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Qin G, Qin Z, Lu C, Ye Z, Elaswad A, Jin Y, Khan MGQ, Su B, Dunham RA. Gene Editing of the Follicle-Stimulating Hormone Gene to Sterilize Channel Catfish, Ictalurus punctatus, Using a Modified Transcription Activator-like Effector Nuclease Technology with Electroporation. Biology 2023; 12:biology12030392. [PMID: 36979084 PMCID: PMC10044888 DOI: 10.3390/biology12030392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
Follicle-stimulating hormone (fsh) plays an important role in sexual maturation in catfish. Knocking out the fsh gene in the fish zygote should suppress the reproduction of channel catfish (Ictalurus punctatus). In this study, transcription activator-like effector nuclease (TALEN) plasmids targeting the fsh gene were electroporated into fertilized eggs with the standard double electroporation technique. Targeted fsh cleavage efficiency was 63.2% in P1fsh-knockout catfish. Ten of fifteen (66.7%) control pairs spawned, and their eggs had 32.3–74.3% average hatch rates in 2016 and 2017. Without hormone therapy, the spawning rates of P1 mutants ranged from 33.3 to 40.0%, with an average egg hatching rate of 0.75%. After confirmation of the low fertility of P1 mutants in 2016, human chorionic gonadotropin (HCG) hormone therapy improved the spawning rates by 80% for female mutants and 88.9% for male mutants, and the mean hatch rate was 35.0% for F1 embryos, similar to that of the controls (p > 0.05). Polymerase chain reaction (PCR) identification showed no potential TALEN plasmid integration into the P1 channel catfish genome. Neither the P1 nor the F1 mutant fish showed any noticeable changes in in body weight, survival rate, and hatching rate when the reproductive gene was knocked out. F1 families had a mean inheritance rate of 50.3%. The results brought us one step closer to allowing implementation of certain genetic techniques to aquaculture and fisheries management, while essentially eliminating the potential environment risk posed by transgenic, hybrid, and exotic fish as well as domestic fish.
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Ahammad AKS, Hasan NA, Bashar A, Haque MM, Abualreesh MH, Islam MM, Datta BK, Rabbi MF, Khan MGQ, Alam MS. Diallel Cross Application and Histomolecular Characterization: An Attempt to Develop Reference Stock of Labeo ariza. Biology 2022; 11:biology11050691. [PMID: 35625419 PMCID: PMC9138064 DOI: 10.3390/biology11050691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/20/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022]
Abstract
The objective of the present study was to evaluate the growth performance and genetic variation in diallel crosses of Ariza labeo (Labeo ariza) originating from three geographically separated rivers (Atrai, Jamuna and Kangsha) in Bangladesh. Intra (G1K♀K♂, G2J♀J♂, and G3A♀A♂) and inter (G4K♀A♂, G5K♀J♂, G6A♀K♂, G7A♀J♂, G8J♀K♂, and G9J♀A♂) stocks were produced following diallel cross (sex ratio—1:1 and n = 48; 16 from each river). Reproductive and growth performance, muscle cellularity and genetic variation following genotyping of eight microsatellite markers (Lr1, Lr2, Lr3, Lr22, Lr24, Lr27, Lr28 and Lr29) and analysis of all crossbreeds was performed. The fertilization (95% ± 2.11%), hatching (88% ± 1.03%), and survival rates (82% ± 1.88%) of G4K♀A♂ were higher compared to other groups. With respect to length and weight gains (2.67 ± 0.4 cm and 3.39 ± 0.2 g), SGR (3.23% ± 0.20%), and heterosis (8.87% and 24.74%) G4K♀A♂ was the superior group. A higher number of hyperplastic muscle fibers, mean number of alleles (2.75) and mean observed heterozygosity (0.417) from G4K♀A♂ could be interpreted to mean that G4K♀A♂ comprise better performance efficiency compared to others and are considered for continuing the L. ariza stock improvement program.
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Affiliation(s)
- A. K. Shakur Ahammad
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.M.I.); (B.K.D.); (M.F.R.); (M.G.Q.K.); (M.S.A.)
- Correspondence: ; Tel.: +880-171-959-9249
| | - Neaz A. Hasan
- Department of Aquaculture, Bangladesh Agricultural University, Mymensingh 2200, Bangladesh; (N.A.H.); (A.B.); (M.M.H.)
| | - Abul Bashar
- Department of Aquaculture, Bangladesh Agricultural University, Mymensingh 2200, Bangladesh; (N.A.H.); (A.B.); (M.M.H.)
| | - Mohammad Mahfujul Haque
- Department of Aquaculture, Bangladesh Agricultural University, Mymensingh 2200, Bangladesh; (N.A.H.); (A.B.); (M.M.H.)
| | - Muyassar H. Abualreesh
- Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah 22254, Saudi Arabia;
| | - Md. Mehefuzul Islam
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.M.I.); (B.K.D.); (M.F.R.); (M.G.Q.K.); (M.S.A.)
| | - Biraj Kumar Datta
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.M.I.); (B.K.D.); (M.F.R.); (M.G.Q.K.); (M.S.A.)
| | - Md. Fazla Rabbi
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.M.I.); (B.K.D.); (M.F.R.); (M.G.Q.K.); (M.S.A.)
| | - Mohd Golam Quader Khan
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.M.I.); (B.K.D.); (M.F.R.); (M.G.Q.K.); (M.S.A.)
| | - Md. Samsul Alam
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh; (M.M.I.); (B.K.D.); (M.F.R.); (M.G.Q.K.); (M.S.A.)
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Gautam S, Setu S, Khan MGQ, Khan MB. Analysis of the health, economic and environmental impacts of COVID-19: The Bangladesh perspective. Geosystems and Geoenvironment 2022. [PMCID: PMC8562041 DOI: 10.1016/j.geogeo.2021.100011] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Although COVID-19 has given an opportunity to the earth to restore her ecosystem, its role in bringing changes in every sector including social, economic, agricultural, industrial, education and health is enormous. The study was conducted to assess the socio-economic impacts of COVID-19 in Bangladesh by collecting data from different sources. The result depicted that during the first wave of COVID-19, the detection rate was less than 5%, exceeding almost 30% after detecting the deadlier Indian variant where 65% of the death is noticed by the people older than 50 years. Among all the frontline service providers during Covid, the highest rate of death was observed for doctors in Bangladesh. This study also discussed the impact of COVID-19 on mental health and found that women faced more depression and anxiety than men as well as 43% of children had subthreshold mental disturbances. Three-fourths of the adolescents have been distressed with household stress during the pandemic. Women and girls have encountered increased domestic violence whereas early marriages dropped out many rural girls from education. Decreasing remittance from non-residents and shutting down of RMG industry resulted loss of job and have badly affected economic section. Almost 20 million workers lost their jobs in Bangladesh from the informal sector. Moreover, the healthcare workers who have treated the corona virus patients have been socially stigmatized due to the fear of infection. Corona Virus has jeopardized the agriculture sector and 66% farmers (53% crop and vegetables, 99% fish farmers) got lower price than they used to get in a normal situation. Together with Government, non-government organizations, researchers, doctors, industrialists, international organization as well as individuals should come forward to handle this pandemic.
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Syaifudin M, Bekaert M, Taggart JB, Bartie KL, Wehner S, Palaiokostas C, Khan MGQ, Selly SLC, Hulata G, D'Cotta H, Baroiller JF, McAndrew BJ, Penman DJ. Species-Specific Marker Discovery in Tilapia. Sci Rep 2019; 9:13001. [PMID: 31506510 PMCID: PMC6737103 DOI: 10.1038/s41598-019-48339-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 07/22/2019] [Indexed: 11/12/2022] Open
Abstract
Tilapias (family Cichlidae) are of importance in aquaculture and fisheries. Hybridisation and introgression are common within tilapia genera but are difficult to analyse due to limited numbers of species-specific genetic markers. We tested the potential of double digested restriction-site associated DNA (ddRAD) sequencing for discovering single nucleotide polymorphism (SNP) markers to distinguish between 10 tilapia species. Analysis of ddRAD data revealed 1,371 shared SNPs in the de novo-based analysis and 1,204 SNPs in the reference-based analysis. Phylogenetic trees based on these two analyses were very similar. A total of 57 species-specific SNP markers were found among the samples analysed of the 10 tilapia species. Another set of 62 species-specific SNP markers was identified from a subset of four species which have often been involved in hybridisation in aquaculture: 13 for Oreochromis niloticus, 23 for O. aureus, 12 for O. mossambicus and 14 for O. u. hornorum. A panel of 24 SNPs was selected to distinguish among these four species and validated using 91 individuals. Larger numbers of SNP markers were found that could distinguish between the pairs of species within this subset. This technique offers potential for the investigation of hybridisation and introgression among tilapia species in aquaculture and in wild populations.
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Affiliation(s)
- Mochamad Syaifudin
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom.,Program Study of Aquaculture, Agriculture Faculty, Universitas Sriwijaya, South Sumatra, Indonesia
| | - Michaël Bekaert
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - John B Taggart
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - Kerry L Bartie
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - Stefanie Wehner
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom.,Max Planck Institute of Psychiatry, 80804, Munich, Germany
| | - Christos Palaiokostas
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - M G Q Khan
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom.,Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Sarah-Louise C Selly
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - Gideon Hulata
- Institute of Animal Science, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7505101, Israel
| | - Helena D'Cotta
- ISEM, Univ. Montpellier, CNRS, IRD, EPHE, Montpellier, France.,CIRAD, Campus Int. Baillarguet, 34398, Montpellier, France
| | - Jean-Francois Baroiller
- ISEM, Univ. Montpellier, CNRS, IRD, EPHE, Montpellier, France.,CIRAD, Campus Int. Baillarguet, 34398, Montpellier, France
| | - Brendan J McAndrew
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - David J Penman
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom.
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Abstract
Background: Hilsa shad (
Tenualosa ilisha), a widely distributed migratory fish, contributes substantially to the economy of Bangladesh. The harvest of hilsa from inland waters has been fluctuating due to anthropological and climate change-induced degradation of the riverine habitats. The whole genome sequence of this valuable fish could provide genomic tools for sustainable harvest, conservation and productivity cycle maintenance. Here, we report the first draft genome of
T. ilisha from the Bay of Bengal, the largest reservoir of the migratory fish. Methods: A live specimen of
T. ilisha was collected from the Bay of Bengal. The whole genome sequencing was performed by the Illumina HiSeqX platform (2 × 150 paired end configuration). We assembled the short reads using SOAPdenovo2 genome assembler and predicted protein coding genes by AUGUSTUS. The completeness of the
T. ilisha genome assembly was evaluated by BUSCO (Benchmarking Universal Single Copy Orthologs). We identified single nucleotide polymorphisms (SNPs) by calling them directly from unassembled sequence reads using discoSnp++. Results: We assembled the draft genome of 710.28 Mb having an N50 scaffold length of 64157 bp and GC content of 42.95%. A total of 37,450 protein coding genes were predicted of which 29,339 (78.34%) were annotated with other vertebrate genomes. We also identified 792,939 isolated SNPs with transversion:transition ratio of 1:1.8. The BUSCO evaluation showed 78.1% completeness of this genome. Conclusions: The genomic data generated in this study could be used as a reference to identify genes associated with physiological and ecological adaptations, population connectivity, and migration behaviour of this biologically and economically important anadromous fish species of the Clupeidae family.
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Affiliation(s)
- Md Bazlur Rahman Mollah
- Poultry Biotechnology and Genomics Laboratory, Department of Poultry Science, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Mohd Golam Quader Khan
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Md Shahidul Islam
- Department of Biotechnology, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Md Samsul Alam
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
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