Thousand-kernel weight(TKW)is a measure of grain weight,a target of wheat breeding.The object of this study was to fine-map a stable quantitative trait loci(QTL)for TKW and identify its candidate gene in a recombinant...Thousand-kernel weight(TKW)is a measure of grain weight,a target of wheat breeding.The object of this study was to fine-map a stable quantitative trait loci(QTL)for TKW and identify its candidate gene in a recombinant inbred line(RIL)population derived from the cross of Kenong 9204(KN9204)and Jing411(J411).On a high-density genetic linkage map,24,26 and 25 QTL were associated with TKW,kernel length(KL),and kernel width(KW),respectively.A major and stable QTL,QTkw-2D,was mapped to an8.3 cM interval on chromosome arm 2DL.By saturation of polymorphic markers in its target region,QTkw-2D was confined to a 9.13 Mb physical interval using a secondary mapping population derived from a residually heterozygous line(F6:7).This interval was further narrowed to 2.52 Mb using QTkw-2D near-isogenic lines(NILs).NILs~(KN9204)had higher fresh and dry weights than NILsJ411at various grain-filling stages.The TKW and KW of NILs~(KN9204)were much higher than those of NILsJ411in field trials.By comparison of both DNA sequence and expression between KN9204 and J411,TraesCS2D02G460300.1(TraesKN2D01HG49350)was assigned as a candidate gene for QTkw-2D.This was confirmed by RNA sequencing(RNA-seq)of QTkw-2D NILs.These results provide the basis of map-based cloning of QTkw-2D,and DNA markers linked to the candidate gene may be used in marker-assisted selection.展开更多
Studying the regulatory mechanisms that drive nitrogen-use efficiency(NUE)in crops is important for sustainable agriculture and environmental protection.In this study,we generated a high-quality genome assembly for th...Studying the regulatory mechanisms that drive nitrogen-use efficiency(NUE)in crops is important for sustainable agriculture and environmental protection.In this study,we generated a high-quality genome assembly for the high-NUE wheat cultivar Kenong 9204 and systematically analyzed genes related to nitrogen uptake and metabolism.By comparative analyses,we found that the high-affinity nitrate transporter gene family had expanded in Triticeae.Further studies showed that subsequent functional differentiation endowed the expanded family members with saline inducibility,providing a genetic basis for improving the adaptability of wheat to nitrogen deficiency in various habitats.To explore the genetic and molecular mechanisms of high NUE,we compared genomic and transcriptomic data from the high-NUE cultivar Kenong 9204(KN9204)and the low-NUE cultivar Jing 411 and quantified their nitrogen accumulation under high-and low-nitrogen conditions.Compared with Jing 411,KN9204 absorbed significantly more nitrogen at the reproductive stage after shooting and accumulated it in the shoots and seeds.Transcriptome data analysis revealed that nitrogen deficiency clearly suppressed the expression of genes related to cell division in the young spike of Jing 411,whereas this suppression of gene expression was much lower in KN9204.In addition,KN9204 maintained relatively high expression of NPF genes for a longer time than Jing 411 during seed maturity.Physiological and transcriptome data revealed that KN9204 was more tolerant of nitrogen deficiency than Jing 411,especially at the reproductive stage.The high NUE of KN9204 is an integrated effect controlled at different levels.Taken together,our data provide new insights into the molecular mechanisms of NUE and important gene resources for improving wheat cultivars with a higher NUE trait.展开更多
A better understanding of wheat functional genomics can improve targeted breeding for better agronomic traits and environmental adaptation.However,the lack of gene-indexed mutants and the low transformation efficiency...A better understanding of wheat functional genomics can improve targeted breeding for better agronomic traits and environmental adaptation.However,the lack of gene-indexed mutants and the low transformation efficiency of wheat limit in-depth gene functional studies and genetic manipulation for breeding.In this study,we created a library for KN9204,a popular wheat variety in northern China,with a reference genome,transcriptome,and epigenome of different tissues,using ethyl methyl sulfonate(EMS)mutagenesis.This library contains a vast developmental diversity of critical tissues and transition stages.Exome capture sequencing of 2090 mutant lines using KN9204 genome-designed probes revealed that 98.79%of coding genes had mutations,and each line had an average of 1383 EMS-type SNPs.We identified new allelic variations for crucial agronomic trait-related genes such as Rht-D1,Q,TaTB1,and WFZP.We tested 100 lines with severemutations in 80 NAC transcription factors(TFs)under drought and salinity stress and identified 13 lines with altered sensitivity.Further analysis of three lines using transcriptome and chromatin accessibility data revealed hundreds of direct NAC targets with altered transcription patterns under salt or drought stress,including SNAC1,DREB2B,CML16,and ZFP182,factors known to respond to abiotic stress.Thus,we have generated and indexed a KN9204 EMS mutant library that can facilitate functional genomics research and offer resources for genetic manipulation of wheat.展开更多
基金jointly supported by the National Natural Science Foundation of China(32272056,U22A6009,31671673,and 31871612)Hebei Natural Science Foundation(C2021205013,C2022204202)+1 种基金Talents Program of Hebei Agricultural University in China(YJ2021016)China Agriculture Research System of MOF and MARA(CARS-03)。
文摘Thousand-kernel weight(TKW)is a measure of grain weight,a target of wheat breeding.The object of this study was to fine-map a stable quantitative trait loci(QTL)for TKW and identify its candidate gene in a recombinant inbred line(RIL)population derived from the cross of Kenong 9204(KN9204)and Jing411(J411).On a high-density genetic linkage map,24,26 and 25 QTL were associated with TKW,kernel length(KL),and kernel width(KW),respectively.A major and stable QTL,QTkw-2D,was mapped to an8.3 cM interval on chromosome arm 2DL.By saturation of polymorphic markers in its target region,QTkw-2D was confined to a 9.13 Mb physical interval using a secondary mapping population derived from a residually heterozygous line(F6:7).This interval was further narrowed to 2.52 Mb using QTkw-2D near-isogenic lines(NILs).NILs~(KN9204)had higher fresh and dry weights than NILsJ411at various grain-filling stages.The TKW and KW of NILs~(KN9204)were much higher than those of NILsJ411in field trials.By comparison of both DNA sequence and expression between KN9204 and J411,TraesCS2D02G460300.1(TraesKN2D01HG49350)was assigned as a candidate gene for QTkw-2D.This was confirmed by RNA sequencing(RNA-seq)of QTkw-2D NILs.These results provide the basis of map-based cloning of QTkw-2D,and DNA markers linked to the candidate gene may be used in marker-assisted selection.
基金supported by the National Natural Science Foundation of China(grant nos.31921005 and 31991211)the Strategic Priority Research Program of the Chinese Academy of Sciences(grant nos.XDA24010104,XDA24010204,and XDA24030102)+1 种基金the Special Information Program of the Chinese Academy of Sciences(grant no.XXH13506-408)the China Agricultural Research System(grant no.CARS-03).
文摘Studying the regulatory mechanisms that drive nitrogen-use efficiency(NUE)in crops is important for sustainable agriculture and environmental protection.In this study,we generated a high-quality genome assembly for the high-NUE wheat cultivar Kenong 9204 and systematically analyzed genes related to nitrogen uptake and metabolism.By comparative analyses,we found that the high-affinity nitrate transporter gene family had expanded in Triticeae.Further studies showed that subsequent functional differentiation endowed the expanded family members with saline inducibility,providing a genetic basis for improving the adaptability of wheat to nitrogen deficiency in various habitats.To explore the genetic and molecular mechanisms of high NUE,we compared genomic and transcriptomic data from the high-NUE cultivar Kenong 9204(KN9204)and the low-NUE cultivar Jing 411 and quantified their nitrogen accumulation under high-and low-nitrogen conditions.Compared with Jing 411,KN9204 absorbed significantly more nitrogen at the reproductive stage after shooting and accumulated it in the shoots and seeds.Transcriptome data analysis revealed that nitrogen deficiency clearly suppressed the expression of genes related to cell division in the young spike of Jing 411,whereas this suppression of gene expression was much lower in KN9204.In addition,KN9204 maintained relatively high expression of NPF genes for a longer time than Jing 411 during seed maturity.Physiological and transcriptome data revealed that KN9204 was more tolerant of nitrogen deficiency than Jing 411,especially at the reproductive stage.The high NUE of KN9204 is an integrated effect controlled at different levels.Taken together,our data provide new insights into the molecular mechanisms of NUE and important gene resources for improving wheat cultivars with a higher NUE trait.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA24010204)to J.X.,the Hebei Natural Science Foundation(C2021205013)"Full-time introduction of high-end talent research project"(2020HBQZYC004)to X.-g.L.+3 种基金the National Natural Science Foundation of China(U22A6009)to J.-m.L.the Research Program for Network Security and Information of the Chinese Academy of Sciences(CAS-WX2021SF-0109)to F.H.and J.X.the National Key Research and Developmental Program of China(2021YFD1201500)to J.X.a China Postdoctoral Science Foundation-funded project(2020M680742)to D.-z.W.
文摘A better understanding of wheat functional genomics can improve targeted breeding for better agronomic traits and environmental adaptation.However,the lack of gene-indexed mutants and the low transformation efficiency of wheat limit in-depth gene functional studies and genetic manipulation for breeding.In this study,we created a library for KN9204,a popular wheat variety in northern China,with a reference genome,transcriptome,and epigenome of different tissues,using ethyl methyl sulfonate(EMS)mutagenesis.This library contains a vast developmental diversity of critical tissues and transition stages.Exome capture sequencing of 2090 mutant lines using KN9204 genome-designed probes revealed that 98.79%of coding genes had mutations,and each line had an average of 1383 EMS-type SNPs.We identified new allelic variations for crucial agronomic trait-related genes such as Rht-D1,Q,TaTB1,and WFZP.We tested 100 lines with severemutations in 80 NAC transcription factors(TFs)under drought and salinity stress and identified 13 lines with altered sensitivity.Further analysis of three lines using transcriptome and chromatin accessibility data revealed hundreds of direct NAC targets with altered transcription patterns under salt or drought stress,including SNAC1,DREB2B,CML16,and ZFP182,factors known to respond to abiotic stress.Thus,we have generated and indexed a KN9204 EMS mutant library that can facilitate functional genomics research and offer resources for genetic manipulation of wheat.
