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Wenne R. Microsatellites as Molecular Markers with Applications in Exploitation and Conservation of Aquatic Animal Populations. Genes (Basel) 2023; 14:genes14040808. [PMID: 37107566 PMCID: PMC10138012 DOI: 10.3390/genes14040808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/28/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
A large number of species and taxa has been studied for genetic polymorphism. Microsatellites have been known as hypervariable neutral molecular markers with the highest resolution power in comparison with any other markers. However, the discovery of a new type of molecular marker—single nucleotide polymorphism (SNP) has put the existing applications of microsatellites to the test. To ensure good resolution power in studies of populations and individuals, a number of microsatellite loci from 14 to 20 was often used, which corresponds to about 200 independent alleles. Recently, these numbers have tended to be increased by the application of genomic sequencing of expressed sequence tags (ESTs), and the choice of the most informative loci for genotyping depends on the aims of research. Examples of successful applications of microsatellite molecular markers in aquaculture, fisheries, and conservation genetics in comparison with SNPs have been summarized in this review. Microsatellites can be considered superior markers in such topics as kinship and parentage analysis in cultured and natural populations, the assessment of gynogenesis, androgenesis and ploidization. Microsatellites can be coupled with SNPs for mapping QTL. Microsatellites will continue to be used in research on genetic diversity in cultured stocks, and also in natural populations as an economically advantageous genotyping technique.
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Affiliation(s)
- Roman Wenne
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
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Weng Z, Yang Y, Wang X, Wu L, Hua S, Zhang H, Meng Z. Parentage Analysis in Giant Grouper ( Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data. Genes (Basel) 2021; 12:genes12071042. [PMID: 34356058 PMCID: PMC8304347 DOI: 10.3390/genes12071042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 12/18/2022] Open
Abstract
Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean Ho = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.
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Affiliation(s)
- Zhuoying Weng
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
| | - Yang Yang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
| | - Xi Wang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
| | - Lina Wu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
| | - Sijie Hua
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
| | - Hanfei Zhang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
| | - Zining Meng
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China; (Z.W.); (Y.Y.); (X.W.); (L.W.); (S.H.); (H.Z.)
- Southern Laboratory of Ocean Science and Engineering, Zhuhai 519000, China
- Correspondence:
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Kim KS, Noh CH, Moon SJ, Han SH, Bang IC. Development of novel tetra- and trinucleotide microsatellite markers for giant grouper Epinephelus lanceolatus using 454 pyrosequencing. Mol Biol Rep 2016; 43:541-8. [PMID: 27059503 DOI: 10.1007/s11033-016-3980-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 04/03/2016] [Indexed: 10/22/2022]
Abstract
Giant grouper (Epinephelus lanceolatus) is a commercially important species, but its wild population has recently been classified as vulnerable. This species has significant potential for use in aquaculture, though a greater understanding of population genetics is necessary for selective breeding programs to minimize kinship for genetically healthy individuals. High-throughput pyrosequencing of genomic DNA was used to identify and characterize novel tetra- and trinucleotide microsatellite markers in giant grouper from Sabah, Malaysia. In total, of 62,763 sequences containing simple sequence repeats (SSRs) were obtained, and 78 SSR loci were selected to possibly contain tetra- and trinucleotide repeats. Of these loci, 16 had tetra- and 8 had trinucleotide repeats, all of which exhibited polymorphisms within easily genotyped regions. A total of 143 alleles were identified with an average of 5.94 alleles per locus, with mean observed and expected heterozygosities of 0.648 and 0.620, respectively. Among of them, 15 microsatellite markers were identified without null alleles and with Hardy-Weinberg equilibrium. These alleles showed a combined non-exclusion probability of 0.01138. The probability of individual identification (PID) value combined with in descending order 12 microsatellite markers was 0.00008, which strongly suggests that the use of the microsatellite markers developed in this study in various combinations would result in a high resolution method for parentage analysis and individual identification. These markers could be used to establish a broodstock management program for giant grouper and to provide a foundation for genetic studies such as population structure, parentage analysis, and kinship selection.
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Affiliation(s)
- Keun-Sik Kim
- East Sea Environment Research Center, East Sea Research Institute, Korea Institute of Ocean Science & Technology, Uljin, 36315, Republic of Korea
| | - Choong Hwan Noh
- East Sea Environment Research Center, East Sea Research Institute, Korea Institute of Ocean Science & Technology, Uljin, 36315, Republic of Korea
| | - Shin-Joo Moon
- Department of Life Science & Biotechnology, Soonchunhyang University, Asan, 31538, Republic of Korea
| | - Seung-Hee Han
- Department of Life Science & Biotechnology, Soonchunhyang University, Asan, 31538, Republic of Korea
| | - In-Chul Bang
- Department of Life Science & Biotechnology, Soonchunhyang University, Asan, 31538, Republic of Korea.
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Nurdalila AA, Bunawan H, Kumar SV, Rodrigues KF, Baharum SN. Homogeneous Nature of Malaysian Marine Fish Epinephelus fuscoguttatus (Perciformes; Serranidae): Evidence Based on Molecular Markers, Morphology and Fourier Transform Infrared Analysis. Int J Mol Sci 2015; 16:14884-900. [PMID: 26147421 PMCID: PMC4519877 DOI: 10.3390/ijms160714884] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 06/04/2015] [Accepted: 06/17/2015] [Indexed: 11/16/2022] Open
Abstract
Taxonomic confusion exists within the genus Epinephelus due to the lack of morphological specializations and the overwhelming number of species reported in several studies. The homogenous nature of the morphology has created confusion in the Malaysian Marine fish species Epinephelus fuscoguttatus and Epinephelus hexagonatus. In this study, the partial DNA sequence of the 16S gene and mitochondrial nucleotide sequences of two gene regions, Cytochrome Oxidase Subunit I and III were used to investigate the phylogenetic relationship between them. In the phylogenetic trees, E. fuscoguttatus was monophyletic with E. hexagonatus species and morphology examination shows that no significant differences were found in the morphometric features between these two taxa. This suggests that E. fuscoguttatus is not distinguishable from E. hexagonatus species, and that E. fuscoguttatus have been identified to be E. hexagonatus species is likely attributed to differences in environment and ability to camouflage themselves under certain conditions. Interestingly, this finding was also supported by Principal Component Analysis on Attenuated Total Reflectance-Fourier-transform Infrared (ATR-FTIR) data analysis. Molecular, morphological and meristic characteristics were combined with ATR-FTIR analysis used in this study offer new perspectives in fish species identification. To our knowledge, this is the first report of an extensive genetic population study of E. fuscoguttatus in Malaysia and this understanding will play an important role in informing genetic stock-specific strategies for the management and conservation of this highly valued fish.
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Affiliation(s)
- A'wani Aziz Nurdalila
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600 Selangor, Malaysia.
| | - Hamidun Bunawan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600 Selangor, Malaysia.
| | - Subbiah Vijay Kumar
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu Sabah, Malaysia.
| | - Kenneth Francis Rodrigues
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu Sabah, Malaysia.
| | - Syarul Nataqain Baharum
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, 43600 Selangor, Malaysia.
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Butler IA, Siletti K, Oxley PR, Kronauer DJC. Conserved microsatellites in ants enable population genetic and colony pedigree studies across a wide range of species. PLoS One 2014; 9:e107334. [PMID: 25244681 PMCID: PMC4170976 DOI: 10.1371/journal.pone.0107334] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 08/15/2014] [Indexed: 01/05/2023] Open
Abstract
Broadly applicable polymorphic genetic markers are essential tools for population genetics, and different types of markers have been developed for this purpose. Microsatellites have been employed as particularly polymorphic markers for over 20 years. However, PCR primers for microsatellite loci are often not useful outside the species for which they were designed. This implies that a new set of loci has to be identified and primers developed for every new study species. To overcome this constraint, we identified 45 conserved microsatellite loci based on the eight currently available ant genomes and designed primers for PCR amplification. Among these loci, we chose 24 for in-depth study in six species covering six different ant subfamilies. On average, 11.16 of these 24 loci were polymorphic and in Hardy-Weinberg equilibrium in any given species. The average number of alleles for these polymorphic loci within single populations of the different species was 4.59. This set of genetic markers will thus be useful for population genetic and colony pedigree studies across a wide range of ant species, supplementing the markers available for previously studied species and greatly facilitating the study of the many ant species lacking genetic markers. Our study shows that it is possible to develop microsatellite loci that are both conserved over a broad range of taxa, yet polymorphic within species. This should encourage researchers to develop similar tools for other large taxonomic groups.
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Affiliation(s)
- Ian A. Butler
- Laboratory of Insect Social Evolution, The Rockefeller University, New York, New York, United States of America
- * E-mail:
| | - Kimberly Siletti
- Laboratory of Insect Social Evolution, The Rockefeller University, New York, New York, United States of America
| | - Peter R. Oxley
- Laboratory of Insect Social Evolution, The Rockefeller University, New York, New York, United States of America
| | - Daniel J. C. Kronauer
- Laboratory of Insect Social Evolution, The Rockefeller University, New York, New York, United States of America
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