Aquaculture,a critical sector for global food security,faces the challenge of meeting growing demand while protecting wild fish populations.Gene editing,a powerful genetic tool,emerges as a potential solution.By modif...Aquaculture,a critical sector for global food security,faces the challenge of meeting growing demand while protecting wild fish populations.Gene editing,a powerful genetic tool,emerges as a potential solution.By modifying key genes in fish,it is expected to rapidly enhance growth rate,disease resistance,and other economically important traits,leading to increased profitability,sustainability,and competitiveness of the industry.This review navigates the complex landscape of genes for important traits,gene editing in aquaculture,exploring successes,challenges,and prospects for improved productivity,sustainability,and resilience.We provide guidance for researchers and stakeholders in identifying and editing genes responsible for important traits,while addressing economic,environmental,regulatory,and ethical considerations.This roadmap paves the way for a future where gene editing empowers aquaculture to meet global food needs while upholding environmental responsibility.展开更多
This study investigates the relationship between polymorphisms in the cathepsin B(ctsb)gene and body weight in Asian seabass(Lates calcarifer).Despite the economic significance of this species,the genetic factors that...This study investigates the relationship between polymorphisms in the cathepsin B(ctsb)gene and body weight in Asian seabass(Lates calcarifer).Despite the economic significance of this species,the genetic factors that influence growth performance in fish remain poorly understood.CTSB,a lysosomal cysteine protease involved in protein degradation and tissue remodelling,is a crucial regulator of growth.We analysed the full-length cDNA of ctsb and mapped it to the major quantitative trait locus(QTL)for growth on linkage group 2 in L.calcarifer.Single nucleotide polymorphisms(SNPs)within ctsb were identified and their associations with body weight were analysed in 298 individuals.Results revealed that SNP1(C>T)in intron 2 of ctsb was significantly correlated with body weight.Quantitative real-time PCR(qRT-PCR)showed that ctsb was expressed in all tissues,with the highest expression in the gills and kidney of developing seabass.Knockdown/overexpression of ctsb in cell lines respectively promoted/inhibited cell proliferation without altering cell size.These findings suggest that ctsb plays a significant role in growth regulation in Asian seabass.This study provides a potential molecular marker for selecting fast-growing Asian seabass.Future research should focus on identifying causal variants in ctsb associated with accelerated growth,conducting in vivo studies,and exploring related signalling pathways.展开更多
Viral nervous necrosis(VNN)disease,caused by the nervous necrosis virus(NNV),is a devastating disease,leading to high mortality rate and huge economical loss in aquaculture.In the past 30 years,many studies on the vir...Viral nervous necrosis(VNN)disease,caused by the nervous necrosis virus(NNV),is a devastating disease,leading to high mortality rate and huge economical loss in aquaculture.In the past 30 years,many studies on the virus,host responses to the virus infection and diagnostics have yielded a lot of knowledge on developing measures to prevent the VNN disease.Although genetic improvement of disease resistance through breeding is inheritable and has long-lasting positive effect on aquaculture,it is a very challenging task in conventional selective breeding for improving disease resistance.With the advances in mapping quantitative trait loci(QTL)and genome wide association studies(GWAS)for NNV resistance in aquaculture species,DNA markers and genes associated with NNV resistance have been identified,making the application of marker-assisted selection(MAS)and genomic selection(GS)for NNV resistance possible.A few genes for NNV resistance are identified and are being used for genome editing to rapidly improve NNV resistance.In this review,we present the current knowledge on the NNV,host responses to NNV infection,diagnostic methods and vaccines available for NNV disease.In addition,we summarize the current status of conventional and molecular breeding for NNV resistance and highlight future directions,including genome editing for improving NNV resistance in aquaculture.展开更多
Iridoviruses are DNA virus and have caused huge economic losses in the aquaculture industry.The aim of this study was to establish a colorimetric loop-mediated isothermal amplification(LAMP)protocol for the on-site de...Iridoviruses are DNA virus and have caused huge economic losses in the aquaculture industry.The aim of this study was to establish a colorimetric loop-mediated isothermal amplification(LAMP)protocol for the on-site detection of Singapore grouper iridovirus(SGIV).The SGIV-VP61 gene was chosen as the target gene to develop a colorimetric LAMP assay.The optimized condition of the colorimetric LAMP assay was incubation at 63℃ for 1 h.Samples infected with SGIV could be detected with the color change from yellow into pink.The sensitivity of the developed assay is 5.66 copies/μL of the viral DNA template.This sensitivity was about 1000 times higher than that of conventional PCR while it was slightly lower than the one-step semi-nested PCR assay.A total of 60 DNA samples extracted from the fin tissue of the SGIV-infected Asian seabass were examined for SGIV by colorimetric LAMP,semi-nested PCR and conventional PCR.The results of the colorimetric LAMP assay showed 94.87%agreement with the semi-nested PCR.In addition,the DNA extraction method using NaOH showed a better performance in the colorimetric LAMP assay.Taken together,the colorimetric LAMP established was a sensitive,rapid and specific method for the detection of SGIV.SGIV was not detected in samples randomly taken from a genetically improved line of the Asian seabass.However,some seabass obtained from the local markets were found to contain SGIV.Thus,the LAMP assay has the potential application in the diagnosis of iridovirus diseases in the aquaculture industry.展开更多
Asian seabass(Lates calcarifer)is an important foodfish species.It has been cultured in Singapore since the 1980s.A selective breeding program to improve growth,meat quality and disease resistance has been ongoing in ...Asian seabass(Lates calcarifer)is an important foodfish species.It has been cultured in Singapore since the 1980s.A selective breeding program to improve growth,meat quality and disease resistance has been ongoing in Singapore since 2004.In 2012,outbreaks of the big belly disease(BBD)occurred in two batches of offspring generated by a mass-cross among F1 brooders in a hatchery.After the outbreaks,only 437 survived in 6000 F2 juveniles.Molecular parentage analysis with 10 microsatellites revealed that four parents(F1)produced high percentage of offspring that survived the BBD outbreaks.Eighty-two BBD survivor offspring(F2)were selected based on their growth performance at 90 days post hatch(dph),family origin and allelic diversity.They were used as brooders to generate F3.In a period of five years,these F2 brooders produced six batches of offspring,where no outbreak of BBD occurred.In the same period,outbreaks of BBD occurred in 4 out of 18 batches produced by F2 brooders selected for growth,with mortality rates ranging from 85.1%to 95.4%.In F3,the average body weight(57.1±1.09 g,n=3068)of the line for BBD survival was slightly lower than that(60.6±2.29 g,n=4280)of the line for growth at 90 dph.In both lines,the body weight of F3 was much higher than that(46.90±0.19 g,n=12117)of F2.The genetic diversity in the line for BBD survival(F3)was much lower than that in F3 line for growth due to small founder population.These data indicate that the selection of BBD survival during BBD outbreaks using molecular parentage analysis is effective to reduce BBD outbreaks.Avoiding further reduction of genetic diversity is essential in the line selected for increased survival against BBD.展开更多
Chia(Salvia hispanica)is a functional food crop for humans.Although its seeds contain high omega-3 fatty acids,the seed yield of chia is still low.Genomic resources available for this plant are limited.We report the f...Chia(Salvia hispanica)is a functional food crop for humans.Although its seeds contain high omega-3 fatty acids,the seed yield of chia is still low.Genomic resources available for this plant are limited.We report the first high-quality chromosome-level genome sequence of chia.The assembled genome size was 347.6 Mb and covered 98.1%of the estimated genome size.A total of 31069 protein-coding genes were predicted.The absence of recent whole-genome duplication and the relatively low intensity of transposable element expansion in chia compared to its sister species contribute to its small genome size.Transcriptome sequencing and gene duplication analysis reveal that the expansion of the fab2 gene family is likely to be related to the high content of omega-3 in seeds.The white seed coat color is determined by a single locus on chromosome 4.This study provides novel insights into the evolution of Salvia species and high omega-3 content,as well as valuable genomic resources for genetic improvement of important commercial traits of chia and its related species.展开更多
Simvastatin(SIM),a commonly prescribed drug for lowering serum-lipid,has been detected in many aquatic environments.Exposure to high concentrations of SIM in rats and aquatic organisms resulted in toxicity to hepatocy...Simvastatin(SIM),a commonly prescribed drug for lowering serum-lipid,has been detected in many aquatic environments.Exposure to high concentrations of SIM in rats and aquatic organisms resulted in toxicity to hepatocytes and negative effects on development.However,there is a paucity of studies on the effects of long-term exposure to low concentrations of SIM on aquaculture species.This study aimed to analyze the effects of environmentally relevant concentrations(0.1μg/L and 1μg/L)of SIM exposure for two months on developing Mozambique tilapias.Surprisingly,the growth of male tilapias was enhanced after a 2-month SIM exposure.The analysis of testis histology revealed that after the SIM exposure,the development of the testis was delayed,and sperm production was reduced.Sequencing of testis transcriptomes showed that the exposure to SIM altered the expression of many genes related to the development of testes and spermatogenesis.These data suggest that a 2-month exposure to environmentally relevant concentrations of increases the growth of male tilapias by inhibiting sexual development of males.展开更多
Viral nervous necrosis(VNN)caused by a betanodavirus(NNV)is one of the major diseases in Asian seabass(Lates calcarifer)hatcheries.Our previous studies showed that the tbx21 gene was in a QTL for NNV resistance in lin...Viral nervous necrosis(VNN)caused by a betanodavirus(NNV)is one of the major diseases in Asian seabass(Lates calcarifer)hatcheries.Our previous studies showed that the tbx21 gene was in a QTL for NNV resistance in linkage group 23 in Asian seabass.The expression of this gene was changed in tissues of Asian seabass challenged with NNV.However,the role of tbx21 in NNV resistance remains largely unknown.In this study,tbx21 of Asian seabass was characterized.This gene consists of an ORF of 1866 bp,a 5′UTR of 357 bp,and a 3′UTR of 4674 bp.The TBX21 protein showed substantial amino acid similarity(70-96%)with other fish but exhibited lower identity(47-52%)with mammals.One SNP identified in the first intron was significantly associated with NNV resistance.In healthy fish,tbx21 was expressed in all tissues examined,and was highly expressed in the kidney and liver.The expression of tbx21 increased in the eye,gills,heart,kidney and gut,but decreased in the brain and spleen at five days after NNV challenge.Overexpression of tbx21 reduced the replication of NNV,whereas knockdown increased viral expression and virus titers.These results suggest that tbx21 plays a key role in NNV resistance.The SNP in this gene could be used as a marker to facilitate marker-assisted selection for NNV resistance.Further investigation of polymorphisms in the 5’and 3’UTRs of tbx21 may provide additional insights into the gene's role in NNV resistance.展开更多
文摘Aquaculture,a critical sector for global food security,faces the challenge of meeting growing demand while protecting wild fish populations.Gene editing,a powerful genetic tool,emerges as a potential solution.By modifying key genes in fish,it is expected to rapidly enhance growth rate,disease resistance,and other economically important traits,leading to increased profitability,sustainability,and competitiveness of the industry.This review navigates the complex landscape of genes for important traits,gene editing in aquaculture,exploring successes,challenges,and prospects for improved productivity,sustainability,and resilience.We provide guidance for researchers and stakeholders in identifying and editing genes responsible for important traits,while addressing economic,environmental,regulatory,and ethical considerations.This roadmap paves the way for a future where gene editing empowers aquaculture to meet global food needs while upholding environmental responsibility.
基金supported by the Internal Funds of the Temasek Life Sciences Laboratory(5020),Singapore.
文摘This study investigates the relationship between polymorphisms in the cathepsin B(ctsb)gene and body weight in Asian seabass(Lates calcarifer).Despite the economic significance of this species,the genetic factors that influence growth performance in fish remain poorly understood.CTSB,a lysosomal cysteine protease involved in protein degradation and tissue remodelling,is a crucial regulator of growth.We analysed the full-length cDNA of ctsb and mapped it to the major quantitative trait locus(QTL)for growth on linkage group 2 in L.calcarifer.Single nucleotide polymorphisms(SNPs)within ctsb were identified and their associations with body weight were analysed in 298 individuals.Results revealed that SNP1(C>T)in intron 2 of ctsb was significantly correlated with body weight.Quantitative real-time PCR(qRT-PCR)showed that ctsb was expressed in all tissues,with the highest expression in the gills and kidney of developing seabass.Knockdown/overexpression of ctsb in cell lines respectively promoted/inhibited cell proliferation without altering cell size.These findings suggest that ctsb plays a significant role in growth regulation in Asian seabass.This study provides a potential molecular marker for selecting fast-growing Asian seabass.Future research should focus on identifying causal variants in ctsb associated with accelerated growth,conducting in vivo studies,and exploring related signalling pathways.
基金This study was supported by the internal fund of the Temasek Life Sciences Laboratory,Singapore and a graduate research scholarship from Tropical Marine Science Institute,National University of Singapore.
文摘Viral nervous necrosis(VNN)disease,caused by the nervous necrosis virus(NNV),is a devastating disease,leading to high mortality rate and huge economical loss in aquaculture.In the past 30 years,many studies on the virus,host responses to the virus infection and diagnostics have yielded a lot of knowledge on developing measures to prevent the VNN disease.Although genetic improvement of disease resistance through breeding is inheritable and has long-lasting positive effect on aquaculture,it is a very challenging task in conventional selective breeding for improving disease resistance.With the advances in mapping quantitative trait loci(QTL)and genome wide association studies(GWAS)for NNV resistance in aquaculture species,DNA markers and genes associated with NNV resistance have been identified,making the application of marker-assisted selection(MAS)and genomic selection(GS)for NNV resistance possible.A few genes for NNV resistance are identified and are being used for genome editing to rapidly improve NNV resistance.In this review,we present the current knowledge on the NNV,host responses to NNV infection,diagnostic methods and vaccines available for NNV disease.In addition,we summarize the current status of conventional and molecular breeding for NNV resistance and highlight future directions,including genome editing for improving NNV resistance in aquaculture.
基金This study was supported by the National Natural Science Foundation of China(41806161)the internal funds of Temasek Life Sciences Lab,Singapore.
文摘Iridoviruses are DNA virus and have caused huge economic losses in the aquaculture industry.The aim of this study was to establish a colorimetric loop-mediated isothermal amplification(LAMP)protocol for the on-site detection of Singapore grouper iridovirus(SGIV).The SGIV-VP61 gene was chosen as the target gene to develop a colorimetric LAMP assay.The optimized condition of the colorimetric LAMP assay was incubation at 63℃ for 1 h.Samples infected with SGIV could be detected with the color change from yellow into pink.The sensitivity of the developed assay is 5.66 copies/μL of the viral DNA template.This sensitivity was about 1000 times higher than that of conventional PCR while it was slightly lower than the one-step semi-nested PCR assay.A total of 60 DNA samples extracted from the fin tissue of the SGIV-infected Asian seabass were examined for SGIV by colorimetric LAMP,semi-nested PCR and conventional PCR.The results of the colorimetric LAMP assay showed 94.87%agreement with the semi-nested PCR.In addition,the DNA extraction method using NaOH showed a better performance in the colorimetric LAMP assay.Taken together,the colorimetric LAMP established was a sensitive,rapid and specific method for the detection of SGIV.SGIV was not detected in samples randomly taken from a genetically improved line of the Asian seabass.However,some seabass obtained from the local markets were found to contain SGIV.Thus,the LAMP assay has the potential application in the diagnosis of iridovirus diseases in the aquaculture industry.
文摘Asian seabass(Lates calcarifer)is an important foodfish species.It has been cultured in Singapore since the 1980s.A selective breeding program to improve growth,meat quality and disease resistance has been ongoing in Singapore since 2004.In 2012,outbreaks of the big belly disease(BBD)occurred in two batches of offspring generated by a mass-cross among F1 brooders in a hatchery.After the outbreaks,only 437 survived in 6000 F2 juveniles.Molecular parentage analysis with 10 microsatellites revealed that four parents(F1)produced high percentage of offspring that survived the BBD outbreaks.Eighty-two BBD survivor offspring(F2)were selected based on their growth performance at 90 days post hatch(dph),family origin and allelic diversity.They were used as brooders to generate F3.In a period of five years,these F2 brooders produced six batches of offspring,where no outbreak of BBD occurred.In the same period,outbreaks of BBD occurred in 4 out of 18 batches produced by F2 brooders selected for growth,with mortality rates ranging from 85.1%to 95.4%.In F3,the average body weight(57.1±1.09 g,n=3068)of the line for BBD survival was slightly lower than that(60.6±2.29 g,n=4280)of the line for growth at 90 dph.In both lines,the body weight of F3 was much higher than that(46.90±0.19 g,n=12117)of F2.The genetic diversity in the line for BBD survival(F3)was much lower than that in F3 line for growth due to small founder population.These data indicate that the selection of BBD survival during BBD outbreaks using molecular parentage analysis is effective to reduce BBD outbreaks.Avoiding further reduction of genetic diversity is essential in the line selected for increased survival against BBD.
基金supported by Internal Funds of the Temasek Life Sciences Laboratory(5020).
文摘Chia(Salvia hispanica)is a functional food crop for humans.Although its seeds contain high omega-3 fatty acids,the seed yield of chia is still low.Genomic resources available for this plant are limited.We report the first high-quality chromosome-level genome sequence of chia.The assembled genome size was 347.6 Mb and covered 98.1%of the estimated genome size.A total of 31069 protein-coding genes were predicted.The absence of recent whole-genome duplication and the relatively low intensity of transposable element expansion in chia compared to its sister species contribute to its small genome size.Transcriptome sequencing and gene duplication analysis reveal that the expansion of the fab2 gene family is likely to be related to the high content of omega-3 in seeds.The white seed coat color is determined by a single locus on chromosome 4.This study provides novel insights into the evolution of Salvia species and high omega-3 content,as well as valuable genomic resources for genetic improvement of important commercial traits of chia and its related species.
基金supported by the internal fund of the Temasek Life Sciences Laboratory,Singapore.
文摘Simvastatin(SIM),a commonly prescribed drug for lowering serum-lipid,has been detected in many aquatic environments.Exposure to high concentrations of SIM in rats and aquatic organisms resulted in toxicity to hepatocytes and negative effects on development.However,there is a paucity of studies on the effects of long-term exposure to low concentrations of SIM on aquaculture species.This study aimed to analyze the effects of environmentally relevant concentrations(0.1μg/L and 1μg/L)of SIM exposure for two months on developing Mozambique tilapias.Surprisingly,the growth of male tilapias was enhanced after a 2-month SIM exposure.The analysis of testis histology revealed that after the SIM exposure,the development of the testis was delayed,and sperm production was reduced.Sequencing of testis transcriptomes showed that the exposure to SIM altered the expression of many genes related to the development of testes and spermatogenesis.These data suggest that a 2-month exposure to environmentally relevant concentrations of increases the growth of male tilapias by inhibiting sexual development of males.
文摘Viral nervous necrosis(VNN)caused by a betanodavirus(NNV)is one of the major diseases in Asian seabass(Lates calcarifer)hatcheries.Our previous studies showed that the tbx21 gene was in a QTL for NNV resistance in linkage group 23 in Asian seabass.The expression of this gene was changed in tissues of Asian seabass challenged with NNV.However,the role of tbx21 in NNV resistance remains largely unknown.In this study,tbx21 of Asian seabass was characterized.This gene consists of an ORF of 1866 bp,a 5′UTR of 357 bp,and a 3′UTR of 4674 bp.The TBX21 protein showed substantial amino acid similarity(70-96%)with other fish but exhibited lower identity(47-52%)with mammals.One SNP identified in the first intron was significantly associated with NNV resistance.In healthy fish,tbx21 was expressed in all tissues examined,and was highly expressed in the kidney and liver.The expression of tbx21 increased in the eye,gills,heart,kidney and gut,but decreased in the brain and spleen at five days after NNV challenge.Overexpression of tbx21 reduced the replication of NNV,whereas knockdown increased viral expression and virus titers.These results suggest that tbx21 plays a key role in NNV resistance.The SNP in this gene could be used as a marker to facilitate marker-assisted selection for NNV resistance.Further investigation of polymorphisms in the 5’and 3’UTRs of tbx21 may provide additional insights into the gene's role in NNV resistance.
