The transition from dormancy to germination marks the initial stage of the plant life cycle,with its intensity,synchronicity,and timing being critical for crop growth,development,and adaptation to complex climate cond...The transition from dormancy to germination marks the initial stage of the plant life cycle,with its intensity,synchronicity,and timing being critical for crop growth,development,and adaptation to complex climate conditions.This review synthesizes recent advances with classic molecular mechanisms of dormancy and germination,including environmental responses and signaling cascades.We integrate these independent studies to provide a comprehensive perspective on the complex regulatory networks and discuss novel insights into how rice seeds perceive and respond to environmental cues during this transition,particularly focusing on stress tolerance to temperature and flooding.We aim to bridge the understanding of the molecular mechanisms of dormancy and germination with their breeding applications.Specifically,we discuss gene targets and feasible strategies for the genetic improvement of pre-harvest sprouting and direct-seeded rice,two key traits essential for climate resilience,both of which involve dormancy and germination.Finally,we propose the concept of engineering germination-smart varieties endowed with intelligent environmental adaptation.展开更多
Previously, we found 123 transcription factors（TFs） as candidate regulators of secondary cell wall（SCW）formation in rice by using phylogenetic and co-expression network analyses. Among them, we examined in this wo...Previously, we found 123 transcription factors（TFs） as candidate regulators of secondary cell wall（SCW）formation in rice by using phylogenetic and co-expression network analyses. Among them, we examined in this work the role of OsIDD_2, a zinc finger and indeterminate domain（IDD） family TF. Its overexpressors showed dwarfism, fragile leaves, and decreased lignin content, which are typical phenotypes of plants defective in SCW formation, whereas its knockout plants showed slightly increased lignin content.The RNA-seq and quantitative reverse transcription polymerase chain reaction analyses confirmed that some lignin biosynthetic genes were downregulated in the OsIDD_2-overexpressing plants, and revealed the same case for other genes involved in cellulose synthesis and sucrose metabolism. The transient expression assay using rice protoplasts revealed that OsIDD_2 negatively regulates the transcription of genes involved in lignin biosynthesis, cinnamyl alcohol dehydrogenase 2 and 3（CAD_2 and 3）, and sucrose metabolism, sucrose synthase 5（SUS_5）, whereas an Alpha Screen assay, which can detect the interaction between TFs and their target DNA sequences, directly confirmed the interaction between OsIDD_2 and the target sequences located in the promoter regions of CAD_2 and CAD_3. Based on these observations, we conclude that OsIDD_2 is negatively involved in SCW formation and other biological events by downregulating its target genes.展开更多
Improving grain quality is a primary objective in contemporary rice breeding.Japanese modern rice breeding has developed two different types of rice,eating and sake-brewing rice,with different grain characteristics,in...Improving grain quality is a primary objective in contemporary rice breeding.Japanese modern rice breeding has developed two different types of rice,eating and sake-brewing rice,with different grain characteristics,indicating the selection of variant gene alleles during the breeding process.Given the critical importance of promptly and efficiently identifying genes selected in past breeding for future molecular breeding,we conducted genome scans for divergence,genome-wide association studies,and map-based cloning.Consequently,we successfully identified two genes,OsMnS and OsWOX9D,both contributing to rice grain traits.OsMnS encodes a mannan synthase that increases the white core frequency in the endosperm,a desirable trait for sake brewing but decreases the grain appearance quality.OsWOX9D encodes a grass-specific homeobox-containing transcription factor,which enhances grain width for better sake brewing.Furthermore,haplotype analysis revealed that their defective alleles were selected in East Asia,but not Europe,during modern improvement.In addition,our analyses indicate that a reduction in grain mannan content during African rice domestication may also be caused a defective OsMnS allele due to breeding selection.This study not only reveals the delicate balance between grain appearance quality and nutrition in rice but also provides a new strategy for isolating causal genes underlying complex traits,based on the concept of“breeding-assisted genomics”in plants.展开更多
Flowering time is a crucial rice trait that influences its adaptation to various environments,cropping schedules,and agronomic characteristics.Rice breeders have exploited spontaneous mutations in heading date genes t...Flowering time is a crucial rice trait that influences its adaptation to various environments,cropping schedules,and agronomic characteristics.Rice breeders have exploited spontaneous mutations in heading date genes to regulate the flowering time.In the present study,we investigated how breeders in Fukui Prefecture regulated days to heading while developing promising rice varieties.Genome-wide association studies(GWAS)identified Hd1,Hd16,and Hd18 as the major genes controlling days to heading in the population.However,we suspected that this highly bred population might exhibit genomic stratification,which could lead to spurious or false correlations in the GWAS.Thus,we also conducted correlation and partial correlation analyses,which uncovered another key heading date gene,Hd17,that GWAS failed to detect because of its linkage disequilibrium with the major effect gene Hd16.Examination of haplotype frequencies across different breeding periods revealed that the early-heading Hd16(Hd16(E))and late-heading Hd17(Hd17(L))were increasingly co-selected in the Hd1 functional population.Varieties carrying this Hd16(E)/Hd17(L)combination exhibited days to heading in the range of 70–80,which corresponds to the peak temperature and sunshine period and is also optimal for grain quality and yield components in the Fukui environment.The present study highlights that it is imperative to remain vigilant for Type I(false positives)and Type II(false negatives)errors when performing GWAS on highly bred populations and to implement appropriate countermeasures by accounting for gene-by-gene interactions established through the breeding process.We also discuss the effectiveness of Hd16(E),which is not used outside Japan for subtle days to heading control but is widely used in Japan at certain latitudes.展开更多
Increasing the yield is one of the most important goals of crop improvement.Since the beginning of rice cultivation thousands of years ago,many efforts have been made to increase rice yield.One of the successes in thi...Increasing the yield is one of the most important goals of crop improvement.Since the beginning of rice cultivation thousands of years ago,many efforts have been made to increase rice yield.One of the successes in this history was the Green Revolution.This tremendous improvement in the 1960s was achieved by increasing rice and wheat production through the development and widespread adoption of semi-dwarf varieties with the extensive use of fertilizers(Hedden,2003).Dwarfism in crops lowers the center of gravity of the plant body,reducing the risk of lodging and enabling farmers to use more fertilizer to increase yields.Semi-dwarf mutations in both rice and wheat created during the Green Revolution are related to the plant growth hormone gibberellin(GA).Although other mechanisms cause dwarf mutants,only GA-related semi-dwarf mutants were selected during the Green Revolution(Wang et al.,2021).While GA-related abnormalities only make plants shorter,most cases caused by other mechanisms involve not only dwarfism but also other morphological abnormalities.展开更多
基金supported by the National Natural Science Foundation of China(grants 32372107 and 32172059)the Applied Basic Research Plan of Liaoning Province(grant 2022JH2/101300172)+2 种基金Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science(24K01886 and 23K23560)the commissioned research fund provided by F-REl(JPFR2303010and JPFR25020105)the joint researchprogram of the J-GlycoNet cooperative network,which is accredited by the Minister of Education,Culture,Sports,Science and Technology,MEXT,Japan,as a Joint Usage/Research Center.
文摘The transition from dormancy to germination marks the initial stage of the plant life cycle,with its intensity,synchronicity,and timing being critical for crop growth,development,and adaptation to complex climate conditions.This review synthesizes recent advances with classic molecular mechanisms of dormancy and germination,including environmental responses and signaling cascades.We integrate these independent studies to provide a comprehensive perspective on the complex regulatory networks and discuss novel insights into how rice seeds perceive and respond to environmental cues during this transition,particularly focusing on stress tolerance to temperature and flooding.We aim to bridge the understanding of the molecular mechanisms of dormancy and germination with their breeding applications.Specifically,we discuss gene targets and feasible strategies for the genetic improvement of pre-harvest sprouting and direct-seeded rice,two key traits essential for climate resilience,both of which involve dormancy and germination.Finally,we propose the concept of engineering germination-smart varieties endowed with intelligent environmental adaptation.
基金supported by grants from Grant-in-Aid for JSPS Research Fellow (JP15J03980 to H.Y.)Series of single-year grants (26-1393 to K.H.)+1 种基金Grants-in-Aid for Scientific Research on Innovative Areas (No.3806 to M.M. and M. U.-T.)the Grant-in-Aid for Scientific Research (A) (JP26252001 to M.M.) and (B) (JP16H04907 to M. U.-T.)
文摘Previously, we found 123 transcription factors（TFs） as candidate regulators of secondary cell wall（SCW）formation in rice by using phylogenetic and co-expression network analyses. Among them, we examined in this work the role of OsIDD_2, a zinc finger and indeterminate domain（IDD） family TF. Its overexpressors showed dwarfism, fragile leaves, and decreased lignin content, which are typical phenotypes of plants defective in SCW formation, whereas its knockout plants showed slightly increased lignin content.The RNA-seq and quantitative reverse transcription polymerase chain reaction analyses confirmed that some lignin biosynthetic genes were downregulated in the OsIDD_2-overexpressing plants, and revealed the same case for other genes involved in cellulose synthesis and sucrose metabolism. The transient expression assay using rice protoplasts revealed that OsIDD_2 negatively regulates the transcription of genes involved in lignin biosynthesis, cinnamyl alcohol dehydrogenase 2 and 3（CAD_2 and 3）, and sucrose metabolism, sucrose synthase 5（SUS_5）, whereas an Alpha Screen assay, which can detect the interaction between TFs and their target DNA sequences, directly confirmed the interaction between OsIDD_2 and the target sequences located in the promoter regions of CAD_2 and CAD_3. Based on these observations, we conclude that OsIDD_2 is negatively involved in SCW formation and other biological events by downregulating its target genes.
文摘Improving grain quality is a primary objective in contemporary rice breeding.Japanese modern rice breeding has developed two different types of rice,eating and sake-brewing rice,with different grain characteristics,indicating the selection of variant gene alleles during the breeding process.Given the critical importance of promptly and efficiently identifying genes selected in past breeding for future molecular breeding,we conducted genome scans for divergence,genome-wide association studies,and map-based cloning.Consequently,we successfully identified two genes,OsMnS and OsWOX9D,both contributing to rice grain traits.OsMnS encodes a mannan synthase that increases the white core frequency in the endosperm,a desirable trait for sake brewing but decreases the grain appearance quality.OsWOX9D encodes a grass-specific homeobox-containing transcription factor,which enhances grain width for better sake brewing.Furthermore,haplotype analysis revealed that their defective alleles were selected in East Asia,but not Europe,during modern improvement.In addition,our analyses indicate that a reduction in grain mannan content during African rice domestication may also be caused a defective OsMnS allele due to breeding selection.This study not only reveals the delicate balance between grain appearance quality and nutrition in rice but also provides a new strategy for isolating causal genes underlying complex traits,based on the concept of“breeding-assisted genomics”in plants.
基金supported by Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science[grant numbers JP22H02294 to M.M.JP24H02257,JP21K14758,to M.S.+2 种基金JP21K15120,24K01886 to H.Y]by Cross-ministerial Moonshot Agriculture,Forestry and Fisheries Research and Development Program,“Technologies for Smart Bio-industry and Agriculture”(funding agency:Bio-oriented Technology Research Advancement Institution)grant to H.Y.(JPJ009237)by the commissioned research fund provided by F-REI(JPFR24020105)to M.S.
文摘Flowering time is a crucial rice trait that influences its adaptation to various environments,cropping schedules,and agronomic characteristics.Rice breeders have exploited spontaneous mutations in heading date genes to regulate the flowering time.In the present study,we investigated how breeders in Fukui Prefecture regulated days to heading while developing promising rice varieties.Genome-wide association studies(GWAS)identified Hd1,Hd16,and Hd18 as the major genes controlling days to heading in the population.However,we suspected that this highly bred population might exhibit genomic stratification,which could lead to spurious or false correlations in the GWAS.Thus,we also conducted correlation and partial correlation analyses,which uncovered another key heading date gene,Hd17,that GWAS failed to detect because of its linkage disequilibrium with the major effect gene Hd16.Examination of haplotype frequencies across different breeding periods revealed that the early-heading Hd16(Hd16(E))and late-heading Hd17(Hd17(L))were increasingly co-selected in the Hd1 functional population.Varieties carrying this Hd16(E)/Hd17(L)combination exhibited days to heading in the range of 70–80,which corresponds to the peak temperature and sunshine period and is also optimal for grain quality and yield components in the Fukui environment.The present study highlights that it is imperative to remain vigilant for Type I(false positives)and Type II(false negatives)errors when performing GWAS on highly bred populations and to implement appropriate countermeasures by accounting for gene-by-gene interactions established through the breeding process.We also discuss the effectiveness of Hd16(E),which is not used outside Japan for subtle days to heading control but is widely used in Japan at certain latitudes.
基金supported by JSPS KAKENHI grants 21K15120 and 24K01886(to H.Y.)and 22H02294(to M.M.)from the Ministry of Education,Culture,Sports,Science and Technology of Japanby the Cross-ministerial Moonshot Agriculture,Forestry and Fisheries Research and Development Program"Technologies for Smart Bio-industry and Agriculture"(funding agency:Bio-oriented Technology Research Advancement Institution)grant JPJ009237(to H.Y.)from the Cabinet Office,Government of Japan+1 种基金by the Priority Research Project(foR-F)of Fukushima University(262Q001 to H.Y.and M.M.)by the commissioned research fund provided by F-REI(JPFR23030101 to H.Y.and M.M.).
文摘Increasing the yield is one of the most important goals of crop improvement.Since the beginning of rice cultivation thousands of years ago,many efforts have been made to increase rice yield.One of the successes in this history was the Green Revolution.This tremendous improvement in the 1960s was achieved by increasing rice and wheat production through the development and widespread adoption of semi-dwarf varieties with the extensive use of fertilizers(Hedden,2003).Dwarfism in crops lowers the center of gravity of the plant body,reducing the risk of lodging and enabling farmers to use more fertilizer to increase yields.Semi-dwarf mutations in both rice and wheat created during the Green Revolution are related to the plant growth hormone gibberellin(GA).Although other mechanisms cause dwarf mutants,only GA-related semi-dwarf mutants were selected during the Green Revolution(Wang et al.,2021).While GA-related abnormalities only make plants shorter,most cases caused by other mechanisms involve not only dwarfism but also other morphological abnormalities.
