Pre-harvest sprouting(PHS)is a disadvantageous trait in cereal production worldwide,causing large economic losses each year.Its regulation mechanism is still unclear.We generated the Oryza sativa Viviparous1(OsVP1)mut...Pre-harvest sprouting(PHS)is a disadvantageous trait in cereal production worldwide,causing large economic losses each year.Its regulation mechanism is still unclear.We generated the Oryza sativa Viviparous1(OsVP1)mutant using gene editing technique,which shows increased PHS compared with that of the wild type Nipponbare.OsVP1 is localized mainly in the nucleus and expressed in various tissues and organs.Expression of Seed dormancy 4(Sdr4),a key gene controlling PHS,was sharply reduced in OsVP1 mutants.OsVP1 bound to the specific motif CACCTG in the promoter of Sdr4 and activated its expression in rice protoplasts.Overexpression of Sdr4 reduced the high seed germination rate of OsVP1 mutant cr-osvp1-1,showing that Sdr4 acts as a downstream target of OsVP1.Both OsVP1 and Sdr4 loss-of-function mutants were insensitive to exogenous ABA and employed the ABA signaling pathway in regulating seed dormancy.These findings shed light on the control of seed dormancy aimed at preventing PHS in rice.展开更多
The mesocotyl,a structure located between the basal part of the seminal root and the coleoptile node of seedlings,contributes to pushing the shoot tip through the soil surface,a function that is essential for the unif...The mesocotyl,a structure located between the basal part of the seminal root and the coleoptile node of seedlings,contributes to pushing the shoot tip through the soil surface,a function that is essential for the uniform emergence of direct-seeded rice.Its elongation is inhibited by light and induced in darkness.This investigation of an indica rice(P25)with vigorous mesocotyl elongation was aimed at identifying the"omics"basis of its lightinduced growth inhibition.A transcriptomic comparison between mesocotyl tissues that had developed in the dark and then been exposed to light identified many differentially expressed genes(DEGs)and differentially abundant micro RNAs(mi RNAs).Degradome sequencing analysis revealed 27 negative mi RNA-target pairs.A co-expression regulatory network was constructed based on the mi RNAs,their corresponding targets,and DEGs with a common Gene Ontology term.It suggested that auxin and light,probably antagonistically,affect mesocotyl elongation by regulating polyamine oxidase activity.展开更多
A mechanized direct seeding of rice with less labor and water usage,has been widely adopted.However,this approach requires varieties that exhibit uniform seedling emergence.Mesocotyl elongation(ME)offers the main driv...A mechanized direct seeding of rice with less labor and water usage,has been widely adopted.However,this approach requires varieties that exhibit uniform seedling emergence.Mesocotyl elongation(ME)offers the main drive of fast emergence of rice seedlings from soils;nevertheless,its genetic basis remains unknown.Here,we identify a major rice quantitative trait locus Mesocotyl Elongation1(qME1),an allele of the Green Revolution gene Semi-Dwarf1(SD1),encoding GA20-oxidase for gibberellin(GA)biosynthesis.ME1 expression is strongly induced by soil depth and ethylene.When rice grains are direct-seeded in soils,the ethylene core signaling factor OsEIL1 directly promotes ME1 transcription,accelerating bioactive GA biosynthesis.The GAs further degrade the DELLA protein SLENDER RICE 1(SLR1),alleviating its inhibition of rice PHYTOCHROME-INTERACTING FACTOR-LIKE13(OsPIL13)to activate the downstream expansion gene OsEXPA4 and ultimately promote rice seedling ME and emergence.The ancient traits of long mesocotyl and strong emergence ability in wild rice and landrace were gradually lost in company with the Green Revolution dwarf breeding process,and an elite ME1-R allele(D349H)is found in some modern Geng varieties(long mesocotyl lengths)in northern China,which can be used in the direct seeding and dwarf breeding of Geng varieties.Furthermore,the ectopic and high expression of ME1 driven by mesocotyl-specific promoters resulted in rice plants that could be direct-seeded without obvious plant architecture or yield penalties.Collectively,we reveal the molecular mechanism of rice ME,and provide useful information for breeding new Green Revolution varieties with long mesocotyl suitable for direct-seeding practice.展开更多
Under conditions of labor or resource scarcity,direct seeding,rather than transplantation,is the preferred mode of rice(Oryza sativa)cultivation.This approach requires varieties that exhibit uniform seedling emergence...Under conditions of labor or resource scarcity,direct seeding,rather than transplantation,is the preferred mode of rice(Oryza sativa)cultivation.This approach requires varieties that exhibit uniform seedling emergence.Mesocotyl elongation(ME),the main driver of rapid emergence of rice seedlings from soil,is enhanced by darkness and inhibited by light.Plant polyamine oxidases(PAOs)oxidize polyamines(PAs)and release H2O2,Here,we established that OsPAO5 expression in rice seedlings is increased in the presence of light and inhibited by darkness.To determine its role in ME,we created OsPAO5 mutants using CRISPR/Cas9.Compared with the wild type,pao5 mutants had longer mesocotyls,released less H2O2,and synthesized more ethylene.The mutant seedlings emerged at a higher and more uniform rate,indicating their potential for use in direct seeding.Nucleotide polymorphism analysis revealed that an SNP(PAO5-578G/A)located 578 bp upstream of the OsPAO5 start codon alters its expression,and was selected during rice mesocotyl domestication.The PAO5-578G genotype conferring a long mesocotyl mainly exists in wild rice,most Aus accessions,and some Geng(Japonica)accessions.Intriguingly,knocking out OsPAO5 can remarkably increase the grain weight,grain number,and yield potential.In summary,we developed a novel strategy to obtain elite rice with higher emergence vigor and yield potential,which can be conveniently and widely used to breed varieties of direct-seeding rice.展开更多
Dear Editor,Rice (Oryza sativa)is a model monocot plant for biological studies due to its relatively small genome,rich germplasm resources,and high-efficiency transformation methods.Although significant progress has b...Dear Editor,Rice (Oryza sativa)is a model monocot plant for biological studies due to its relatively small genome,rich germplasm resources,and high-efficiency transformation methods.Although significant progress has been made in rice genomics and functional genomics research (Li et al.,2018),large-scale indoor research toward better understanding of rice biology is hampered by its long growth period and extreme dependence on the natural environment for cultivation.There are some rice germplasms that have a short growth period and short plant height,such as Kitaake.展开更多
The percentage of amylose in the endosperm of rice(Oryza sativa)largely determines grain cooking and eating qualities.Granule-bound starch synthase I(GBSSI)and GBSSII are responsible for amylose biosynthesis in the en...The percentage of amylose in the endosperm of rice(Oryza sativa)largely determines grain cooking and eating qualities.Granule-bound starch synthase I(GBSSI)and GBSSII are responsible for amylose biosynthesis in the endosperm and leaf,respectively.Here,we identified OsGBP,a rice GBSS-binding protein that interacted with GBSSI and GBSSII in vitro and in vivo.The total starch and amylose contents in osgbp mutants were significantly lower than those of wild type in leaves and grains,resulting in reduced grain weight and quality.The carbohydrate-binding module 48(CBM48)domain present in the C-terminus of OsGBP is crucial for OsGBP binding to starch.In the osgbp mutant,the extent of GBSSI and GBSSII binding to starch in the leaf and endospermwas significantly lower than wild type.Our data suggest that OsGBP plays an important role in leaf and endosperm starch biosynthesis by mediating the binding of GBSS proteins to developing starch granules.This elucidation of the function of OsGBP enhances our understanding of the molecular basis of starch biosyn-thesis in rice and contributes information that can be potentially used for the genetic improvement of yield and grain quality.展开更多
Pentatricopeptide repeat(PPR)proteins play important roles in the post-transcriptional modification of organellar RNAs in plants.However,the function of most PPR proteins remains unknown.Here,we characterized the rice...Pentatricopeptide repeat(PPR)proteins play important roles in the post-transcriptional modification of organellar RNAs in plants.However,the function of most PPR proteins remains unknown.Here,we characterized the rice(Oryza sativa L.)chlorophyll deficient 4(cde4)mutant which exhibits an albino phenotype during early leaf development,with decreased chlorophyll contents and abnormal chloroplasts at low-temperature(20℃).Positional cloning revealed that CDE4 encodes a P-type PPR protein localized in chloroplasts.In the cde4 mutant,plastid-encoded polymerase(PEP)-dependent transcript levels were significantly reduced,but transcript levels of nuclear-encoded genes were increased compared to wild-type plants at 20℃.CDE4 directly binds to the transcripts of the chloroplast genes rpl2,ndhA,and ndhB.Intron splicing of these transcripts was defective in the cde4 mutant at 20℃,but was normal at 32℃.Moreover,CDE4 interacts with the guanylate kinase VIRESCENT 2(V2);overexpression of V2 enhanced CDE4 protein stability,thereby rescuing the cde4 phenotype at 20℃.Our results suggest that CDE4 participates in plastid RNA splicing and plays an important role in rice chloroplast development under lowtemperature conditions.展开更多
Starch and storage proteins are the main components of rice(Oryza sativa L.)grains.Despite their importance,the molecular regulatory mechanisms of storage protein and starch biosynthesis remain largely elusive.Here,we...Starch and storage proteins are the main components of rice(Oryza sativa L.)grains.Despite their importance,the molecular regulatory mechanisms of storage protein and starch biosynthesis remain largely elusive.Here,we identified a rice opaque endosperm mutant,opaque3(o3),that overaccumulates 57-kDa proglutelins and has significantly lower protein and starch contents than the wild type.The o3 mutant also has abnormal protein body structures and compound starch grains in its endosperm cells.OPAQUE3(O3)encodes a transmembrane basic leucine zipper(bZIP)transcription factor(OsbZIP60)and is localized in the endoplasmic reticulum(ER)and the nucleus,but it is localized mostly in the nucleus under ER stress.We demonstrated that O3 could activate the expression of several starch synthesis-related genes(GBSSI,AGPL2,SBEI,and ISA2)and storage protein synthesis-related genes(OsGluA2,Prol14,and Glb1).O3 also plays an important role in protein processing and export in the ER by directly binding to the promoters and activating the expression of OsBIP1 and PDIL1-1,two major chaperones that assist with folding of immature secretory proteins in the ER of rice endosperm cells.High-temperature conditions aggravate ER stress and result in more abnormal grain development in o3 mutants.We also revealed that OsbZIP50 can assist O3 in response to ER stress,especially under high-temperature conditions.We thus demonstrate that O3 plays a central role in rice grain development by participating simultaneously in the regulation of storage protein and starch biosynthesis and the maintenance of ER homeostasis in endosperm cells.展开更多
基金supported by grants from the National Major Science and Technology Program on New GMO Organism Variety Breeding(2016ZX08001-001)Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences(CAAS)。
文摘Pre-harvest sprouting(PHS)is a disadvantageous trait in cereal production worldwide,causing large economic losses each year.Its regulation mechanism is still unclear.We generated the Oryza sativa Viviparous1(OsVP1)mutant using gene editing technique,which shows increased PHS compared with that of the wild type Nipponbare.OsVP1 is localized mainly in the nucleus and expressed in various tissues and organs.Expression of Seed dormancy 4(Sdr4),a key gene controlling PHS,was sharply reduced in OsVP1 mutants.OsVP1 bound to the specific motif CACCTG in the promoter of Sdr4 and activated its expression in rice protoplasts.Overexpression of Sdr4 reduced the high seed germination rate of OsVP1 mutant cr-osvp1-1,showing that Sdr4 acts as a downstream target of OsVP1.Both OsVP1 and Sdr4 loss-of-function mutants were insensitive to exogenous ABA and employed the ABA signaling pathway in regulating seed dormancy.These findings shed light on the control of seed dormancy aimed at preventing PHS in rice.
基金financially supported by the National S&T Major Project of China(2016ZX08001006)the National Key Research and Development Program of China(2016YFD0101801 and 2017YFD0100300)the Agricultural Science and Technology Innovation Program of CAAS。
文摘The mesocotyl,a structure located between the basal part of the seminal root and the coleoptile node of seedlings,contributes to pushing the shoot tip through the soil surface,a function that is essential for the uniform emergence of direct-seeded rice.Its elongation is inhibited by light and induced in darkness.This investigation of an indica rice(P25)with vigorous mesocotyl elongation was aimed at identifying the"omics"basis of its lightinduced growth inhibition.A transcriptomic comparison between mesocotyl tissues that had developed in the dark and then been exposed to light identified many differentially expressed genes(DEGs)and differentially abundant micro RNAs(mi RNAs).Degradome sequencing analysis revealed 27 negative mi RNA-target pairs.A co-expression regulatory network was constructed based on the mi RNAs,their corresponding targets,and DEGs with a common Gene Ontology term.It suggested that auxin and light,probably antagonistically,affect mesocotyl elongation by regulating polyamine oxidase activity.
基金supported by the National Natural Science Foundation of China(32188102 and 32101763)Zhejang Provincial Science and Technology Project(2020R51007)+1 种基金the Key Research and Development Program of Zhejiang province(2022C02011)the Innovation Program of Chinese Academy of Agricultural Sciences(CAAS-CACB-202402).
文摘A mechanized direct seeding of rice with less labor and water usage,has been widely adopted.However,this approach requires varieties that exhibit uniform seedling emergence.Mesocotyl elongation(ME)offers the main drive of fast emergence of rice seedlings from soils;nevertheless,its genetic basis remains unknown.Here,we identify a major rice quantitative trait locus Mesocotyl Elongation1(qME1),an allele of the Green Revolution gene Semi-Dwarf1(SD1),encoding GA20-oxidase for gibberellin(GA)biosynthesis.ME1 expression is strongly induced by soil depth and ethylene.When rice grains are direct-seeded in soils,the ethylene core signaling factor OsEIL1 directly promotes ME1 transcription,accelerating bioactive GA biosynthesis.The GAs further degrade the DELLA protein SLENDER RICE 1(SLR1),alleviating its inhibition of rice PHYTOCHROME-INTERACTING FACTOR-LIKE13(OsPIL13)to activate the downstream expansion gene OsEXPA4 and ultimately promote rice seedling ME and emergence.The ancient traits of long mesocotyl and strong emergence ability in wild rice and landrace were gradually lost in company with the Green Revolution dwarf breeding process,and an elite ME1-R allele(D349H)is found in some modern Geng varieties(long mesocotyl lengths)in northern China,which can be used in the direct seeding and dwarf breeding of Geng varieties.Furthermore,the ectopic and high expression of ME1 driven by mesocotyl-specific promoters resulted in rice plants that could be direct-seeded without obvious plant architecture or yield penalties.Collectively,we reveal the molecular mechanism of rice ME,and provide useful information for breeding new Green Revolution varieties with long mesocotyl suitable for direct-seeding practice.
基金This work was supported by the National Key Research and Development Program of China(2017YFD0100300 and 2016YFD0101801)the Central Public-interest Scientific Institution Basal Research Fund of China(Y2020YJ09 and Y2020PT07)Agricultural Sciences and Technologies Innovation Program of the Chinese Academy of Agricultural Sciences.
文摘Under conditions of labor or resource scarcity,direct seeding,rather than transplantation,is the preferred mode of rice(Oryza sativa)cultivation.This approach requires varieties that exhibit uniform seedling emergence.Mesocotyl elongation(ME),the main driver of rapid emergence of rice seedlings from soil,is enhanced by darkness and inhibited by light.Plant polyamine oxidases(PAOs)oxidize polyamines(PAs)and release H2O2,Here,we established that OsPAO5 expression in rice seedlings is increased in the presence of light and inhibited by darkness.To determine its role in ME,we created OsPAO5 mutants using CRISPR/Cas9.Compared with the wild type,pao5 mutants had longer mesocotyls,released less H2O2,and synthesized more ethylene.The mutant seedlings emerged at a higher and more uniform rate,indicating their potential for use in direct seeding.Nucleotide polymorphism analysis revealed that an SNP(PAO5-578G/A)located 578 bp upstream of the OsPAO5 start codon alters its expression,and was selected during rice mesocotyl domestication.The PAO5-578G genotype conferring a long mesocotyl mainly exists in wild rice,most Aus accessions,and some Geng(Japonica)accessions.Intriguingly,knocking out OsPAO5 can remarkably increase the grain weight,grain number,and yield potential.In summary,we developed a novel strategy to obtain elite rice with higher emergence vigor and yield potential,which can be conveniently and widely used to breed varieties of direct-seeding rice.
基金grants from the National Natural Science Foundation of China (31521064,91735304,31501279) the Agricultural Science and Technology Innovation Program Cooperation and Innovation Mission (no.CAAS-XTCT2016001).
文摘Dear Editor,Rice (Oryza sativa)is a model monocot plant for biological studies due to its relatively small genome,rich germplasm resources,and high-efficiency transformation methods.Although significant progress has been made in rice genomics and functional genomics research (Li et al.,2018),large-scale indoor research toward better understanding of rice biology is hampered by its long growth period and extreme dependence on the natural environment for cultivation.There are some rice germplasms that have a short growth period and short plant height,such as Kitaake.
基金This work was supported by the National S&T Major Project of China(2016ZX08001006,2016ZX08001001)the National Natural Science Foundation of China(31971925)Agricultural Sciences and Technologies Innovation Program of Chinese Academy of(Agricultural Sciences(CAAS).
文摘The percentage of amylose in the endosperm of rice(Oryza sativa)largely determines grain cooking and eating qualities.Granule-bound starch synthase I(GBSSI)and GBSSII are responsible for amylose biosynthesis in the endosperm and leaf,respectively.Here,we identified OsGBP,a rice GBSS-binding protein that interacted with GBSSI and GBSSII in vitro and in vivo.The total starch and amylose contents in osgbp mutants were significantly lower than those of wild type in leaves and grains,resulting in reduced grain weight and quality.The carbohydrate-binding module 48(CBM48)domain present in the C-terminus of OsGBP is crucial for OsGBP binding to starch.In the osgbp mutant,the extent of GBSSI and GBSSII binding to starch in the leaf and endospermwas significantly lower than wild type.Our data suggest that OsGBP plays an important role in leaf and endosperm starch biosynthesis by mediating the binding of GBSS proteins to developing starch granules.This elucidation of the function of OsGBP enhances our understanding of the molecular basis of starch biosyn-thesis in rice and contributes information that can be potentially used for the genetic improvement of yield and grain quality.
基金This work was supported by the Natural Science Foundation of Zhejiang province(LR20C13002)the special support plan for high level talents in Zhejiang Province(2019R52032)Agricultural Sciences and Technologies Innovation Program of the Chinese Academy of Agricultural Sciences.
文摘Pentatricopeptide repeat(PPR)proteins play important roles in the post-transcriptional modification of organellar RNAs in plants.However,the function of most PPR proteins remains unknown.Here,we characterized the rice(Oryza sativa L.)chlorophyll deficient 4(cde4)mutant which exhibits an albino phenotype during early leaf development,with decreased chlorophyll contents and abnormal chloroplasts at low-temperature(20℃).Positional cloning revealed that CDE4 encodes a P-type PPR protein localized in chloroplasts.In the cde4 mutant,plastid-encoded polymerase(PEP)-dependent transcript levels were significantly reduced,but transcript levels of nuclear-encoded genes were increased compared to wild-type plants at 20℃.CDE4 directly binds to the transcripts of the chloroplast genes rpl2,ndhA,and ndhB.Intron splicing of these transcripts was defective in the cde4 mutant at 20℃,but was normal at 32℃.Moreover,CDE4 interacts with the guanylate kinase VIRESCENT 2(V2);overexpression of V2 enhanced CDE4 protein stability,thereby rescuing the cde4 phenotype at 20℃.Our results suggest that CDE4 participates in plastid RNA splicing and plays an important role in rice chloroplast development under lowtemperature conditions.
基金supported by the National Natural Science Foundation of China(31971925 and 32172080)the Natural Science Foundation of Zhejiang Province(LR20C13002)+1 种基金the Special Support Plan for High-Level Talents in Zhejiang Province(2019R52032)the International Science&Technology Innovation Program of the Chinese Academy of Agricultural Sciences,China(CAAS-ZDRW202109).
文摘Starch and storage proteins are the main components of rice(Oryza sativa L.)grains.Despite their importance,the molecular regulatory mechanisms of storage protein and starch biosynthesis remain largely elusive.Here,we identified a rice opaque endosperm mutant,opaque3(o3),that overaccumulates 57-kDa proglutelins and has significantly lower protein and starch contents than the wild type.The o3 mutant also has abnormal protein body structures and compound starch grains in its endosperm cells.OPAQUE3(O3)encodes a transmembrane basic leucine zipper(bZIP)transcription factor(OsbZIP60)and is localized in the endoplasmic reticulum(ER)and the nucleus,but it is localized mostly in the nucleus under ER stress.We demonstrated that O3 could activate the expression of several starch synthesis-related genes(GBSSI,AGPL2,SBEI,and ISA2)and storage protein synthesis-related genes(OsGluA2,Prol14,and Glb1).O3 also plays an important role in protein processing and export in the ER by directly binding to the promoters and activating the expression of OsBIP1 and PDIL1-1,two major chaperones that assist with folding of immature secretory proteins in the ER of rice endosperm cells.High-temperature conditions aggravate ER stress and result in more abnormal grain development in o3 mutants.We also revealed that OsbZIP50 can assist O3 in response to ER stress,especially under high-temperature conditions.We thus demonstrate that O3 plays a central role in rice grain development by participating simultaneously in the regulation of storage protein and starch biosynthesis and the maintenance of ER homeostasis in endosperm cells.