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Das G, Das SP, Bit A, Sahoo L, Swain SK, Raghavendra CH, Krishnaprasoon NP, Sahoo SK, Das P. Development of novel SSR markers and validation by assessing the genetic diversity of endangered Deccan mahseer, Tor khudree. Mol Biol Rep 2024; 51:290. [PMID: 38329563 DOI: 10.1007/s11033-023-09188-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/20/2023] [Indexed: 02/09/2024]
Abstract
BACKGROUND The Deccan mahseer, Tor khudree (Sykes, 1839) is a potential game and food fish species belonging to the family cyprinidae and is categorized as endangered. Its distribution is restricted to southern part of India, specifically to Peninsular Rivers. This study is first to assess the genetic diversity and differentiation in Tor khudree by developing novel simple sequence repeat (SSR) markers. METHODS AND RESULTS Low depth next generation sequencing followed by sequence analysis in MISA software identified 187,649 SSRs. The novel fourteen validated SSR loci were used for population genetic analysis. All of the SSR loci were highly informative with mean PIC > 0.5. High mean allelic richness (9.29) observed heterozygosity (0.98) and expected heterozygosity (0.79) were observed across the loci. However, genetic differentiation was low but significant (0.052). Negative FIS values were observed in both locus-wise and populations indicating the presence of high heterozygosity. Intrapopulation variation was found to be high (96.29%). The population structure revealed two genetic stocks. CONCLUSIONS The results from the present study including the highly polymorphic markers developed would be a useful resource for further research on population genetics and conservation genetics of the species.
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Affiliation(s)
- Gargee Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | | | - Amrita Bit
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Lakshman Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Subrat Kumar Swain
- Institute of Medical Sciences & SUM Hospital, Siksha O Anusandhan University, Bhubaneswar, India
| | | | - N P Krishnaprasoon
- PMFGR Centre of ICAR-National Bureau of Fish Genetic Resources, CMFRI Campus, Kochi, India
| | - Sangram Ketan Sahoo
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
- Aquaculture Productions and Environment Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India
| | - Paramananda Das
- Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Kausalyaganga, Bhubaneswar, 751002, India.
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2
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Colautti DC, Miranda L, Gonzalez-Castro M, Villanova V, Strüssmann CA, Mancini M, Maiztegui T, Berasain G, Hattori R, Grosman F, Sanzano P, Lozano I, Vegh SL, Salinas V, Del Ponti O, Del Fresno P, Minotti P, Yamamoto Y, Baigún CRM. Evidence of a landlocked reproducing population of the marine pejerrey Odontesthes argentinensis (Actinopterygii; Atherinopsidae). JOURNAL OF FISH BIOLOGY 2020; 96:202-216. [PMID: 31729023 DOI: 10.1111/jfb.14207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
In South America, the order Atheriniformes includes the monophyletic genus Odontesthes with 20 species that inhabit freshwater, estuarine and coastal environments. Pejerrey Odontesthes argentinensis is widely distributed in coastal and estuarine areas of the Atlantic Ocean and is known to foray into estuaries of river systems, particularly in conditions of elevated salinity. However, to our knowledge, a landlocked self-sustaining population has never been recorded. In this study, we examined the pejerrey population of Salada de Pedro Luro Lake (south-east of Buenos Aires Province, Argentina) to clarify its taxonomic identity. An integrative taxonomic analysis based on traditional meristic, landmark-based morphometrics and genetic techniques suggests that the Salada de Pedro Luro pejerrey population represents a novel case of physiological and morphological adaptation of a marine pejerrey species to a landlocked environment and emphasises the environmental plasticity of this group of fishes.
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Affiliation(s)
- Darío C Colautti
- Laboratorio de Ecología de Peces Instituto de Limnología 'Dr. Raúl A. Ringuelet' (ILPLA-CONICET), La Plata, Argentina
| | - Leandro Miranda
- Laboratorio de Ictiofisiología y Acuicultura IIB-INTECH (CONICET-UNSAM), Chascomús, Argentina
| | - Mariano Gonzalez-Castro
- Laboratorio de Biotaxonomía Morfológica y Molecular de Peces, Instituto de Investigaciones Marinas y Costeras (IIMyC-CONICET), Mar del Plata, Argentina
| | - Vanina Villanova
- Laboratorio de Biotecnología Acuática (FCByF-UNR) Centro Científico, Tecnológico y Educativo Acuario del Río Paraná, Rosario, Argentina
- Centro Científico y Tecnológico Conicet Rosario (CCT-Conicet Rosario), Rosario, Argentina
| | - Carlos A Strüssmann
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Miguel Mancini
- Ecología & Acuicultura, Facultad de Agronomía y Veterinaria (UNRC), Río Cuarto, Argentina
| | - Tomas Maiztegui
- Laboratorio de Ecología de Peces Instituto de Limnología 'Dr. Raúl A. Ringuelet' (ILPLA-CONICET), La Plata, Argentina
| | - Gustavo Berasain
- Dirección Provincial de Pesca, Ministerio de agroindustria de la Provincia de Buenos Aires, Lastra y Juarez (7130), Chascomús, Buenos Aires, Argentina
| | - Ricardo Hattori
- São Paulo 31 Fisheries Institute (APTA/SAA), Campos do Jordão, 12460-000, Brazil
| | - Fabian Grosman
- Facultad de Ciencias Veterinarias, Instituto Ecosistemas (UNCPBA-CIC), Tandil, Argentina
| | - Pablo Sanzano
- Facultad de Ciencias Veterinarias, Instituto Ecosistemas (UNCPBA-CIC), Tandil, Argentina
| | - Ismael Lozano
- Laboratorio de Ecotoxicología Acuática, Instituto de Biodiversidad y Biología Experimental Aplicada (IBBEA-CONICET), Ciudad Universitaria, Buenos Aires, Argentina
| | - Sabina L Vegh
- Instituto de Investigaciones en Producción Animal (INPA-CONICET), Buenos Aires, Argentina
| | - Victor Salinas
- Ecología & Acuicultura, Facultad de Agronomía y Veterinaria (UNRC), Río Cuarto, Argentina
| | - Omar Del Ponti
- Departamento de Recursos Naturales, Facultad de Ciencias Exactas y Naturales (UNLPam), Santa Rosa, Argentina
| | - Pamela Del Fresno
- Laboratorio de Ictiofisiología y Acuicultura IIB-INTECH (CONICET-UNSAM), Chascomús, Argentina
| | - Priscila Minotti
- Laboratorio de Ecología, Teledetección y Ecoinformática3iA Instituto de Investigación e Ingeniería Ambiental Universidad Nacional de San Martín Campus Miguelete, Martín, Argentina
| | - Yoji Yamamoto
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Claudio R M Baigún
- Laboratorio de Ecología Pesquera Aplicada, Instituto de Investigación e Ingeniería Ambiental (UNSAM-CONICET), Buenos Aires, Argentina
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Restrepo-Escobar N, Márquez EJ. Microsatellite loci development for three catfish species from northwestern South America. NEOTROPICAL ICHTHYOLOGY 2020. [DOI: 10.1590/1982-0224-2019-0079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT The Neotropical catfish species Ageneiosus pardalis, Pimelodus grosskopfii, and Sorubim cuspicaudus are important fishery resources in Colombia that show historical declines in their capture. This study used next-generation sequencing with 454 FLX technology (Roche Applied Science) and bioinformatics analysis to develop between 18 and 24 microsatellite loci for these species. The novel microsatellite loci showed high values of polymorphic information content -PIC (A. pardalis: 0.601-0.903, P. grosskopfii: 0.748-0.946 and S. cuspicaudus: 0.383-0.876), and the average number of alleles/locus ranged from 7-15 for A. pardalis, 9-30 for P. grosskopfii and 5-14 for S. cuspicaudus. The average observed and expected heterozygosities were respectively, 0.757 ± 0.035 and 0.834 ± 0.015 for A. pardalis; 0.596 ± 0.040 and 0.881 ± 0.009 for P. grosskopfii; and 0.747 ± 0.031 and 0.757 ± 0.025 for S. cuspicaudus. For future studies, these loci can be useful to estimate the genetic diversity and population structure in these three Neotropical catfishes.
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Mastrochirico-Filho VA, Del Pazo F, Hata ME, Villanova GV, Foresti F, Vera M, Martínez P, Porto-Foresti F, Hashimoto DT. Assessing Genetic Diversity for a Pre-Breeding Program in Piaractus mesopotamicus by SNPs and SSRs. Genes (Basel) 2019; 10:genes10090668. [PMID: 31480436 PMCID: PMC6771149 DOI: 10.3390/genes10090668] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/28/2019] [Accepted: 08/28/2019] [Indexed: 11/16/2022] Open
Abstract
The pacu (Piaractus mesopotamicus) is a Neotropical fish with remarkable productive performance for aquaculture. Knowledge of genetic resources in Neotropical fish is essential for their applications in breeding programs. The aim of this study was to characterize the genetic diversity of seven farmed populations of pacu which will constitute the basis for a broodstock foundation for coming breeding programs in Brazil. Analysis of one wild population (Paraná River) was used as a reference to compare genetic parameters in the farmed populations. The analyses were performed using 32 single-nucleotide polymorphisms (SNP) and 8 simple sequence repeat (SSR) markers. No significant differences in genetic diversity between populations estimated through the number of alleles and allelic richness, observed heterozygosity, expected heterozygosity, and minimum allele frequency were detected (p > 0.05). Low genetic diversity was observed in all farmed stocks and the wild population. Moreover, we detected low genetic structure when comparing farmed and wild populations for SNPs (FST = 0.07; K = 3) and SSRs (FST = 0.08; K = 2). Analysis of molecular variance (AMOVA) demonstrated that genetic variation was mostly within populations. Kinship analysis showed that most fish farms included related individuals at a proportion of at least 25%. Our results suggest that the basal broodstock for pacu breeding programs should be founded with individuals from different fish farms for higher genetic diversity and to avoid inbreeding risks.
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Affiliation(s)
| | - Felipe Del Pazo
- Laboratorio Mixto de Biotecnología Acuática - Universidad Nacional de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas - Ministerio de Ciencia, Tecnología e Innovación productiva de Santa Fe. Centro Científico y Tecnológico Acuario del Río Paraná, Rosario, Santa Fe 2000, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Rosario, Santa Fe 2000, Argentina
| | - Milene Elissa Hata
- Aquaculture Center of Unesp, São Paulo State University (Unesp), Jaboticabal, SP 14884-900, Brazil
| | - Gabriela Vanina Villanova
- Laboratorio Mixto de Biotecnología Acuática - Universidad Nacional de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas - Ministerio de Ciencia, Tecnología e Innovación productiva de Santa Fe. Centro Científico y Tecnológico Acuario del Río Paraná, Rosario, Santa Fe 2000, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Rosario, Santa Fe 2000, Argentina
| | - Fausto Foresti
- Institute of Biosciences, São Paulo State University (Unesp), Botucatu, SP 18618-970, Brazil
| | - Manuel Vera
- Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), ES27002 Lugo, Spain
- Instituto de Acuicultura, Universidad de Santiago de Compostela (USC), 15705 Santiago de Compostela, Spain
| | - Paulino Martínez
- Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), ES27002 Lugo, Spain
- Instituto de Acuicultura, Universidad de Santiago de Compostela (USC), 15705 Santiago de Compostela, Spain
| | - Fábio Porto-Foresti
- São Paulo State University (Unesp), School of Sciences, Bauru, SP 17033-360, Brazil
| | - Diogo Teruo Hashimoto
- Aquaculture Center of Unesp, São Paulo State University (Unesp), Jaboticabal, SP 14884-900, Brazil.
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Pimentel JSM, Carmo AO, Rosse IC, Martins APV, Ludwig S, Facchin S, Pereira AH, Brandão-Dias PFP, Abreu NL, Kalapothakis E. High-Throughput Sequencing Strategy for Microsatellite Genotyping Using Neotropical Fish as a Model. Front Genet 2018; 9:73. [PMID: 29593777 PMCID: PMC5855144 DOI: 10.3389/fgene.2018.00073] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 02/19/2018] [Indexed: 01/15/2023] Open
Abstract
Genetic diversity and population studies are essential for conservation and wildlife management programs. However, monitoring requires the analysis of multiple loci from many samples. These processes can be laborious and expensive. The choice of microsatellites and PCR calibration for genotyping are particularly daunting. Here we optimized a low-cost genotyping method using multiple microsatellite loci for simultaneous genotyping of up to 384 samples using next-generation sequencing (NGS). We designed primers with adapters to the combinatorial barcoding amplicon library and sequenced samples by MiSeq. Next, we adapted a bioinformatics pipeline for genotyping microsatellites based on read-length and sequence content. Using primer pairs for eight microsatellite loci from the fish Prochilodus costatus, we amplified, sequenced, and analyzed the DNA of 96, 288, or 384 individuals for allele detection. The most cost-effective methodology was a pseudo-multiplex reaction using a low-throughput kit of 1 M reads (Nano) for 384 DNA samples. We observed an average of 325 reads per individual per locus when genotyping eight loci. Assuming a minimum requirement of 10 reads per loci, two to four times more loci could be tested in each run, depending on the quality of the PCR reaction of each locus. In conclusion, we present a novel method for microsatellite genotyping using Illumina combinatorial barcoding that dispenses exhaustive PCR calibrations, since non-specific amplicons can be eliminated by bioinformatics analyses. This methodology rapidly provides genotyping data and is therefore a promising development for large-scale conservation-genetics studies.
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Affiliation(s)
- Juliana S. M. Pimentel
- Laboratory of Biotechnology and Molecular Markers, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Anderson O. Carmo
- Laboratory of Biotechnology and Molecular Markers, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Izinara C. Rosse
- Laboratory of Biotechnology and Molecular Markers, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Ana P. V. Martins
- Laboratory of Biotechnology and Molecular Markers, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Sandra Ludwig
- Department of Zoology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Susanne Facchin
- Laboratory of Biotechnology and Molecular Markers, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Adriana H. Pereira
- Laboratory of Biotechnology and Molecular Markers, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Pedro F. P. Brandão-Dias
- Laboratory of Biotechnology and Molecular Markers, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Nazaré L. Abreu
- Laboratory of Biotechnology and Molecular Markers, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Evanguedes Kalapothakis
- Laboratory of Biotechnology and Molecular Markers, Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
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