Understanding the genetic basis of phenotypes is of importance in evolutionary biology and for genetic improvement of economically valuable animals.The giant phenotype of the fighting fish,Betta splendens,provides a u...Understanding the genetic basis of phenotypes is of importance in evolutionary biology and for genetic improvement of economically valuable animals.The giant phenotype of the fighting fish,Betta splendens,provides a unique opportunity to explore the genetic architecture of overgrowth in body size.As such,we re-sequenced and analyzed the genomes of 54 fighting fish.Genome-wide FST and selective sweep analyses using 3582429 DNA variants revealed three genomic regions at chr1,chr9,and chr11 that were associated with the giant phenotype.With a total length of~3.5 Mb,these regions showed high divergence between the giant and non-giant bettas.In contrast,no signature of selection was detected in the wild-type fish.Transcriptome analysis of brain and muscle samples from giant and normal bettas identified 14 candidate genes that were likely responsible for the giant phenotype.Overall,our data provide novel insights into the genetic basis of body size variation.The genome sequences,transcriptome sequences,DNA sequence variants,and candidate genes for body size provide valuable resources for further biological and evolutionary studies,as well as for rapid improvement in growth-related traits.展开更多
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
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
The palm family(Arecaceae),consisting of2600 species,is the third most economically important family of plants.The African oil palm(Elaeis guineensis)is one of the most important palms.However,the genome sequences of ...The palm family(Arecaceae),consisting of2600 species,is the third most economically important family of plants.The African oil palm(Elaeis guineensis)is one of the most important palms.However,the genome sequences of palms that are currently available are still limited and fragmented.Here,we report a high-quality chromosome-level reference genome of an oil palm,Dura,assembled by integrating long reads with150 genome coverage.The assembled genome was 1.7 Gb in size,covering 94.5%of the estimated genome,of which 91.6%was assigned into 16 pseudochromosomes and 73.7%was repetitive sequences.Relying on the conserved synteny with oil palm,the existing draft genome sequences of both date palm and coconut were further assembled into chromosomal level.Transposon burst,particularly long terminal repeat retrotransposons,following the last whole-genome duplication,likely explains the genome size variation across palms.Sequence analysis of the VIRESCENS gene in palms suggests that DNA variations in this gene are related to fruit colors.Recent duplications of highly tandemly repeated pathogenesis-related proteins from the same tandem arrays play an important role in defense responses to Ganoderma.Whole-genome resequencing of both ancestral African and introduced oil palms in Southeast Asia reveals that genes under putative selection are notably associated with stress responses,suggesting adaptation to stresses in the new habitat.The genomic resources and insights gained in this study could be exploited for accelerating genetic improvement and understanding the evolution of palms.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
基金supported by the Internal Funds of the Temasek Life Sciences Laboratory(5020)。
文摘Understanding the genetic basis of phenotypes is of importance in evolutionary biology and for genetic improvement of economically valuable animals.The giant phenotype of the fighting fish,Betta splendens,provides a unique opportunity to explore the genetic architecture of overgrowth in body size.As such,we re-sequenced and analyzed the genomes of 54 fighting fish.Genome-wide FST and selective sweep analyses using 3582429 DNA variants revealed three genomic regions at chr1,chr9,and chr11 that were associated with the giant phenotype.With a total length of~3.5 Mb,these regions showed high divergence between the giant and non-giant bettas.In contrast,no signature of selection was detected in the wild-type fish.Transcriptome analysis of brain and muscle samples from giant and normal bettas identified 14 candidate genes that were likely responsible for the giant phenotype.Overall,our data provide novel insights into the genetic basis of body size variation.The genome sequences,transcriptome sequences,DNA sequence variants,and candidate genes for body size provide valuable resources for further biological and evolutionary studies,as well as for rapid improvement in growth-related traits.
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 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 the Internal Funds of the Temasek Life Sciences Laboratory,Singapore(Grant No.5020)Wilmar International,Singapore(Grant No.9200).
文摘The palm family(Arecaceae),consisting of2600 species,is the third most economically important family of plants.The African oil palm(Elaeis guineensis)is one of the most important palms.However,the genome sequences of palms that are currently available are still limited and fragmented.Here,we report a high-quality chromosome-level reference genome of an oil palm,Dura,assembled by integrating long reads with150 genome coverage.The assembled genome was 1.7 Gb in size,covering 94.5%of the estimated genome,of which 91.6%was assigned into 16 pseudochromosomes and 73.7%was repetitive sequences.Relying on the conserved synteny with oil palm,the existing draft genome sequences of both date palm and coconut were further assembled into chromosomal level.Transposon burst,particularly long terminal repeat retrotransposons,following the last whole-genome duplication,likely explains the genome size variation across palms.Sequence analysis of the VIRESCENS gene in palms suggests that DNA variations in this gene are related to fruit colors.Recent duplications of highly tandemly repeated pathogenesis-related proteins from the same tandem arrays play an important role in defense responses to Ganoderma.Whole-genome resequencing of both ancestral African and introduced oil palms in Southeast Asia reveals that genes under putative selection are notably associated with stress responses,suggesting adaptation to stresses in the new habitat.The genomic resources and insights gained in this study could be exploited for accelerating genetic improvement and understanding the evolution of palms.
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.
