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Sumana SL, Wang P, Zhang C, Jing X, Zhu J, Tang Y, Liu W, Su S, Liao Y. Genetic diversity of the common carp black strain population based on mtDNA ( D-loop and cytb). Heliyon 2024; 10:e30307. [PMID: 38774331 PMCID: PMC11107203 DOI: 10.1016/j.heliyon.2024.e30307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/24/2024] Open
Abstract
The common strain black carp (Cyprinus carpio var. baisenensis) is a culturally important carp strain that is raised and cultured in Guangxi Province, China. Its color reflects the interactions between the Burau people and their surrounding environment. The population of the common carp black strain was isolated and cultured in a rice-fish integration system. To explore the genetic diversity and protection of germplasm resources, we analyzed mitochondrial DNA (mtDNA) sequences, specifically the displacement loop (D-loop) and cytochrome b (Cytb), using single-nucleotide polymorphisms (SNP). We compared these sequences with those from four other local common carp populations. The study included a total of 136 adult common carps from five strain populations: the common black carp strain (HJ = 31), Jian (F = 30), Heilongjiang (H = 10), Songpu (S = 31), and Saijiang (SJ = 34). The results of the Cytb and D-loop analyses showed that the Heilongjiang carp (H) and Saijiang (SJ) populations had the highest levels of haplotype diversity (0.867 ± 0.034785) and nucleotide diversity (π = 0.0063 ± 0.000137 and 0.0093 ± 0.000411), respectively. On the other hand, the Common carp black strain population (HJ) exhibited the lowest haplotype diversity in both Cytb and D-loop, with haplotype 2 being the most commonly observed among the populations. Private haplotypes dominated the five common carp populations, which were significantly different at P<0.001. Furthermore, analyzing the coefficient of genetic differentiation (Fst), the highest genetic difference was observed between Saijiang (SJ) and Heilongjiang (H) (Fst = 0.963), whereas the lowest was observed between Songpu (S) and the Common carp black strain population (HJ) (Fst = 0.019) for the Cytb gene sequences. For the D-loop, the Common carp black strain population (HJ) and Songpu (S) (Fst = 0.7) had the highest values, and Heilongjiang (H) and Common black carp strain (HJ) had an Fst of 0.125. Additionally, the AMOVA analysis revealed a higher level of variance for the Cytb and D-loop genes, indicating lower genetic diversity within the local carp community. On the other hand, the phylogenetic tree analysis showed that the five carp populations were closely related and formed a distinct cluster. The distinct cluster of populations suggests a common ancestor or recent gene flow, possibly due to geographic proximity or migration history, and unique genetic characteristics, possibly due to adaptations or selective pressures. The results of this study provide valuable insights into the genetic diversity of the common strain black carp, which can have implications for conservation, breeding programs, evolutionary studies, and fisheries management.
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Affiliation(s)
- Sahr Lamin Sumana
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China
| | - Peipei Wang
- Guangxi Fisheries Introduction and Cultivation Center, Nanning, PR China
| | - Chengfeng Zhang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China
| | - Xiaojun Jing
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, PR China
| | - Jian Zhu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, PR China
| | - Yongkai Tang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, PR China
| | - Wenting Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, PR China
| | - Shengyan Su
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, PR China
| | - Yu Liao
- Guangxi Fisheries Introduction and Cultivation Center, Nanning, PR China
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Dawood A, Shi W. Effect of dietary β-mannanase supplementation on growth performance, digestibility, and gene expression levels of Cyprinus carpio (Linnaeus) fingerlings fed a plant protein-rich diet. Front Vet Sci 2022; 9:956054. [PMID: 36118353 PMCID: PMC9480618 DOI: 10.3389/fvets.2022.956054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/05/2022] [Indexed: 11/23/2022] Open
Abstract
The aim of this study was to assess possible beneficial effects of dietary β-mannanase supplementation on the nutrient digestibility, growth performance, digestive and metabolic enzyme activity, and immune response of common carp (Cyprinus carpio) fed plant protein-rich diets. An experiment was conducted in triplicate, and a total of 225 fingerlings of common carp with an average body weight of 13.17 ± 0.12 g were stocked in 15 fiberglass tanks (15 fish/tank). Five dietary treatments (control 35% crude protein, plant-rich basal diet without supplement and four diets supplemented with β-mannanase from two sources (commercially available and locally isolated), each at two dosage levels (500 and 1,000 U/kg diet) were prepared and fed to respective groups of fish, twice a day (8:00 AM and 4:00 PM) at 4 % body weight. During the trial, changes in the level of DO and temperature ranged from 5.5 to 6.1 mg L-1 and 21.5 to 23.5°C, respectively. At the end of the feeding experiment, all fish in each tank were weighed and counted to determine growth parameters, while for the study of other indices, nine samples/treatment group were selected. The results of the study indicated a positive effect of both sources and dosage levels of β-mannanase supplementation on all studied indices, that is, significantly improved (P < 0.05), growth performance (%weight gain, specific growth rate), survival %, hematological indices (RBC, Hb, HCT, and MCHC), immunological indices (lysozyme activity, WBC, respiratory burst activity, and phagocytic activity), improved apparent digestibility of nutrients (crude protein, crude fat, and carbohydrates), and digestible energy. Furthermore, higher activity (P < 0.05) of the digestive enzymes (cellulase, lipase, and protease) and upregulation of MyoD gene in muscle and TNF-α gene in liver, intestine, and muscle were also observed, while the activity of serum AST (serum aspartate aminotransferase) and ALT (alanine transaminase) as compared to control group was significantly decreased (P < 0.05). Based on the results, β-mannanase supplementation (500 U/kg) could be recommended for obtaining better carp production when low-cost plant protein-rich diets are used.
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Affiliation(s)
- Aneesa Dawood
- Department of Zoology, Quaid-i-Azam University, Islamabad, Pakistan
- Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, United States
| | - Weibin Shi
- Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, United States
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Yáñez JM, Xu P, Carvalheiro R, Hayes B. Genomics applied to livestock and aquaculture breeding. Evol Appl 2022; 15:517-522. [PMID: 35505887 PMCID: PMC9046759 DOI: 10.1111/eva.13378] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- José M. Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias Universidad de Chile
| | - Peng Xu
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms College of Ocean and Earth Sciences Xiamen University Xiamen China
| | - Roberto Carvalheiro
- Departamento de Zootecnia Faculdade de Ciências Agrárias e Veterinárias UNESP – Univ Estadual Paulista Jaboticabal, São Paulo Brazil
- CSIRO Agriculture & Food Hobart Tasmania Australia
| | - Ben Hayes
- Centre for Animal Science Queensland Alliance for Agriculture and Food Innovation The University of Queensland Australia
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Emmenegger EJ, Bueren EK, Jia P, Hendrix N, Liu H. Comparative virulence of spring viremia of carp virus (SVCV) genotypes in two koi varieties. DISEASES OF AQUATIC ORGANISMS 2022; 148:95-112. [PMID: 35297379 DOI: 10.3354/dao03650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Spring viremia of carp virus (SVCV), is a lethal freshwater pathogen of cyprinid fish, and Cyprinus carpio koi is a primary host species. The virus was initially described in the 1960s after outbreaks occurred in Europe, but a global expansion of SVCV has been ongoing since the late 1990s. Genetic typing of SVCV isolates separates them into 4 genotypes that are correlated with geographic origin: Ia (Asia), Ib and Ic (Eastern Europe), and Id (Central Europe). We compared infectivity and virulence of 8 SVCV strains, including 4 uncharacterized Chinese Ia isolates and representatives of genotypes Ia-d in 2 morphologically distinct varieties of koi: long-fin semi-scaled Beni Kikokuryu koi and short-fin fully scaled Sanke koi. Mortality ranged from 4 to 82% in the Beni Kikokuryu koi and 0 to 94% in the Sanke koi following immersion challenge. Genotype Ia isolates of Asian origin had a wide range in virulence (0-94%). Single isolates representing the European genotypes Ib and Ic were moderately virulent (38-56%). Each virus strain produced similar levels of mortality in both koi breeds, with the exception of the SVCV Id strain that appeared to have both moderate and high virulence phenotypes (60% in Beni Kikokuryu koi vs. 87% in Sanke koi). Overall SVCV strain virulence appeared to be a dominant factor in determining disease outcomes, whereas intraspecies variation, based on koi variety, had less of an impact. This study is the first side-by-side comparison of Chinese SVCV isolates and genotype Ia-d strain virulence in a highly susceptible host.
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Kominakis A, Tarsani E, Hager-Theodorides AL, Mastranestasis I, Gkelia D, Hadjigeorgiou I. Genetic differentiation of mainland-island sheep of Greece: Implications for identifying candidate genes for long-term local adaptation. PLoS One 2021; 16:e0257461. [PMID: 34529728 PMCID: PMC8445479 DOI: 10.1371/journal.pone.0257461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 09/01/2021] [Indexed: 11/23/2022] Open
Abstract
In Greece, a number of local sheep breeds are raised in a wide range of ecological niches across the country. These breeds can be used for the identification of genetic variants that contribute to local adaptation. To this end, 50k genotypes of 90 local sheep from mainland Greece (Epirus, n = 35 and Peloponnesus, n = 55) were used, as well as 147 genotypes of sheep from insular Greece (Skyros, n = 21), Lemnos, n = 36 and Lesvos, n = 90). Principal components and phylogenetic analysis along with admixture and spatial point patterns analyses suggested genetic differentiation of 'mainland-island' populations. Genome scans for signatures of selection and genome-wide association analysis (GWAS) pointed to one highly differentiating marker on OAR4 (FST = 0.39, FLK = 21.93, FDR p-value = 0.10) that also displayed genome wide significance (FDR p-value = 0.002) during GWAS. A total number of 6 positional candidate genes (LOC106990429, ZNF804B, TEX47, STEAP4, SRI and ADAM22) were identified within 500 kb flanking regions around the significant marker. In addition, two QTLs related to fat tail deposition are reported in genomic regions 800 kb downstream the significant marker. Based on gene ontology analysis and literature evidence, the identified candidate genes possess biological functions relevant to local adaptation that worth further investigation.
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Affiliation(s)
- Antonios Kominakis
- Department of Animal Science, Agricultural University of Athens, Athens, Greece
| | - Eirini Tarsani
- Department of Animal Science, Agricultural University of Athens, Athens, Greece
| | | | | | - Dimitra Gkelia
- Association of Pastoral Farmers of Epirus, Ioannina, Greece
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Suurväli J, Whiteley AR, Zheng Y, Gharbi K, Leptin M, Wiehe T. The Laboratory Domestication of Zebrafish: From Diverse Populations to Inbred Substrains. Mol Biol Evol 2021; 37:1056-1069. [PMID: 31808937 PMCID: PMC7086173 DOI: 10.1093/molbev/msz289] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We know from human genetic studies that practically all aspects of biology are strongly influenced by the genetic background, as reflected in the advent of “personalized medicine.” Yet, with few exceptions, this is not taken into account when using laboratory populations as animal model systems for research in these fields. Laboratory strains of zebrafish (Danio rerio) are widely used for research in vertebrate developmental biology, behavior, and physiology, for modeling diseases, and for testing pharmaceutic compounds in vivo. However, all of these strains are derived from artificial bottleneck events and therefore are likely to represent only a fraction of the genetic diversity present within the species. Here, we use restriction site-associated DNA sequencing to genetically characterize wild populations of zebrafish from India, Nepal, and Bangladesh, and to compare them to previously published data on four common laboratory strains. We measured nucleotide diversity, heterozygosity, and allele frequency spectra, and find that wild zebrafish are much more diverse than laboratory strains. Further, in wild zebrafish, there is a clear signal of GC-biased gene conversion that is missing in laboratory strains. We also find that zebrafish populations in Nepal and Bangladesh are most distinct from all other strains studied, making them an attractive subject for future studies of zebrafish population genetics and molecular ecology. Finally, isolates of the same strains kept in different laboratories show a pattern of ongoing differentiation into genetically distinct substrains. Together, our findings broaden the basis for future genetic, physiological, pharmaceutic, and evolutionary studies in Danio rerio.
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Affiliation(s)
- Jaanus Suurväli
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Andrew R Whiteley
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, College of Forestry and Conservation, University of Montana, Missoula, MT
| | - Yichen Zheng
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom.,Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Maria Leptin
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Thomas Wiehe
- Institute for Genetics, University of Cologne, Cologne, Germany
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Nishihira T, Urabe M. Morphological and molecular studies of Eudiplozoon nipponicum (Goto, 1891) and Eudiplozoon kamegaii sp. n. (Monogenea; Diplozoidae). Folia Parasitol (Praha) 2020; 67. [PMID: 32764186 DOI: 10.14411/fp.2020.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 03/24/2020] [Indexed: 11/19/2022]
Abstract
Eudiplozoon nipponicum (Goto, 1891) Khotenovsky, 1985 (Monogenea: Diplozoidae), is known to parasitise Cyprinus carpio Linnaeus and species of Carassius. In this study, we conducted a taxonomic re-examination of E. nipponicum using genetic analysis and morphological comparisons from different host species from a single water system. rDNA nucleotide sequences of the internal transcription spacer 2 (ITS-2) region (645 bp) showed interspecific-level genetic differences among diplozoids from species of Carassius and C. carpio (p-distance: 3.1-4.0%) but no difference among those from different species of Carassius (0-0.4%) or between those from C. carpio collected in Asia and Europe (0-1.1%). Large variation was observed among 346 bp cytochrome c oxidase subunit I (COI) sequences (0.3-16.0 %); the topology of the phylogenetic tree showed no relationship to host genera or geographical regions of origin. Morphological observation showed that average clamp size of diplozoids from C. carpio was larger than those from Carassius spp. The number of folds on the hindbody was 10-25 for diplozoids from C. carpio and 12-19 for those from Carassius spp. Thus, our ITS-2 sequence and morphological comparison results indicate that diplozoids from C. carpio and species of Carassius belong to different species. The scientific name E. nipponicum should be applied to the species infected to the type host, Carassius sp. of Nakabo (2013) (Japanese name ginbuna). The diplozoid infecting C. carpio (Eurasian type) should be established as a new species: Eudiplozoon kamegaii sp. n. A neotype of E. nipponicum is designated in this report because the original E. nipponicum specimens are thought to have been lost.
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Affiliation(s)
- Tomoki Nishihira
- Division of Environmental Dynamics, Graduate School of Environmental Science, University of Shiga Prefecture, Hikone-City, Japan
| | - Misako Urabe
- School of Environmental Science, The University of Shiga Prefecture, Hikone-City, Japan
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