Genetic manipulation(either restraint or enhancement)of the biosynthesis pathway ofα-linolenic acid(ALA)in seed oil is an important goal in Brassica napus breeding.B.napus is a tetraploid plant whose genome often har...Genetic manipulation(either restraint or enhancement)of the biosynthesis pathway ofα-linolenic acid(ALA)in seed oil is an important goal in Brassica napus breeding.B.napus is a tetraploid plant whose genome often har-bors four and six homologous copies,respectively,of the two fatty acid desaturases FAD2 and FAD3,which con-trol the last two steps of ALA biosynthesis during seed oil accumulation.In this study,we compared their promoters,coding sequences,and expression levels in three high-ALA inbred lines 2006L,R8Q10,and YH25005,a low-ALA line A28,a low-ALA/high-oleic-acid accession SW,and the wildtype ZS11.The expression levels of most FAD2 and FAD3 homologs in the three high-ALA accessions were higher than those in ZS11 and much higher than those in A28 and SW.The three high-ALA accessions shared similar sequences with the pro-moters and CDSs of BnFAD3.C4 and BnFAD3.A3.In A28 and SW,substitution of three amino acid residues in BnFAD2.A5 and BnFAD2.C5,an absence of BnFAD2.C1 locus,and a 549 bp long deletion on the BnFAD3.A3 promoter were detected.The profile of BnFAD2 mutation in the two low-ALA accessions A28 and SW is different from that reported in previous studies.The mutations in BnFAD3 in the high-ALA accessions are reported for thefirst time.In identifying the sites of these mutations,we provide detailed information to aid the design of mole-cular markers for accelerated breeding schemes.展开更多
Plant height is a key plant architectural trait that affects the seed yield,harvest index and lodging resistance in Brassica napus L.,although the genetic mechanisms affecting plant height remain unclear.Here,a semi-d...Plant height is a key plant architectural trait that affects the seed yield,harvest index and lodging resistance in Brassica napus L.,although the genetic mechanisms affecting plant height remain unclear.Here,a semi-dwarf mutant,df34,was obtained by ethyl methanesulphonate-induced mutagenesis.Genetic analysis showed that the semi-dwarf phenotype is controlled by one semi-dominant gene,which was located on chromosome C03 using a bulked segregant analysis coupled with whole-genome sequencing,and this gene was named BnaSD.C3.Then BnaSD.C3 was fine-mapped to a 297.35-kb segment of the“Darmor-bzh”genome,but there was no potential candidate gene for the semi-dwarf trait underlying this interval.Furthermore,the interval was aligned to the Zhongshuang 11 reference genome.Finally,combining structural variation analysis,transcriptome sequencing,phytohormone analyses and gene annotation information,BnaC03G0466900ZS and BnaC03G0478900ZS were determined to be the most likely candidate genes affecting the plant height of df34.This study provides a novel major locus for breeding and new insights into the genetic architecture of plant height in B.napus.展开更多
Seed weight is a component of seed yield in rapeseed(Brassica napus L.).Although quantitative trait loci(QTL)for seed weight have been reported in rapeseed,only a few causal quantitative trait genes(QTGs)have been ide...Seed weight is a component of seed yield in rapeseed(Brassica napus L.).Although quantitative trait loci(QTL)for seed weight have been reported in rapeseed,only a few causal quantitative trait genes(QTGs)have been identified,resulting in a limitation in understanding of seed weight regulation.We constructed a gene coexpression network at the early seed developmental stage using transcripts of 20,408 genes in QTL intervals and 1017 rapeseed homologs of known genes from other species.Among the 10 modules in this gene coexpression network,modules 1 and 2 were core modules and contained genes involved in source–flow–sink processes such as synthesis and transportation of fatty acid and protein,and photosynthesis.A hub gene SERINE CARBOXYPEPTIDASE-LIKE 19(SCPL19)was identified by candidate gene association analysis in rapeseed and functionally investigated using Arabidopsis T-DNA mutant and overexpression lines.Our study demonstrates the power of gene coexpression analysis to prioritize candidate genes from large candidate QTG sets and enhances the understanding of molecular mechanism for seed weight at the early developmental stage in rapeseed.展开更多
Seed number per silique(SNPS)is one of seed yield components in rapeseed,but its genetic mechanism remains elusive.Here a double haploid(DH)population derived from a hybrid between female 6Q006with 35–40 SNPS and mal...Seed number per silique(SNPS)is one of seed yield components in rapeseed,but its genetic mechanism remains elusive.Here a double haploid(DH)population derived from a hybrid between female 6Q006with 35–40 SNPS and male 6W26 with 10–15 SNPS was investigated for SNPS in the year 2017,2018,2019 and 2021,and genotyped with Brassica 60K Illumina Infinium SNP array.An overlapping major QTL(qSNPS.C09)explaining 51.50%of phenotypic variance on average was narrowed to a 0.90 Mb region from 44.87 Mb to 45.77 Mb on chromosome C09 by BSA-seq.Subsequently,two DEGs in this interval were detected between extreme individuals in DH and F_2populations by transcriptome sequencing at7 and 14 days after pollination siliques.Of which,BnaC09g45400D encoded an adenine phosphoribosyltransferase 5(APT5)has a 48-bp InDel variation in the promoter of two parents.Candidate gene association analysis showed that this InDel variation was associated with SNPS in a nature population of rapeseed,where 54 accessions carrying the same haplotype as parent 6Q006 had higher SNPS than103 accessions carrying the same haplotype as parent 6W26.Collectively,the findings are helpful for rapeseed molecular breeding of SNPS,and provide new insight into the genetic and molecular mechanism of SNPS in rapeseed.展开更多
Ascorbate peroxidase(APX)is a crucial H2O2 scavenger that utilizes ascorbic acid as an electron donor and plays a significant role in plant stress resistance.This study aims to identify and characterize the Brassica n...Ascorbate peroxidase(APX)is a crucial H2O2 scavenger that utilizes ascorbic acid as an electron donor and plays a significant role in plant stress resistance.This study aims to identify and characterize the Brassica napus L.APX gene family through genome and transcriptome sequencing,while also revealing their expression profile under low-temperature stress via transcriptome and proteome analysis.The results indicate the presence of 18 genes with three different conserved domains distributed in Brassica napus L.,which can be classified into three major branches based on phylogenetic analysis.Eleven members were predicted to have the low-temperature response component(LTR).Most APX genes exhibit up-regulated transcriptional expression under low temperature stress,particularly APX2,APX4,APX12,and APX18.In terms of proteomics data,only six members(APX2,APX4,APX8,APX12,APX17,and APX18)showed temporal specificity in their expression patterns.Therefore,this study provides valuable insights into the complexity of the APX family in the functional characterization of its genes for future research.展开更多
Gibberellin 2-oxidases(GA2ox)are important enzymes that maintain the balance of bioactive GAs in plants.GA2ox genes have been identified and characterized in many plants,but these genes were not investigated in Brassi...Gibberellin 2-oxidases(GA2ox)are important enzymes that maintain the balance of bioactive GAs in plants.GA2ox genes have been identified and characterized in many plants,but these genes were not investigated in Brassica napus.Here,we identified 31 GA2ox genes in B.napus and 15 of these BnaGA2ox genes were distributed in the A and C subgenomes.Subcellular localization predictions suggested that all BnaGA2ox proteins were localized in the cytoplasm,and gene structure analysis showed that the BnaGA2ox genes contained 2–4 exons.Phylogenetic analysis indicated that BnGA2ox family proteins in monocotyledons and dicotyledons can be divided into four groups,including two C_(19)-GA2ox and two C_(20)-GA2ox clades.Group 4 is a C_(20)-GA2ox Class discovered recently.Most BnaGA2ox genes had a syntenic relationship with AtGA2ox genes.BnaGA2ox genes in the C subgenome had experienced stronger selection pressure than genes in the A subgenome.BnaGA2ox genes were highly expressed in specific tissues such as those involved in growth and development,and most of them were mainly involved in abiotic responses,regulation of phytohormones and growth and development.Our study provided a valuable evolutionary analysis of GA2ox genes in monocotyledons and dicotyledons,as well as an insight into the biological functions of GA2ox family genes in B.napus.展开更多
Oilseed rape(Brassica napus L.) is an allotetraploid(AACC,2n=38) crop,valued for its edible oil and protein content.seed yield and nutritional composition of rapeseed are influenced by its yield and oil quality traits...Oilseed rape(Brassica napus L.) is an allotetraploid(AACC,2n=38) crop,valued for its edible oil and protein content.seed yield and nutritional composition of rapeseed are influenced by its yield and oil quality traits.However,the genetic basis of yield-related and oil-quality traits remain ambiguous.A panel of 266 diversified oilseed rape accessions was genotyped using 223 simple sequence repeat(SSR) markers covering all 19 chromosomes to identify significant markers associated with yield and quality traits.Twelve yield-related and six quality traits were investigated in two consecutive years(2014 and 2015),with three replications in two environments(Changshun,CS;and Qinghe,QH).Using the model GLM with population structure and kinship(Q+K),a total of 25 significant SSR markers(P <0.001) were detected to be associated with these twelve yield-related and six quality traits,explaining 4.56%-19.17% of the phenotypic variation for each trait.Based on these markers,BnaA03g23490D, BnaC09g46370D,BnaA07g37150D,BnaA01g32590D, and BnaC09g37280D were identified as pleiotropic genes controlling multiple traits.These candidate genes illustrated the potential for the genetic understanding of yield and oil quality traits.Most importantly,these significant markers can be used for marker-assisted breeding of oilseed rape in different environments.展开更多
基金The study was financially supported by Projects from Shaanxi Province(2021LLRH-07-03-01 and 2023-ZDLNY-07)Yangling Seed Industry Innovation(YLzy-yc2021-01).The funders had no role in study design,data collection and analysis,decision to publish,or preparation of the manuscript.
文摘Genetic manipulation(either restraint or enhancement)of the biosynthesis pathway ofα-linolenic acid(ALA)in seed oil is an important goal in Brassica napus breeding.B.napus is a tetraploid plant whose genome often har-bors four and six homologous copies,respectively,of the two fatty acid desaturases FAD2 and FAD3,which con-trol the last two steps of ALA biosynthesis during seed oil accumulation.In this study,we compared their promoters,coding sequences,and expression levels in three high-ALA inbred lines 2006L,R8Q10,and YH25005,a low-ALA line A28,a low-ALA/high-oleic-acid accession SW,and the wildtype ZS11.The expression levels of most FAD2 and FAD3 homologs in the three high-ALA accessions were higher than those in ZS11 and much higher than those in A28 and SW.The three high-ALA accessions shared similar sequences with the pro-moters and CDSs of BnFAD3.C4 and BnFAD3.A3.In A28 and SW,substitution of three amino acid residues in BnFAD2.A5 and BnFAD2.C5,an absence of BnFAD2.C1 locus,and a 549 bp long deletion on the BnFAD3.A3 promoter were detected.The profile of BnFAD2 mutation in the two low-ALA accessions A28 and SW is different from that reported in previous studies.The mutations in BnFAD3 in the high-ALA accessions are reported for thefirst time.In identifying the sites of these mutations,we provide detailed information to aid the design of mole-cular markers for accelerated breeding schemes.
基金the National Natural Science Foundation of China(32172065 and 32172095)the earmarked Fund for China Agriculture Research System(CARS-12)+1 种基金the Central Public-interest Scientific Institution Basal Research Fund,China(Y2022QC21)the Jiangsu Collaborative Innovation Center for Modern Crop Production,China。
文摘Plant height is a key plant architectural trait that affects the seed yield,harvest index and lodging resistance in Brassica napus L.,although the genetic mechanisms affecting plant height remain unclear.Here,a semi-dwarf mutant,df34,was obtained by ethyl methanesulphonate-induced mutagenesis.Genetic analysis showed that the semi-dwarf phenotype is controlled by one semi-dominant gene,which was located on chromosome C03 using a bulked segregant analysis coupled with whole-genome sequencing,and this gene was named BnaSD.C3.Then BnaSD.C3 was fine-mapped to a 297.35-kb segment of the“Darmor-bzh”genome,but there was no potential candidate gene for the semi-dwarf trait underlying this interval.Furthermore,the interval was aligned to the Zhongshuang 11 reference genome.Finally,combining structural variation analysis,transcriptome sequencing,phytohormone analyses and gene annotation information,BnaC03G0466900ZS and BnaC03G0478900ZS were determined to be the most likely candidate genes affecting the plant height of df34.This study provides a novel major locus for breeding and new insights into the genetic architecture of plant height in B.napus.
基金provided by the National Natural Science Foundation of China(32201776)the Natural Science Foundation of Chongqing(cstc2019jcyj-bsh X0055,cstc2019jcyj-zdxm X0012)。
文摘Seed weight is a component of seed yield in rapeseed(Brassica napus L.).Although quantitative trait loci(QTL)for seed weight have been reported in rapeseed,only a few causal quantitative trait genes(QTGs)have been identified,resulting in a limitation in understanding of seed weight regulation.We constructed a gene coexpression network at the early seed developmental stage using transcripts of 20,408 genes in QTL intervals and 1017 rapeseed homologs of known genes from other species.Among the 10 modules in this gene coexpression network,modules 1 and 2 were core modules and contained genes involved in source–flow–sink processes such as synthesis and transportation of fatty acid and protein,and photosynthesis.A hub gene SERINE CARBOXYPEPTIDASE-LIKE 19(SCPL19)was identified by candidate gene association analysis in rapeseed and functionally investigated using Arabidopsis T-DNA mutant and overexpression lines.Our study demonstrates the power of gene coexpression analysis to prioritize candidate genes from large candidate QTG sets and enhances the understanding of molecular mechanism for seed weight at the early developmental stage in rapeseed.
基金supported by the National Basic Research Program of China(2015CB150201)the Natural Science Foundation of Chongqing(cstc2019jcyj-bshX0055,cstc2019jcyj-zdxmX0012cstc2020jcyj-msxmX0461)。
文摘Seed number per silique(SNPS)is one of seed yield components in rapeseed,but its genetic mechanism remains elusive.Here a double haploid(DH)population derived from a hybrid between female 6Q006with 35–40 SNPS and male 6W26 with 10–15 SNPS was investigated for SNPS in the year 2017,2018,2019 and 2021,and genotyped with Brassica 60K Illumina Infinium SNP array.An overlapping major QTL(qSNPS.C09)explaining 51.50%of phenotypic variance on average was narrowed to a 0.90 Mb region from 44.87 Mb to 45.77 Mb on chromosome C09 by BSA-seq.Subsequently,two DEGs in this interval were detected between extreme individuals in DH and F_2populations by transcriptome sequencing at7 and 14 days after pollination siliques.Of which,BnaC09g45400D encoded an adenine phosphoribosyltransferase 5(APT5)has a 48-bp InDel variation in the promoter of two parents.Candidate gene association analysis showed that this InDel variation was associated with SNPS in a nature population of rapeseed,where 54 accessions carrying the same haplotype as parent 6Q006 had higher SNPS than103 accessions carrying the same haplotype as parent 6W26.Collectively,the findings are helpful for rapeseed molecular breeding of SNPS,and provide new insight into the genetic and molecular mechanism of SNPS in rapeseed.
基金supported by the Fundamental Research Project of Shanxi Province(202203021211276)Major Program of Shanxi Province(202201140601025-5)The Science and Technology Innovated Project of Shanxi Agricultural University(CXGC2023050).
文摘Ascorbate peroxidase(APX)is a crucial H2O2 scavenger that utilizes ascorbic acid as an electron donor and plays a significant role in plant stress resistance.This study aims to identify and characterize the Brassica napus L.APX gene family through genome and transcriptome sequencing,while also revealing their expression profile under low-temperature stress via transcriptome and proteome analysis.The results indicate the presence of 18 genes with three different conserved domains distributed in Brassica napus L.,which can be classified into three major branches based on phylogenetic analysis.Eleven members were predicted to have the low-temperature response component(LTR).Most APX genes exhibit up-regulated transcriptional expression under low temperature stress,particularly APX2,APX4,APX12,and APX18.In terms of proteomics data,only six members(APX2,APX4,APX8,APX12,APX17,and APX18)showed temporal specificity in their expression patterns.Therefore,this study provides valuable insights into the complexity of the APX family in the functional characterization of its genes for future research.
基金supported by the Chongqing Academy of Agricultural Sciences Youth Innovation Team Project(NKY-2018QC01)Chongqing Finance Special Project(NKY-2022AC002)+2 种基金the Natural Science Foundation Project of Yongchuan(2021yc-jckx20013)the Technology Innovation and Application Development(Surface)Project of Yongchuan(2021yc-cxfz30007)the National Oilseed Rape Industrial Technology System Sanxia Comprehensive Experiment Station Project(CARS-13).
文摘Gibberellin 2-oxidases(GA2ox)are important enzymes that maintain the balance of bioactive GAs in plants.GA2ox genes have been identified and characterized in many plants,but these genes were not investigated in Brassica napus.Here,we identified 31 GA2ox genes in B.napus and 15 of these BnaGA2ox genes were distributed in the A and C subgenomes.Subcellular localization predictions suggested that all BnaGA2ox proteins were localized in the cytoplasm,and gene structure analysis showed that the BnaGA2ox genes contained 2–4 exons.Phylogenetic analysis indicated that BnGA2ox family proteins in monocotyledons and dicotyledons can be divided into four groups,including two C_(19)-GA2ox and two C_(20)-GA2ox clades.Group 4 is a C_(20)-GA2ox Class discovered recently.Most BnaGA2ox genes had a syntenic relationship with AtGA2ox genes.BnaGA2ox genes in the C subgenome had experienced stronger selection pressure than genes in the A subgenome.BnaGA2ox genes were highly expressed in specific tissues such as those involved in growth and development,and most of them were mainly involved in abiotic responses,regulation of phytohormones and growth and development.Our study provided a valuable evolutionary analysis of GA2ox genes in monocotyledons and dicotyledons,as well as an insight into the biological functions of GA2ox family genes in B.napus.
基金supported by National Natural Science Foundation of China(No.32070217)Subsidy project from NSFC of Guizhou Academy of Agricultural Sciences(No.[2021]50)+2 种基金The Scientific and Technological Key Program of Guizhou province(No.Qiankehezhicheng[2022]Key 031,025and 026)The Agricultural Scientific and Technological Research Projects of Guizhou province(No.Qiankehezhicheng[2020]1Y109 and 1Y106Youth Foundation of Guizhou Academy of Agricultural Sciences(No.[2021]07).
文摘Oilseed rape(Brassica napus L.) is an allotetraploid(AACC,2n=38) crop,valued for its edible oil and protein content.seed yield and nutritional composition of rapeseed are influenced by its yield and oil quality traits.However,the genetic basis of yield-related and oil-quality traits remain ambiguous.A panel of 266 diversified oilseed rape accessions was genotyped using 223 simple sequence repeat(SSR) markers covering all 19 chromosomes to identify significant markers associated with yield and quality traits.Twelve yield-related and six quality traits were investigated in two consecutive years(2014 and 2015),with three replications in two environments(Changshun,CS;and Qinghe,QH).Using the model GLM with population structure and kinship(Q+K),a total of 25 significant SSR markers(P <0.001) were detected to be associated with these twelve yield-related and six quality traits,explaining 4.56%-19.17% of the phenotypic variation for each trait.Based on these markers,BnaA03g23490D, BnaC09g46370D,BnaA07g37150D,BnaA01g32590D, and BnaC09g37280D were identified as pleiotropic genes controlling multiple traits.These candidate genes illustrated the potential for the genetic understanding of yield and oil quality traits.Most importantly,these significant markers can be used for marker-assisted breeding of oilseed rape in different environments.
