Accurate genomic information is essential for advancing genetic breeding research in specific rice varieties.This study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bi...Accurate genomic information is essential for advancing genetic breeding research in specific rice varieties.This study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bio HiFi,Hi-C,and ONT(Oxford Nanopore Technologies)ultra-long sequencing technologies,annotating 43037 gene structures.Subsequently,utilizing this genome along with transcriptomic and metabolomic techniques,we explored ZH8015's response to brown planthopper(BPH)infestation.Continuous transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH feeding.Enrichment analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall formation.Metabolomic results demonstrated marked increases in levels of several monosaccharides,which are components of the cell wall and dramatic changes in flavonoid contents.Omics association analysis identified differentially expressed genes associated with key metabolites,shedding light on ZH8015's response to BPH infestation.In summary,this study constructed a reliable genome sequence resource for ZH8015,and the preliminary multi-omics results will guide future insect-resistant breeding research.展开更多
Grain size is one of key agronomic traits associated with grain yield and grain quality. Both major quantitative trait loci GS3 and GL3.1 play a predominant role in negative regulation of grain size. In this study, a ...Grain size is one of key agronomic traits associated with grain yield and grain quality. Both major quantitative trait loci GS3 and GL3.1 play a predominant role in negative regulation of grain size. In this study, a CRISPR/Cas9-mediated multiplex genome editing system was used to simultaneously edit GS3 and GL3.1 in a typical japonica rice Nipponbare. In T1 generation, we found that gs3 formed slender grain with lower chalkiness percentage, while gs3gl3.1 produced larger grain with higher chalkiness percentage. In terms of other agronomic traits, flag leaf size, grain number and grain yield of both gs3 and gs3gl3.1 mutants were affected. It is noteworthy that gs3 and gs3gl3.1 mutants both led to dramatical reduction of grain number, thereby decreased grain yield. In conclusion, these results indicated that knockout of GS3 and GL3.1 could rapidly improve grain size, but probably have some negative influences on grain quality and grain yield.展开更多
Rice(Oryza sativa L.)is an important cereal crop,consumed as a staple by more than 50%of the global population(Gathala et al,2011).In Asian countries,the rice production increased to 695.5 million tones in the last ye...Rice(Oryza sativa L.)is an important cereal crop,consumed as a staple by more than 50%of the global population(Gathala et al,2011).In Asian countries,the rice production increased to 695.5 million tones in the last years,and this increasing was caused by the main source of income and employment in these countries.Breeding high-yielding hybrid rice is a potentially promising solution for addressing food shortages caused by marked increases in the global population.Recent progress in DNA marker technology and the construction of linkage maps has enabled the detection of quantitative trait loci(QTLs)that regulate different agronomic traits applicable to breeding(Parida et al,2006;Zhang et al,2017).展开更多
Grain size is one of the critical agronomic traits governing grain yield and quality in rice.However,the underlying genetic mechanisms that control grain size in rice are poorly understood.We used an introgression lin...Grain size is one of the critical agronomic traits governing grain yield and quality in rice.However,the underlying genetic mechanisms that control grain size in rice are poorly understood.We used an introgression line derived from Zhonghui 8015 and Oryza rufipogon Griff.This introgression line was evaluated under two different environmental conditions to dissect the quantitative trait loci controlling grain size.Genome-wide association study(GWAS)was performed using 28193 SNPs through a general linear model,and 56 significant SNPs on different loci associated with the 4 grain size traits were detected.Cloned genes including GS3 and q GL3 showed substantial effects on grain length and size.Seven new stable loci were identified with pleiotropic effects on grain size.Haplotype,gene expression analyses,combined gene-based associations,and functional annotations permitted the shortlisting of important dominant genes including GS3 and q GL3.展开更多
Many excellent genes in wild rice have been lost during the domestication of wild rice to cultivated rice.In this study,introgression lines(ILs)were produced with a wild rice(Oryza rufipogon)accession,BJ194,as a donor...Many excellent genes in wild rice have been lost during the domestication of wild rice to cultivated rice.In this study,introgression lines(ILs)were produced with a wild rice(Oryza rufipogon)accession,BJ194,as a donor parent and an indica restorer line,Zhonghui 8015(ZH8015),as a recipient parent to map QTLs for plant height.We identified four QTLs(qPH3.1,qPH3.2,qPH2,and qPH8)related to plant height distributed on chromosomes 2,3 and 8.Furthermore,we sequenced and analyzed qPH3.2 located in the interval of RM15753-RM3525,and found this QTL may be a new locus regulating rice plant height.展开更多
To investigate the genetic bases of grain weight(GW),a set of 76 chromosome segment substitution lines(CSSLs,BC4F5)were developed from the cross between Xieqingzao B(XQZB)and Zhonghui 9308(ZH9308)using a marker-assist...To investigate the genetic bases of grain weight(GW),a set of 76 chromosome segment substitution lines(CSSLs,BC4F5)were developed from the cross between Xieqingzao B(XQZB)and Zhonghui 9308(ZH9308)using a marker-assisted selection(MAS).All substituted segments represented by 120 markers in those lines covered 96.7%of the donor parent(ZH9308).Consequently,two QTLs(qTGW1 and qTGW6)for 1000-grain weight(TGW)were preliminarily mapped on chromosomes 1 and 6,respectively.The line CSSL7 was selected for further mapping of qGL1.4/qTGW1.As a result,qGL1.4 was validated and narrowed to a 1.4 Mb interval between markers InDel15 and RM11872 using secondary F2,and narrowed to a 500 kb in F2:3 populations between markers RM11824 and RM11842.In F4:5 secondary population,using homozygous recombinant strategy,qGL1.4 was finally fine-mapped to a 286.4 kb region between markers D-12 and TG-57.In addition,a near-isogenic line(NIL)harbouring qGL1.4 was developed using MAS approach,which showed enhanced grain length compared with ZH9308 without changing other traits.In summary,these results lay a foundation for the genetic isolation of qGL1.4 and molecular breeding in rice.展开更多
基金supported by the Chinese Academy of Agricultural Sciences Innovation Project(Grant No.CAASASTIP-2013CNRRI)Fundamental Research Funds for Central Public Welfare Research Institutes of Chinese Rice Research Institute(Grant No.CPSIBRF-CNRRI-202102)。
文摘Accurate genomic information is essential for advancing genetic breeding research in specific rice varieties.This study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bio HiFi,Hi-C,and ONT(Oxford Nanopore Technologies)ultra-long sequencing technologies,annotating 43037 gene structures.Subsequently,utilizing this genome along with transcriptomic and metabolomic techniques,we explored ZH8015's response to brown planthopper(BPH)infestation.Continuous transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH feeding.Enrichment analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall formation.Metabolomic results demonstrated marked increases in levels of several monosaccharides,which are components of the cell wall and dramatic changes in flavonoid contents.Omics association analysis identified differentially expressed genes associated with key metabolites,shedding light on ZH8015's response to BPH infestation.In summary,this study constructed a reliable genome sequence resource for ZH8015,and the preliminary multi-omics results will guide future insect-resistant breeding research.
基金supported by the National Nature Science Foundation of China(Grant Nos.31521064 and 31961143016)Technological Innovation Project of Chinese Academy of Agricultural Sciences(Grant No.CAASASTIP-2013-CNRRI)+2 种基金Major Transgenic Projects of China(Grant No.2016ZX08001-002)National Key Research and Development Program(Grant No.2016YFD0101801)the Natural Science Foundation of Innovation Research Group(Grant No.31521064)。
文摘Grain size is one of key agronomic traits associated with grain yield and grain quality. Both major quantitative trait loci GS3 and GL3.1 play a predominant role in negative regulation of grain size. In this study, a CRISPR/Cas9-mediated multiplex genome editing system was used to simultaneously edit GS3 and GL3.1 in a typical japonica rice Nipponbare. In T1 generation, we found that gs3 formed slender grain with lower chalkiness percentage, while gs3gl3.1 produced larger grain with higher chalkiness percentage. In terms of other agronomic traits, flag leaf size, grain number and grain yield of both gs3 and gs3gl3.1 mutants were affected. It is noteworthy that gs3 and gs3gl3.1 mutants both led to dramatical reduction of grain number, thereby decreased grain yield. In conclusion, these results indicated that knockout of GS3 and GL3.1 could rapidly improve grain size, but probably have some negative influences on grain quality and grain yield.
文摘Rice(Oryza sativa L.)is an important cereal crop,consumed as a staple by more than 50%of the global population(Gathala et al,2011).In Asian countries,the rice production increased to 695.5 million tones in the last years,and this increasing was caused by the main source of income and employment in these countries.Breeding high-yielding hybrid rice is a potentially promising solution for addressing food shortages caused by marked increases in the global population.Recent progress in DNA marker technology and the construction of linkage maps has enabled the detection of quantitative trait loci(QTLs)that regulate different agronomic traits applicable to breeding(Parida et al,2006;Zhang et al,2017).
基金supported by the National Key Research and Development Program(Grant No.2016YFD0101801)the Major Project of the Genetically Modified and National Key Transgenic Research Projects,China(Grant No.2016ZX08001-002)+2 种基金the National Natural Science Foundation of China(Grant No.31521064)Chinese Academy of Agricultural Sciences Innovation Project(CAASASTIP-2013-CNRRI)Fundamental Research Expenses of Central Public Welfare Research Institutions 2017 RG001-1.
文摘Grain size is one of the critical agronomic traits governing grain yield and quality in rice.However,the underlying genetic mechanisms that control grain size in rice are poorly understood.We used an introgression line derived from Zhonghui 8015 and Oryza rufipogon Griff.This introgression line was evaluated under two different environmental conditions to dissect the quantitative trait loci controlling grain size.Genome-wide association study(GWAS)was performed using 28193 SNPs through a general linear model,and 56 significant SNPs on different loci associated with the 4 grain size traits were detected.Cloned genes including GS3 and q GL3 showed substantial effects on grain length and size.Seven new stable loci were identified with pleiotropic effects on grain size.Haplotype,gene expression analyses,combined gene-based associations,and functional annotations permitted the shortlisting of important dominant genes including GS3 and q GL3.
基金supported by the National Natural Science Foundation of China (Grant No. 31961143016)the National Rice Industry Technology System of China (Grant No.CARS-01-03)+2 种基金the ‘14th Five-Year Plan’ Major Special Projects for Breeding New Rice Varieties of Zhejiang Province, China (Grant No. 2021C02063-1)the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (Grant No. CAAS-ASTIP2013-CNRRI)Hainan Yazhou Bay Seed Laboratory Oratory, China (Grant No. B21HJ0219)
文摘Many excellent genes in wild rice have been lost during the domestication of wild rice to cultivated rice.In this study,introgression lines(ILs)were produced with a wild rice(Oryza rufipogon)accession,BJ194,as a donor parent and an indica restorer line,Zhonghui 8015(ZH8015),as a recipient parent to map QTLs for plant height.We identified four QTLs(qPH3.1,qPH3.2,qPH2,and qPH8)related to plant height distributed on chromosomes 2,3 and 8.Furthermore,we sequenced and analyzed qPH3.2 located in the interval of RM15753-RM3525,and found this QTL may be a new locus regulating rice plant height.
基金supported by the Natural Science Foundation of China(Grant No.31961143016)the National Key Research and Development Program(Grant No.2016YFD0101801)+1 种基金the Fundamental Research Funds of Central Public Welfare Research Institutions(Grant No.CPSIBRF-CNRRI-202102)the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Science(Grant No.CAAS-ASTIP-2013-CNRRI).
文摘To investigate the genetic bases of grain weight(GW),a set of 76 chromosome segment substitution lines(CSSLs,BC4F5)were developed from the cross between Xieqingzao B(XQZB)and Zhonghui 9308(ZH9308)using a marker-assisted selection(MAS).All substituted segments represented by 120 markers in those lines covered 96.7%of the donor parent(ZH9308).Consequently,two QTLs(qTGW1 and qTGW6)for 1000-grain weight(TGW)were preliminarily mapped on chromosomes 1 and 6,respectively.The line CSSL7 was selected for further mapping of qGL1.4/qTGW1.As a result,qGL1.4 was validated and narrowed to a 1.4 Mb interval between markers InDel15 and RM11872 using secondary F2,and narrowed to a 500 kb in F2:3 populations between markers RM11824 and RM11842.In F4:5 secondary population,using homozygous recombinant strategy,qGL1.4 was finally fine-mapped to a 286.4 kb region between markers D-12 and TG-57.In addition,a near-isogenic line(NIL)harbouring qGL1.4 was developed using MAS approach,which showed enhanced grain length compared with ZH9308 without changing other traits.In summary,these results lay a foundation for the genetic isolation of qGL1.4 and molecular breeding in rice.
