23) ◽

pp. 3489-3498 ◽

Cited By ~ 11

Author(s):

Yuankun Wang ◽

Ziqiang Xia ◽

Dong Wang

Keyword(s):

Yangtze River ◽

The Yangtze River ◽

Chinese Sturgeon ◽

Spawning Habitat ◽

Acipenser Sinensis

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Cross-species amplification and characterization of microsatellite loci in Pinus mugo Turra

Biologia ◽

10.2478/s11756-013-0189-z ◽

2013 ◽

Vol 68 (4) ◽

Cited By ~ 8

Author(s):

Konrad Celiński ◽

Ewa Pawlaczyk ◽

Aleksandra Wojnicka-Półtorak ◽

Ewa Chudzińska ◽

Wiesław Prus-Głowacki

Keyword(s):

Microsatellite Markers ◽

Polymorphic Information Content ◽

Pinus Mugo ◽

Genetic Studies ◽

Transfer Rates ◽

Isolation And Characterization ◽

Nuclear Microsatellite ◽

European Mountain ◽

High Level

AbstractPinus mugo (dwarf mountain pine) is an important component of European mountain ecosystems. However, little is known about the present genetic structure and population differentiation of this species at the DNA level, possibly due to a lack of nuclear microsatellite markers (SSR) developed for Pinus mugo. Therefore in this study we transferred microsatellite markers originally developed for Pinus sylvestris and Pinus taeda to Pinus mugo. This cross-species amplification approach is much faster and less expensive than isolation and characterization of new microsatellite markers. The transfer rates from the source species to Pinus mugo were moderately low (26%). There were no differences in microsatellite repeat motifs between the source species and Pinus mugo. Nuclear microsatellite markers successfully transferred to Pinus mugo can be applied to various genetic studies on this species, due to the high level of their polymorphism and high value of polymorphic information content.

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Development of 17 Novel Cross-Species Microsatellite Markers for Dabry’s Sturgeon (Acipenser dabryanus) from Chinese Sturgeon (Acipenser sinensis) via Next-Generation Sequencing

Pakistan Journal of Zoology ◽

10.17582/journal.pjz/2019.51.6.sc4 ◽

2019 ◽

Vol 51 (6) ◽

Author(s):

Yacheng Hu ◽

Xueqing Liu ◽

Jing Yang ◽

Kan Xiao ◽

Binzhong Wang ◽

...

Keyword(s):

Next Generation Sequencing ◽

Microsatellite Markers ◽

Next Generation ◽

Chinese Sturgeon ◽

Acipenser Sinensis ◽

Generation Sequencing ◽

Dabry’S Sturgeon

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Development and characterization of 29 polymorphic microsatellite loci of Megalobrama pellegrini by next-generation sequencing technology and cross-species amplification in related species

10.7287/peerj.preprints.2490 ◽

2016 ◽

Author(s):

Wen Song ◽

Dongmei Zhu ◽

Yefeng Lv ◽

Weimin Wang

Keyword(s):

Microsatellite Markers ◽

Microsatellite Loci ◽

Related Species ◽

Polymorphic Information Content ◽

Sequencing Technology ◽

Next Generation Sequencing Technology ◽

Expected Heterozygosity ◽

Polymorphic Microsatellite ◽

Generation Sequencing

Megalobrama pellegrini is one of the economically important freshwater fish in China. Here, we developed 29 polymorphic microsatellite loci of M. pellegrini. The number of alleles (Na), effective number of alleles (Ne), observed heterozygosity (HO), expected heterozygosity (HE) and polymorphic information content (PIC) ranged from 3 to 11 (mean±SD 5.4828±1.9571), 2.8708 to 9.6257 (mean±SD 5.0865±1.6681), 0.4333 to 0.9333 (mean±SD 0.7874±0.1213), 0.6627 to 0.9113 (mean±SD 0.7946±0.0751) and 0.5785 to 0.8868 (mean±SD 0.7439±0.0950), respectively. Cross-species amplification was successful at most loci for related species such as M. amblycephala, M. hoffmanni, M. skolkovii and Parabramis pekinensis. The transferability rate of the 29 polymorphic microsatellite markers in M. amblycephala, M. hoffmanni, M. skolkovii and P. pekinensis were 96.55%, 86.21%, 86.21% and 75.86%, respectively. These polymorphic microsatellites are not only useful in genetic study and conservation of M. pellegrini, but also an effective tool for identifying the related species. We could use 5 microsatellite markers (HHF-63, HHF-104, HHF-113, HHF-148, HHF-163) to distinguish the 5 species.

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