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Yang YC, Chu PY, Chen CC, Yang WC, Hsu TH, Gong HY, Liao IC, Huang CW. Transcriptomic Insights and the Development of Microsatellite Markers to Assess Genetic Diversity in the Broodstock Management of Litopenaeus stylirostris. Animals (Basel) 2024; 14:1685. [PMID: 38891732 PMCID: PMC11171113 DOI: 10.3390/ani14111685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/22/2024] [Accepted: 06/02/2024] [Indexed: 06/21/2024] Open
Abstract
The Pacific blue shrimp (Litopenaeus stylirostris) is a premium product in the international seafood market. However, intensified farming has increased disease incidence and reduced genetic diversity. In this study, we developed a transcriptome database for L. stylirostris and mined microsatellite markers to analyze their genetic diversity. Using the Illumina HiSeq 4000 platform, we identified 53,263 unigenes from muscle, hepatopancreas, the intestine, and lymphoid tissues. Microsatellite analysis identified 36,415 markers from 18,657 unigenes, predominantly dinucleotide repeats. Functional annotation highlighted key disease resistance pathways and enriched categories. The screening and PCR testing of 42 transcriptome-based and 58 literature-based markers identified 40 with successful amplification. The genotyping of 200 broodstock samples revealed that Na, Ho, He, PIC, and FIS values were 3, 0.54 ± 0.05, 0.43 ± 0.09, 0.41 ± 0.22, and 0.17 ± 0.27, respectively, indicating moderate genetic variability and significant inbreeding. Four universal microsatellite markers (CL1472.Contig13, CL517.Contig2, Unigene5692, and Unigene7147) were identified for precise diversity analysis in Pacific blue, Pacific white (Litopenaeus vannamei), and black tiger shrimps (Penaeus monodon). The transcriptome database supports the development of markers and functional gene analysis for selective breeding programs. Our findings underscore the need for an appropriate genetic management system to mitigate inbreeding depression, reduce disease susceptibility, and preserve genetic diversity in farmed shrimp populations.
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Affiliation(s)
- Ya-Chi Yang
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan; (Y.-C.Y.); (P.-Y.C.); (C.-C.C.); (T.-H.H.); (H.-Y.G.)
| | - Pei-Yun Chu
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan; (Y.-C.Y.); (P.-Y.C.); (C.-C.C.); (T.-H.H.); (H.-Y.G.)
| | - Che-Chun Chen
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan; (Y.-C.Y.); (P.-Y.C.); (C.-C.C.); (T.-H.H.); (H.-Y.G.)
| | - Wen-Chin Yang
- Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Academia Sinica Road, Sec. 2, Nankang, Taipei 11529, Taiwan;
| | - Te-Hua Hsu
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan; (Y.-C.Y.); (P.-Y.C.); (C.-C.C.); (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan;
| | - Hong-Yi Gong
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan; (Y.-C.Y.); (P.-Y.C.); (C.-C.C.); (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan;
| | - I Chiu Liao
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan;
| | - Chang-Wen Huang
- Department of Aquaculture, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan; (Y.-C.Y.); (P.-Y.C.); (C.-C.C.); (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Beining Road, Jhongjheng District, Keelung City 20224, Taiwan;
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Chan S, Pan YJ, Lu A, Huang CW, Liao JL, Chang JS, Dur G. Establishing an astaxanthin-rich live feed strain of Pseudodiaptomus annandalei. Sci Rep 2024; 14:8671. [PMID: 38622162 PMCID: PMC11018791 DOI: 10.1038/s41598-024-59224-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/08/2024] [Indexed: 04/17/2024] Open
Abstract
This study aimed to establish an astaxanthin-rich strain of the calanoid copepod Pseudodiaptomus annandalei, through selective breeding based on RGB (red, green and blue) value, a parameter indicating color intensity. We evaluated the RGB value frequency distributions of the copepod populations, and selected individuals with the highest 10% and the lowest 10% RGB value over six generations. The RGB value, nauplii production, clutch interval and clutch number were assessed, and the genetic gain was calculated across generations (G0-G5). Two strains of copepods were selected and defined as dark body copepod strain (DBS) and light body copepod strain (LBS) at the end of experiment. Results revealed significantly lower RGB values (male: 121.5 ± 14.1; female: 108.8 ± 15) in the G5 DBS population compared to the G0 (male: 163.9 ± 13.1; female: 162.2 ± 14.6), with higher genetic gains of RGB values during G0 to G2. While DBS females exhibited longer clutch intervals in the G3 and G4, there was no significant difference in nauplii production between the two strains across all generations. Significantly higher astaxanthin content was found in the DBS copepods (0.04 μg/ ind.) compared to the LBS copepods (0.01 μg/ ind.) and the non-selective copepods (0.02 μg/ ind.) 20 months post selective breeding, validating the stability of the desired trait in the DBS strain. This study successfully established an astaxanthin-rich strain of P. annandalei, which provides implications for enhancing marine and brackish larviculture production.
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Affiliation(s)
- Sen Chan
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan, R.O.C
| | - Yen-Ju Pan
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan, R.O.C..
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan, R.O.C..
| | - Ang Lu
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan, R.O.C
| | - Chang-Wen Huang
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan, R.O.C
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan, R.O.C
| | - Ji-Long Liao
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan, R.O.C
| | - Jui-Sheng Chang
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan, R.O.C
| | - Gaël Dur
- Creative Science Unit (Geoscience), Faculty of Science, Shizuoka University, Shizuoka, Japan
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Lee JW, Shim I, Park K. Proposing Effective Ecotoxicity Test Species for Chemical Safety Assessment in East Asia: A Review. TOXICS 2023; 12:30. [PMID: 38250986 PMCID: PMC10819827 DOI: 10.3390/toxics12010030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024]
Abstract
East Asia leads the global chemical industry, but environmental chemical risk in these countries is an emerging concern. Despite this, only a few native species that are representative of East Asian environments are listed as test species in international guidelines compared with those native to Europe and America. This review suggests that Zacco platypus, Misgurnus anguillicaudatus, Hydrilla verticillata, Neocaridina denticulata spp., and Scenedesmus obliquus, all resident to East Asia, are promising test species for ecotoxicity tests. The utility of these five species in environmental risk assessment (ERA) varies depending on their individual traits and the state of ecotoxicity research, indicating a need for different applications of each species according to ERA objectives. Furthermore, the traits of these five species can complement each other when assessing chemical effects under diverse exposure scenarios, suggesting they can form a versatile battery for ERA. This review also analyzes recent trends in ecotoxicity studies and proposes emerging research issues, such as the application of alternative test methods, comparative studies using model species, the identification of specific markers for test species, and performance of toxicity tests under environmentally relevant conditions. The information provided on the utility of the five species and alternative issues in toxicity tests could assist in selecting test species suited to study objectives for more effective ERA.
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Affiliation(s)
- Jin Wuk Lee
- Research of Environmental Health, National Institute of Environmental Research, Incheon 404-708, Republic of Korea; (I.S.); (K.P.)
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Feng D, Gao X, Kong W, Wu Z, Yan C, Liu Y, Xing K, Sun Y, Zhang J. An extracellular Cu/Zn superoxide dismutase from Neocaridina denticulata sinensis: cDNA cloning, mRNA expression and characterizations of recombinant protein. FISH & SHELLFISH IMMUNOLOGY 2022; 128:547-556. [PMID: 35998869 DOI: 10.1016/j.fsi.2022.08.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
Neocaridina denticulata sinensis possesses characters of rapid growth, tenacious vitality, short growth cycle, transparent, and easy feeding. Therefore, it is gradually being developed into an animal model for basic research on decapod crustaceans. Herein, a Cu/Zn superoxide dismutase (Cu/Zn-SOD), named as Nd-ecCu/Zn-SOD, was identified and characterized from N. denticulata sinensis. The full-length cDNA sequence of Nd-ecCu/Zn-SOD is 829 bp containing a 684 bp open reading frame, which encodes a protein of 227 amino acid residues with a typical Sod_Cu domain. The quantitative real-time PCR analysis showed that Nd-ecCu/Zn-SOD mRNA was expressed in all the tested tissues. Under challenge with copper, the mRNA expression of Nd-ecCu/Zn-SOD reached the maximum at 6 h, and decreased until 24 h. After 24 h of exposure, its expression was up-regulated significantly at 36 h. After then its expression sharply decreased with a comeback at 48 h. The result indicated that Nd-ecCu/Zn-SOD might play an important role in the stress response of N. denticulata sinensis. The expression of Nd-ecCu/Zn-SOD in gills challenged with Vibrio parahaemolyticus changed in a time-dependent manner. Nd-ecCu/Zn-SOD was lowly expressed in early developmental stages by RNA-Seq technology, yet it showed that a cyclical rise and fall occurred between middle stages and late stages. In addition, Nd-ecCu/Zn-SOD was recombinantly expressed using E. coli and the recombinant protein was purified as a single band on SDS-PAGE. The recombinant Nd-ecCu/Zn-SOD (rNd-ecCu/Zn-SOD) existed enzymatic activity under a wide range of temperature and pH. The exposure of metal ions was found that Zn2+, Mg2+, Ca2+, Ba2+, and Cu2+ could inhibit the enzymatic activity of rNd-ecCu/Zn-SOD, and Mn2+ increased the enzymatic activity of rNd-ecCu/Zn-SOD. These results indicate that Nd-ecCu/Zn-SOD may play a pivotal role in resistant against oxidative damage and act as a biomarker under stressful environment.
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Affiliation(s)
- Dandan Feng
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China
| | - Xi Gao
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China
| | - Weihua Kong
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China
| | - Zixuan Wu
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China
| | - Congcong Yan
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China
| | - Yujie Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China
| | - Kefan Xing
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China
| | - Yuying Sun
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China; Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Hebei University, Baoding, 071002, China.
| | - Jiquan Zhang
- School of Life Sciences, Institute of Life Sciences and Green Development, Engineering Laboratory of Microbial Breeding and Preservation of Hebei Province, Hebei University, Baoding, 071002, China.
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Duan B, Mu S, Guan Y, Liu W, Kang T, Cheng Y, Li Z, Tian Y, Kang X. Development of Microsatellite Markers Based on Transcriptome Sequencing and Evaluation of Genetic Diversity in Swimming Crab (Portunus trituberculatus). Front Genet 2022; 13:932173. [PMID: 35923702 PMCID: PMC9340201 DOI: 10.3389/fgene.2022.932173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/16/2022] [Indexed: 12/02/2022] Open
Abstract
P. trituberculatus is an economically important mariculture species in China. Evaluating its genetic diversity and population structure can contribute to the exploration of germplasm resources and promote sustainable aquaculture production. In this study, a total of 246,243 SSRs were generated by transcriptome sequencing of P. trituberculatus. Among the examined 254,746 unigenes, 66,331 had more than one SSR. Among the different SSR motif types, dinucleotide repeats (110,758, 44.98%) were the most abundant. In 173 different base repeats, A/T (96.86%), AC/GT (51.46%), and ACC/GGT (26.20%) were dominant in mono-, di-, and trinucleotide, respectively. GO annotations showed 87,079 unigenes in 57 GO terms. Cellular process, cell, and binding were the most abundant terms in biological process, cellular component, and molecular function categories separately. A total of 34,406 annotated unigenes were classified into 26 functional categories according to the functional annotation analysis of KOG, of which “general function prediction only” was the biggest category (6,028 unigenes, 17.52%). KEGG pathway annotations revealed the clustering of 34,715 unigenes into 32 different pathways. Nineteen SSRs were identified as polymorphic and, thus, used to assess the genetic diversity and structure of 240 P. trituberculatus individuals from four populations in the Bohai Sea. Genetic parameter analysis showed a similar level of genetic diversity within wild populations, and the cultured population indicated a reduction in genetic diversity compared with wild populations. The pairwise FST values were between 0.001 and 0.04 with an average of 0.0205 (p < 0.05), suggesting a low but significant level of genetic differentiation among the four populations. Structure analysis demonstrated that the four populations were classified into two groups including the cultured group and other populations. The phylogenetic tree and PCA revealed that a vast number of samples were clustered together and that cultivated individuals were distributed more centrally than wild individuals. The findings contribute to the further assessment of germplasm resources and assist to provide valuable SSRs for marker-assisted breeding of P. trituberculatus in the future.
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Affiliation(s)
- Baohua Duan
- College of Life Sciences, Hebei University, Baoding, China
| | - Shumei Mu
- College of Life Sciences, Hebei University, Baoding, China
| | - Yueqiang Guan
- College of Life Sciences, Hebei University, Baoding, China
| | - Weibiao Liu
- College of Life Sciences, Hebei University, Baoding, China
| | - Tongxu Kang
- College of Life Sciences, Hebei University, Baoding, China
| | - Yana Cheng
- College of Life Sciences, Hebei University, Baoding, China
| | - Zejian Li
- Bureau of Agricultural and Rural Affairs of Huanghua City, Huanghua, China
| | - Yang Tian
- Hebei Fishery Technology Extension Station, Shijiazhuang, China
| | - Xianjiang Kang
- College of Life Sciences, Hebei University, Baoding, China
- Institute of Life Science and Green Development, Hebei University, Baoding, China
- Hebei Innovation Center for Bioengineering and Biotechnology, Hebei University, Baoding, China
- *Correspondence: Xianjiang Kang,
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Genome-Wide Survey and Development of the First Microsatellite Markers Database ( AnCorDB) in Anemone coronaria L. Int J Mol Sci 2022; 23:ijms23063126. [PMID: 35328546 PMCID: PMC8949970 DOI: 10.3390/ijms23063126] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 12/31/2022] Open
Abstract
Anemone coronaria L. (2n = 2x = 16) is a perennial, allogamous, highly heterozygous plant marketed as a cut flower or in gardens. Due to its large genome size, limited efforts have been made in order to develop species-specific molecular markers. We obtained the first draft genome of the species by Illumina sequencing an androgenetic haploid plant of the commercial line “MISTRAL® Magenta”. The genome assembly was obtained by applying the MEGAHIT pipeline and consisted of 2 × 106 scaffolds. The SciRoKo SSR (Simple Sequence Repeats)-search module identified 401.822 perfect and 188.987 imperfect microsatellites motifs. Following, we developed a user-friendly “Anemone coronaria Microsatellite DataBase” (AnCorDB), which incorporates the Primer3 script, making it possible to design couples of primers for downstream application of the identified SSR markers. Eight genotypes belonging to eight cultivars were used to validate 62 SSRs and a subset of markers was applied for fingerprinting each cultivar, as well as to assess their intra-cultivar variability. The newly developed microsatellite markers will find application in Breeding Rights disputes, developing genetic maps, marker assisted breeding (MAS) strategies, as well as phylogenetic studies.
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Klein K, Heß S, Nungeß S, Schulte-Oehlmann U, Oehlmann J. Particle shape does not affect ingestion and egestion of microplastics by the freshwater shrimp Neocaridina palmata. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:62246-62254. [PMID: 34189691 PMCID: PMC8589796 DOI: 10.1007/s11356-021-15068-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/18/2021] [Indexed: 06/01/2023]
Abstract
The ingestion of microplastics (MPs) is well documented for various animals and spherical MPs (beads) in many studies. However, the retention time and egestion of MPs have been examined less, especially for irregular MPs (fragments) which are predominantly found in the environment. Furthermore, the accumulation of such particles in the gastrointestinal tract is likely to determine whether adverse effects are induced. To address this, we investigated if the ingestion and egestion of beads are different to those of fragments in the freshwater shrimp Neocaridina palmata. Therefore, organisms were exposed to 20-20,000 particles L-1 of either polyethylene (PE) beads (41 μm and 87 μm) or polyvinyl chloride (PVC) fragments (<63 μm). Moreover, shrimps were exposed to 20,000 particles L-1 of either 41 μm PE and 11 μm polystyrene (PS) beads or the PVC fragments for 24 h, followed by a post-exposure period of 4 h to analyze the excretion of particles. To simulate natural conditions, an additional fragment ingestion study was performed in the presence of food. After each treatment, the shrimps were analyzed for retained or excreted particles. Our results demonstrate that the ingestion of beads and fragments were concentration-dependent. Shrimps egested 59% of beads and 18% of fragments within 4 h. Particle shape did not significantly affect MP ingestion or egestion, but size was a relevant factor. Medium- and small-sized beads were frequently ingested. Furthermore, fragment uptake decreased slightly when co-exposed to food, but was not significantly different to the treatments without food. Finally, the investigations highlight that the assessment of ingestion and egestion rates can help to clarify whether MPs remain in specific organisms and, thereby, become a potential health threat.
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Affiliation(s)
- Kristina Klein
- Faculty of Biological Sciences, Department Aquatic Ecotoxicology, Goethe University Frankfurt, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany.
| | - Sebastian Heß
- Faculty of Biological Sciences, Department Aquatic Ecotoxicology, Goethe University Frankfurt, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany
| | - Sandra Nungeß
- Faculty of Biological Sciences, Department Aquatic Ecotoxicology, Goethe University Frankfurt, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany
| | - Ulrike Schulte-Oehlmann
- Faculty of Biological Sciences, Department Aquatic Ecotoxicology, Goethe University Frankfurt, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany
| | - Jörg Oehlmann
- Faculty of Biological Sciences, Department Aquatic Ecotoxicology, Goethe University Frankfurt, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany
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Salgotra RK, Thompson M, Chauhan BS. Unravelling the genetic potential of untapped crop wild genetic resources for crop improvement. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01242-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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He Z, Zhao J, Chen X, Liao M, Xue Y, Zhou J, Chen H, Chen G, Zhang S, Sun C. The Molecular Mechanism of Hemocyte Immune Response in Marsupenaeus japonicus Infected With Decapod Iridescent Virus 1. Front Microbiol 2021; 12:710845. [PMID: 34512588 PMCID: PMC8427283 DOI: 10.3389/fmicb.2021.710845] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
As a new type of shrimp lethal virus, decapod iridescent virus 1 (DIV1) has caused huge economic losses to shrimp farmers in China. Up to now, DIV1 has been detected in a variety of shrimps, but there is no report in Marsupenaeus japonicus. In the current study, we calculated the LC50 to evaluate the toxicity of DIV1 to M. japonicus and determined through nested PCR that M. japonicus can be the host of DIV1. Through enzyme activity study, it was found that DIV1 can inhibit the activities of superoxide dismutase, catalase, lysozyme, and phenoloxidase, which could be a way for DIV1 to achieve immune evasion. In a comprehensive study on the transcriptomic changes of M. japonicus in response to DIV1 infection, a total of 52,287 unigenes were de novo assembled, and 20,342 SSR markers associated with these unigenes were obtained. Through a comparative transcriptomic analysis, 6,900 differentially expressed genes were identified, including 3,882 upregulated genes and 3,018 downregulated genes. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that some GO terms related to virus invasion, replication, and host antiviral infection were promoted under DIV1 infection, such as carbohydrate binding, chitin binding, chitin metabolic process, and DNA replication initiation, and some KEGG pathways related to immune response were significantly influenced by DIV1 infection, including Toll and IMD signaling pathway, JAK-STAT signaling pathway, IL-17 signaling pathway, C-type lectin receptor signaling pathway, complement and coagulation cascades, antigen processing and presentation, necroptosis, apoptosis, NOD-like receptor signaling pathway, apoptosis-multiple species, and TNF signaling pathway. Further analysis showed that STAT, Dorsal, Relish, heat shock protein 70 (HSP70), C-type lectins, and caspase play an important role in DIV1 infection. This is the first detailed study of DIV1 infection in M. japonicus, which initially reveals the molecular mechanism of DIV1 infection in M. japonicus by using the transcriptome analysis of hemocytes combined with enzyme activity study.
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Affiliation(s)
- Zihao He
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Jichen Zhao
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Xieyan Chen
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Minze Liao
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Yuan Xue
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Jianing Zhou
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Haozhen Chen
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China
| | - Guoliang Chen
- Haimao Seed Technology Group Co., Ltd., Zhanjiang, China
| | - Shuang Zhang
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Aquatic Animals Precision Nutrition and High Efficiency Feed Engineering Research Center of Guangdong Province, Zhanjiang, China
| | - Chengbo Sun
- College of Fisheries, Guangdong Ocean University, Zhanjiang, China.,Guangdong Provincial Laboratory of Southern Marine Science and Engineering, Zhanjiang, China.,Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, China
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All Shades of Shrimp: Preferences of Colour Morphs of a Freshwater Shrimp Neocaridina davidi (Decapoda, Atyidae) for Substrata of Different Colouration. Animals (Basel) 2021; 11:ani11041071. [PMID: 33918889 PMCID: PMC8069546 DOI: 10.3390/ani11041071] [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: 02/17/2021] [Revised: 04/01/2021] [Accepted: 04/07/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Examination of preferences of an aquarium “Red Cherry” shrimp for differently coloured backgrounds revealed common traits, irrespective of shrimp body colouration. The shrimp selected dark backgrounds and coarse patterns over light and fine patterned substrata. Thus, the use of materials with dark and uniform colouration can contribute to designing proper monitoring tools to detect biological invasions after releasing this pet into the wild, as well as to provide shrimp with comfortable conditions in captivity. Abstract An ornamental freshwater shrimp, Neocaridina davidi, is popular as an aquarium hobby and, therefore, a potentially invasive species. There is a growing need for proper management of this species to determine not only their optimum breeding conditions, but also their ability to colonise novel environments. We tested habitat preferences of colour morphs (brown, red, white) of N. davidi for substratum colour (black, white, grey shades, red) and fine or coarse chess-board patterns to recognise their suitable captivity conditions and predict their distribution after potential release into nature. We conducted laboratory choice experiments (n = 8) with three individuals of the same morph exposed for two hours to a range of backgrounds. Shrimp preferred dark backgrounds over light ones irrespective of their own colouration and its match with the background colour. Moreover, the brown and red morphs, in contrast to the white morph, preferred the coarse background pattern over the finer pattern. This suggests that the presence of dark, uniform substrata (e.g., rocks, macrophytes) will favour N. davidi. Nevertheless, the polymorphism of the species has little effect on its total niche breadth, and thus its invasive potential.
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Siregar P, Suryanto ME, Chen KHC, Huang JC, Chen HM, Kurnia KA, Santoso F, Hussain A, Ngoc Hieu BT, Saputra F, Audira G, Roldan MJM, Fernandez RA, Macabeo APG, Lai HT, Hsiao CD. Exploiting the Freshwater Shrimp Neocaridina denticulata as Aquatic Invertebrate Model to Evaluate Nontargeted Pesticide Induced Toxicity by Investigating Physiologic and Biochemical Parameters. Antioxidants (Basel) 2021; 10:391. [PMID: 33807713 PMCID: PMC7999401 DOI: 10.3390/antiox10030391] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/27/2021] [Accepted: 03/02/2021] [Indexed: 12/21/2022] Open
Abstract
As a nicotinoid neurotoxic insecticide, imidacloprid (IMI) works by disrupting nerve transmission via nicotinic acetylcholine receptor (nAChR). Although IMI is specifically targeting insects, nontarget animals such as the freshwater shrimp, Neocaridina denticulata, could also be affected, thus causing adverse effects on the aquatic environment. To investigate IMI toxicity on nontarget organisms like N. denticulata, their physiology (locomotor activity, heartbeat, and gill ventilation) and biochemical factors (oxidative stress, energy metabolism) after IMI exposure were examined. IMI exposure at various concentrations (0.03125, 0.0625, 0.125, 0.25, 0.5, and 1 ppm) to shrimp after 24, 48, 72 h led to dramatic reduction of locomotor activity even at low concentrations. Meanwhile, IMI exposure after 92 h caused reduced heartbeat and gill ventilation at high concentrations. Biochemical assays were performed to investigate oxidative stress and energy metabolism. Interestingly, locomotion immobilization and cardiac activity were rescued after acetylcholine administration. Through molecular docking, IMI demonstrated high binding affinity to nAChR. Thus, locomotor activity and heartbeat in shrimp after IMI exposure may be caused by nAChR blockade and not alterations caused by oxidative stress and energy metabolism. To summarize, N. denticulata serves as an excellent and sensitive aquatic invertebrate model to conduct pesticide toxicity assays that encompass physiologic and biochemical examinations.
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Affiliation(s)
- Petrus Siregar
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 320314, Taiwan; (P.S.); (B.T.N.H.); (G.A.)
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 320314, Taiwan; (M.E.S.); (K.A.K.); (F.S.); (A.H.); (F.S.)
| | - Michael Edbert Suryanto
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 320314, Taiwan; (M.E.S.); (K.A.K.); (F.S.); (A.H.); (F.S.)
| | - Kelvin H.-C. Chen
- Department of Applied Chemistry, National Pingtung University, Pingtung 900391, Taiwan; (K.H.-C.C.); (J.-C.H.)
| | - Jong-Chin Huang
- Department of Applied Chemistry, National Pingtung University, Pingtung 900391, Taiwan; (K.H.-C.C.); (J.-C.H.)
| | - Hong-Ming Chen
- Department of Aquatic Biosciences, National Chiayi University, 300 University Rd., Chiayi 60004, Taiwan;
| | - Kevin Adi Kurnia
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 320314, Taiwan; (M.E.S.); (K.A.K.); (F.S.); (A.H.); (F.S.)
| | - Fiorency Santoso
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 320314, Taiwan; (M.E.S.); (K.A.K.); (F.S.); (A.H.); (F.S.)
| | - Akhlaq Hussain
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 320314, Taiwan; (M.E.S.); (K.A.K.); (F.S.); (A.H.); (F.S.)
| | - Bui Thi Ngoc Hieu
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 320314, Taiwan; (P.S.); (B.T.N.H.); (G.A.)
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 320314, Taiwan; (M.E.S.); (K.A.K.); (F.S.); (A.H.); (F.S.)
| | - Ferry Saputra
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 320314, Taiwan; (M.E.S.); (K.A.K.); (F.S.); (A.H.); (F.S.)
| | - Gilbert Audira
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 320314, Taiwan; (P.S.); (B.T.N.H.); (G.A.)
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 320314, Taiwan; (M.E.S.); (K.A.K.); (F.S.); (A.H.); (F.S.)
| | - Marri Jmelou M. Roldan
- Faculty of Pharmacy and The Graduate School, University of Santo Tomas, Manila 1008, Philippines;
| | - Rey Arturo Fernandez
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila 1008, Philippines;
| | - Allan Patrick G. Macabeo
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila 1008, Philippines;
| | - Hong-Thih Lai
- Department of Aquatic Biosciences, National Chiayi University, 300 University Rd., Chiayi 60004, Taiwan;
| | - Chung-Der Hsiao
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 320314, Taiwan; (P.S.); (B.T.N.H.); (G.A.)
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 320314, Taiwan; (M.E.S.); (K.A.K.); (F.S.); (A.H.); (F.S.)
- Center for Nanotechnology, Chung Yuan Christian University, Chung-Li 320314, Taiwan
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Salgotra RK, Stewart CN. Functional Markers for Precision Plant Breeding. Int J Mol Sci 2020; 21:E4792. [PMID: 32640763 PMCID: PMC7370099 DOI: 10.3390/ijms21134792] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/19/2020] [Accepted: 07/02/2020] [Indexed: 01/24/2023] Open
Abstract
Advances in molecular biology including genomics, high-throughput sequencing, and genome editing enable increasingly faster and more precise cultivar development. Identifying genes and functional markers (FMs) that are highly associated with plant phenotypic variation is a grand challenge. Functional genomics approaches such as transcriptomics, targeting induced local lesions in genomes (TILLING), homologous recombinant (HR), association mapping, and allele mining are all strategies to identify FMs for breeding goals, such as agronomic traits and biotic and abiotic stress resistance. The advantage of FMs over other markers used in plant breeding is the close genomic association of an FM with a phenotype. Thereby, FMs may facilitate the direct selection of genes associated with phenotypic traits, which serves to increase selection efficiencies to develop varieties. Herein, we review the latest methods in FM development and how FMs are being used in precision breeding for agronomic and quality traits as well as in breeding for biotic and abiotic stress resistance using marker assisted selection (MAS) methods. In summary, this article describes the use of FMs in breeding for development of elite crop cultivars to enhance global food security goals.
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Affiliation(s)
- Romesh K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Chatha, Jammu 190008, India
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
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