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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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Vaini JO, Mota KG, Ojeda AP, Barreiros JP, Moreira RG, Hilsdorf AWS. Development and characterization of 20 polymorphic microsatellite markers for Epinephelus marginatus (Lowe, 1834) (Perciformes: Epinephelidae) using 454 pyrosequencing. Genet Mol Biol 2019; 42:74-79. [PMID: 30776048 PMCID: PMC6428119 DOI: 10.1590/1678-4685-gmb-2018-0067] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 04/26/2018] [Indexed: 11/23/2022] Open
Abstract
The dusky grouper, Epinephelus marginatus, is a well-known and
widespread marine fish assessed as endangered by the International Union for the
Conservation of Nature. Analyzing the genetic diversity of this species is,
therefore, of utmost importance and necessary for conservation purposes.
Microsatellites are molecular tools with advantages that are ideal for
population analyses. This study provides the first set of species-specific
microsatellite loci for E. marginatus that can be applied when
assessing both intra- and interpopulation genetic variation. Twenty
microsatellite loci were isolated and characterized for the dusky grouper by
genotyping 20 individuals obtained from the North Eastern Atlantic Ocean (n = 4)
and from the South Western Atlantic Ocean (n = 16). The number of alleles per
locus varied from 2 to 11, while the observed and expected heterozygosities
ranged from 0.25 to 0.94 and 0.34 to 0.89, respectively. The polymorphic
information content varied from moderately to highly informative. This suite of
markers provides the first specific nuclear tools for E.
marginatus and, thus, allows to assess with more specificity
different populations’ structures.
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Affiliation(s)
- Jussara Oliveira Vaini
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes, Mogi das Cruzes, SP, Brazil
| | - Kenneth Gabriel Mota
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes, Mogi das Cruzes, SP, Brazil
| | - Alejandra Paola Ojeda
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes, Mogi das Cruzes, SP, Brazil
| | - João Pedro Barreiros
- Centro de Ecologia, Evolução e Alterações Ambientais, Universidade dos Açores, Angra do Heroísmo, Portugal
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LIU HONGGAO, YANG ZHI, TANG HUIYUAN, GONG YUN, WAN LI. Microsatellite development and characterization for Saurogobio dabryi Bleeker, 1871 in a Yangtze river-connected lake, China. J Genet 2017. [DOI: 10.1007/s12041-016-0733-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Li L, Fang Z, Zhou J, Chen H, Hu Z, Gao L, Chen L, Ren S, Ma H, Lu L, Zhang W, Peng H. An accurate and efficient method for large-scale SSR genotyping and applications. Nucleic Acids Res 2017; 45:e88. [PMID: 28184437 PMCID: PMC5449614 DOI: 10.1093/nar/gkx093] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/01/2017] [Indexed: 01/10/2023] Open
Abstract
Accurate and efficient genotyping of simple sequence repeats (SSRs) constitutes the basis of SSRs as an effective genetic marker with various applications. However, the existing methods for SSR genotyping suffer from low sensitivity, low accuracy, low efficiency and high cost. In order to fully exploit the potential of SSRs as genetic marker, we developed a novel method for SSR genotyping, named as AmpSeq-SSR, which combines multiplexing polymerase chain reaction (PCR), targeted deep sequencing and comprehensive analysis. AmpSeq-SSR is able to genotype potentially more than a million SSRs at once using the current sequencing techniques. In the current study, we simultaneously genotyped 3105 SSRs in eight rice varieties, which were further validated experimentally. The results showed that the accuracies of AmpSeq-SSR were nearly 100 and 94% with a single base resolution for homozygous and heterozygous samples, respectively. To demonstrate the power of AmpSeq-SSR, we adopted it in two applications. The first was to construct discriminative fingerprints of the rice varieties using 3105 SSRs, which offer much greater discriminative power than the 48 SSRs commonly used for rice. The second was to map Xa21, a gene that confers persistent resistance to rice bacterial blight. We demonstrated that genome-scale fingerprints of an organism can be efficiently constructed and candidate genes, such as Xa21 in rice, can be accurately and efficiently mapped using an innovative strategy consisting of multiplexing PCR, targeted sequencing and computational analysis. While the work we present focused on rice, AmpSeq-SSR can be readily extended to animals and micro-organisms.
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Affiliation(s)
- Lun Li
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China
| | - Zhiwei Fang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China
| | - Junfei Zhou
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China
| | - Hong Chen
- Center for Development of Science and Technology, Ministry of Agriculture, P.R. China, Beijing 100122, China
| | - Zhangfeng Hu
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China
| | - Lifen Gao
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China
| | - Lihong Chen
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China
| | - Sheng Ren
- Division of Biomedical Informatics, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45229-3026, USA.,Department of Mathematical Sciences, McMicken College of Arts & Sciences, University of Cincinnati, 2815 Commons Way, Cincinnati, OH 45221-0025, USA
| | - Hongyu Ma
- Thermo Fisher Scientific, Building 6, No. 27, Xin Jinqiao Rd., Pudong, Shanghai 201206, China
| | - Long Lu
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China.,Division of Biomedical Informatics, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45229-3026, USA
| | - Weixiong Zhang
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China.,Department of Computer Science and Engineering, Washington University in St Louis, MO 63130, USA.,Department of Genetics, Washington University School of Medicine, St Louis, MO 63130, USA
| | - Hai Peng
- Institute for Systems Biology, Jianghan University, Wuhan, Hubei 430056, China
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