Iron is an essential element for plant growth and development. Iron homeostasis in plants is tightly regulated at both transcriptional and posttranscriptional level. Several bHLH transcription factors involved in iron...Iron is an essential element for plant growth and development. Iron homeostasis in plants is tightly regulated at both transcriptional and posttranscriptional level. Several bHLH transcription factors involved in iron homeostasis have been identified recently. However, their regulatory mechanisms remain unknown. In this work, we demonstrate that the transcription factor FIT interacted with AtbHLH38 and AtbHLH39 and directly conferred the expression regulation of iron uptake genes for iron homeostasis in Arabidopsis. Yeast two-hybrid analysis and transient expression in Arabidopsis protoplasts showed that AtbHLH38 or AtbHLH39 interacted with FIT, a central transcription factor involved in iron homeostasis in Arabidopsis. Expression of FIT/AtbHLH38 or FIT/AtbHLH39 in yeast cells activated GUS expression driven by ferric chelate reductase （FRO2） and ferrous transporter （IRT1） promoters. Overexpression of FITwith either AtbHLH38 or AtbHLH39 in plants converted the expression of the iron uptake genes FRO2 and IRT1 from induced to constitutive. Further analysis revealed that FRO2 and IRT1 were not regulated at the posttranscriptional level in these plants because IRT1 protein accumulation and high ferric chelate reductase activity were detected in the overexpression plants under both iron deficiency and iron sufficiency. The double overexpression plants accumulated more iron in their shoots than wild type or the plants overexpressing either AtbHLH38, AtbHLH39 or FIT. Our data support that ferric-chelate reductase FRO2 and ferrous-transporter IRT1 are the targets of the three transcription factors and the transcription of FRO2 and IRT1 is directly regulated by a complex of FIT/AtbHLH38 or FIT/AtbHLH39.展开更多
The inducible CRISPR activation(CRISPR-a)system offers unparalleled precision and versatility for regu-lating endogenous genes,making it highly sought after in plant research.In this study,we developed a chem-ically i...The inducible CRISPR activation(CRISPR-a)system offers unparalleled precision and versatility for regu-lating endogenous genes,making it highly sought after in plant research.In this study,we developed a chem-ically inducible CRISPR-a tool for plants called ER-Tag by combining the LexA-VP16-ER inducible system with the SunTag CRISPR-a system.We systematically compared different induction strategies and achieved high efficiency in target gene activation.We demonstrated that guide RNAs can be multiplexed and pooled for large-scale screening of effective morphogenic genes and gene pairs involved in plant regeneration.Further experiments showed that induced activation of these morphogenic genes can accelerate regenera-tion and improve regeneration efficiency in both eudicot and monocot plants,including alfalfa,woodland strawberry,and sheepgrass.Our study expands the CRISPR toolset in plants and provides a powerful new strategy for studying gene function when constitutive expression is not feasible or ideal.展开更多
Natural rubber(NR)is an irreplaceable biopolymer of economic and strategic importance owing to its unique physical and chemical properties.The Parárubber tree(Hevea brasiliensis(Willd.ex A.Juss.)Müll.Arg.)is...Natural rubber(NR)is an irreplaceable biopolymer of economic and strategic importance owing to its unique physical and chemical properties.The Parárubber tree(Hevea brasiliensis(Willd.ex A.Juss.)Müll.Arg.)is currently the exclusive commercial source of NR,and it is primarily grown in plantations restricted to the tropical and subtropical areas of Southeast Asia.However,current Parárubber production barely meets the sharply increasing global industrial demand for rubber.Petroleum-based synthetic rubber(SR)has been used to supplement the shortage of NR but its industrial performance is not comparable to that of NR.Thus,there is an urgent need to develop new productive rubber crops with broader environmental adaptability.This review summarizes the current research progress on alternative rubberproducing plants,including horticultural plants(Taraxacum kok-saghyz Rodin and Lactuca L.species),woody plants(Parthenium argentatum A.Gray and Eucommia ulmoides Oliv.),and other plant species with potential for NR production.With an emphasis on the molecular basis of NR biosynthesis revealed by a multi-omics approach,we highlight new integrative strategies and biotechnologies for exploring the mechanism of NR biosynthesis with a broader scope,which may accelerate the breeding and improvement of new rubber crops.展开更多
Fruit color is an important horticultural trait,which greatly affects consumer preferences.In tomato,fruit color is determined by the accumulation of different pigments,such as carotenoids in the pericarp and f lavono...Fruit color is an important horticultural trait,which greatly affects consumer preferences.In tomato,fruit color is determined by the accumulation of different pigments,such as carotenoids in the pericarp and f lavonoids in the peel,along with the degradation of chlorophyll during fruit ripening.Since fruit color is a multigenic trait,it takes years to introgress all color-related genes in a single genetic background via traditional crossbreeding,and the avoidance of linkage drag during this process is difficult.Here,we proposed a rapid breeding strategy to generate tomato lines with different colored fruits from red-fruited materials by CRISPR/Cas9-mediated multiplex gene editing of three fruit color-related genes(PSY1,MYB12,and SGR1).Using this strategy,the red-fruited cultivar‘Ailsa Craig’has been engineered to a series of tomato genotypes with different fruit colors,including yellow,brown,pink,light-yellow,pink-brown,yellow-green,and light green.Compared with traditional crossbreeding,this strategy requires less time and can obtain transgene-free plants with different colored fruits in less than 1 year.Most importantly,it does not alter other important agronomic traits,like yield and fruit quality.Our strategy has great practical potential for tomato breeding and serves as a reference for improving multigene-controlled traits of horticultural crops.展开更多
Dear Editor,Genome editing has revolutionized speed breeding by enabling researchers to alter the genome directly as desired(Gao,2021).The most widely used CRISPR–Cas9 technology has mainly been applied to engineer n...Dear Editor,Genome editing has revolutionized speed breeding by enabling researchers to alter the genome directly as desired(Gao,2021).The most widely used CRISPR–Cas9 technology has mainly been applied to engineer null mutations in coding sequences,with the goal of creating loss-of-function alleles.Recently,upstream regulatory elements of the promoter region and 50 upstream open reading frame(uORF)have been engineered to generate gain-of-function alleles,producing versatile cis-regulatory effects,usually through changes in gene expression levels(Rodrıguez-Leal et al.,2017;Zhang et al.,2018;Song et al.,2022).展开更多
The architecture of the panicle, including grain size and panicle morphology, directly determines grain yield. Panicle erectness, which is selected for achieving ideal plant arehitecture in the northern part of China,...The architecture of the panicle, including grain size and panicle morphology, directly determines grain yield. Panicle erectness, which is selected for achieving ideal plant arehitecture in the northern part of China, has drawn increasing attention of rice breeders. Here, dense and erect panicle 2 （dep2） mutant, which shows a dense and erect panicle phenotype, was identified. DEP2 encodes a plant-specific protein without any known functional domain. Expression profiling of DEP2 revealed that it is highly expressed in young tissues, with most abundance in young panicles. Morphological and expression analysis indicated that mutation in DEP2 mainly affects the rapid elongation of rachis and primary and secondary branches, but does not impair the initiation or formation of panicle primordia. Further analysis suggests that decrease of panicle length in dep2 is caused by a defect in cell proliferation during the exponential elongation of panicle. Despite a more compact plant type in the dep2 mutant, no significant alteration in grain production was found between wild type and dep2 mutant. Therefore, the study of DEP2 not only strengthens our understanding of the molecular genetic basis of panicle architecture but also has important implications for rice breeding.展开更多
Polyamines are implicated in regulating various developmental processes in plants, but their exact roles and how they govern these processes still remain elusive. We report here an Arabidopsis bushy and dwarf mutant, ...Polyamines are implicated in regulating various developmental processes in plants, but their exact roles and how they govern these processes still remain elusive. We report here an Arabidopsis bushy and dwarf mutant, bud2, which results from the complete deletion of one member of the small gene family that encodes S-adenosylmethionine decarboxylases （SAMDCs） necessary for the formation of the indispensable intermediate in the polyamine biosynthetic pathway. The bud2 plant has enlarged vascular systems in inflorescences, roots, and petioles, and an altered homeostasis ofpolyamines. The double mutant of bud2 and samdcl, a knockdown mutant of another SAMDC member, is embryo lethal, demonstrating that SAMDCs are essential for plant embryogenesis. Our results suggest that polyamines are required for the normal growth and development of higher plants.展开更多
Brassinosteroids （BRs） are a major group of plant hormones that regulate plant growth and development. BRI1, a protein localized to the plasma membrane, functions as a BR receptor and it has been proposed that its k...Brassinosteroids （BRs） are a major group of plant hormones that regulate plant growth and development. BRI1, a protein localized to the plasma membrane, functions as a BR receptor and it has been proposed that its kinase activity has an essential role in BR-regulated plant growth and development. Here we report the isolation and molecular characterization of a new allele of bril, bril-301, which shows moderate morphological phenotypes and a reduced response to BRs under normal growth conditions. Sequence analysis identified a two-base alteration from GG to AT, resulting in a conversion of 989G to 9891 in the BRI1 kinase domain. An in vitro assay of kinase activity showed that bril-301 has no detectable autophosphorylation activity or phosphorylation activity towards the BRI1 substrates TTL and BAK1. Furthermore, our results suggest that bril-301, even with extremely impaired kinase activity, still retains partial function in regulating plant growth and development, which raises the question of whether BRI1 kinase activity is essential for BR-mediated growth and development in higher plants.展开更多
Thiamine （vitamin B1） is an essential compound for organisms. It contains a pyrimidine ring structure and a thiazole ring structure. These two moieties of thiamine are synthesized independently and then coupled toge...Thiamine （vitamin B1） is an essential compound for organisms. It contains a pyrimidine ring structure and a thiazole ring structure. These two moieties of thiamine are synthesized independently and then coupled together. Here we report the molecular characterization of AtTHIC, which is involved in thiamine biosynthesis in Arabidopsis. AtTHIC is similar to Escherichia coli ThiC, which is involved in pyrimidine biosynthesis in prokaryotes. Heterologous expression of AtTHIC could functionally complement the thiC knock-out mutant of E. coll. Downregulation of AtTHIC expression by T-DNA insertion at its promoter region resulted in a drastic reduction of thiamine content in plants and the knock-down mutant thicl showed albino （white leaves） and lethal phenotypes under the normal culture conditions. The thicl mutant could be rescued by supplementation of thiamine and its defect functions could be complemented by expression ofAtTHIC cDNA. Transient expression analysis revealed that the AtTHIC protein targets plastids and chloroplasts. AtTHIC was strongly expressed in leaves, flowers and siliques and the transcription of AtTHIC was downregulated by extrinsic thiamine. In conclusion, AtTHIC is a gene involved in pyrimidine synthesis in the thiamine biosynthesis pathway of Arabidopsis, and our results provide some new clues for elucidating the pathway of thiamine biosynthesis in plants.展开更多
The ratio of auxin and cytokinin plays a crucial role in regulating aerial architecture by promoting or repressing axillary bud outgrowth. We have previously identified an Arabidopsis mutant bud2 that displays altered...The ratio of auxin and cytokinin plays a crucial role in regulating aerial architecture by promoting or repressing axillary bud outgrowth. We have previously identified an Arabidopsis mutant bud2 that displays altered root and shoot architecture, which results from the loss-of-function of S-adenosylmethionine decarboxylase 4 （SAMDC4）. In this study, we demonstrate that BUD2 could be induced by auxin, and the induction is dependent on auxin signaling. The mutation of BUD2 results in hyposensitivity to auxin and hypersensitivity to cytokinin, which is confirmed by callus induction assays. Our study suggests that polyamines may play their roles in regulating the plant architecture through affecting the homeostasis of cytokinins and sensitivities to auxin and cytokinin.展开更多
Phased small interfering RNAs(phasiRNAs) are abundantly expressed in anthers and linked to environment-related male fertility in grasses, yet how they function under different environmental conditions remains unclear....Phased small interfering RNAs(phasiRNAs) are abundantly expressed in anthers and linked to environment-related male fertility in grasses, yet how they function under different environmental conditions remains unclear. Here, we identified a rice(Oryza sativa) low temperature-induced Argonaute(AGO) protein, OsAGO1d, that is responsible for generating phasiRNAs and preserving male fertility at low temperature. Loss of OsAGO1d function causes low-temperature male sterility associated with delayed programmed cell death of tapetal cells during anther development. OsAGO1d binds miR2118 and miR2275 family members and triggers phasiRNA biogenesis;it also binds 21-nt phasiRNAs with a 5′ terminal U. In total, phasiRNAs from 972loci are OsAGO1d-dependent. OsAGO1d protein moves from anther wall cells into meiocytes, where it loads miR2275 to produce 24-nt phasiRNAs. Together, our results show that OsAGO1d acts as a mobile signal to fine-tune phasiRNA production and this function is important for male fertility at low temperature.展开更多
Pollen germination and embryogenesis are important to sexual plant reproduction. The processes require a large number of genes to be expressed. Transcription of eukaryotic nuclear genes is accomplished by three conser...Pollen germination and embryogenesis are important to sexual plant reproduction. The processes require a large number of genes to be expressed. Transcription of eukaryotic nuclear genes is accomplished by three conserved RNA polymerases acting in association with a set of auxiliary general transcription factors （GTFs）, including B-type GTFs. The roles of B-type GTFs in plant reproduction remain poorly understood. Here we report functional characterization of a novel plant-specific TFIIB-related gene PTF2 in Arabidopsis. Mutation in PTF2 caused failure of pollen germination. Pollen-rescue revealed that the mutation also disrupted embryogenesis and resulted in seed abortion. PTF2 is expressed prolifically in developing pollen and the other tissues with active cell division and differentiation, including embryo and shoot apical meristem. The PTF2 protein shares a lower amino acid sequence similarity with other known TFIIB and TFIIB-related proteins in Arabidopsis. It can interact with TATA-box binding protein 2 （TBP2） and bind to the double- stranded DNA （dsDNA） as the other known TFIIB and TFIIB-related proteins do. In addition, PTF2 can form a homodimer and interact with the subunits of RNA polymerases （RNAPs）, implying that it may be involved in the RNAPs transcription. These results suggest that PTF2 plays crucial roles in pollen germination and embryogenesis in Arabidopsis, possibly by regulating gene expression through interaction with TBP2 and the subunits of RNAPs.展开更多
E3 ligases are key enzymes required for protein degradation.Here,we identified a C3H2C3 RING domaincontaining E3 ubiquitin ligase gene named GhATL68b.It is preferentially and highly expressed in developing cotton fibe...E3 ligases are key enzymes required for protein degradation.Here,we identified a C3H2C3 RING domaincontaining E3 ubiquitin ligase gene named GhATL68b.It is preferentially and highly expressed in developing cotton fiber cells and shows greater conservation in plants than in animals or archaea.The four orthologous copies of this gene in various diploid cottons and eight in the allotetraploid G.hirsutum were found to have originated from a single common ancestor that can be traced back to Chlamydomonas reinhardtii at about 992 million years ago.Structural variations in the GhATL68b promoter regions of G.hirsutum,G.herbaceum,G.arboreum,and G.raimondii are correlated with significantly different methylation patterns.Homozygous CRISPR-Cas9 knockout cotton lines exhibit significant reductions in fiber quality traits,including upper-half mean length,elongation at break,uniformity,and mature fiber weight.In vitro ubiquitination and cell-free protein degradation assays revealed that GhATL68b modulates the homeostasis of 2,4-dienoyl-CoA reductase,a rate-limiting enzyme for theβ-oxidation of polyunsaturated fatty acids(PUFAs),via the ubiquitin proteasome pathway.Fiber cells harvested from these knockout mutants contain significantly lower levels of PUFAs important for production of glycerophospholipids and regulation of plasma membrane fluidity.The fiber growth defects of the mutant can be fully rescued by the addition of linolenic acid(C18:3),the most abundant type of PUFA,to the ovule culture medium.This experimentally characterized C3H2C3 type E3 ubiquitin ligase involved in regulating fiber cell elongation may provide us with a new genetic target for improved cotton lint production.展开更多
Gene innovation plays an essential role in trait evolution.Rhizobial symbioses,the most important N2-fixing agent in agricultural systems that exists mainly in Leguminosae,is one of the most attractive evolution event...Gene innovation plays an essential role in trait evolution.Rhizobial symbioses,the most important N2-fixing agent in agricultural systems that exists mainly in Leguminosae,is one of the most attractive evolution events.However,the gene innovations underlying Leguminosae root nodule symbiosis(RNS)remain largely unknown.Here,we investigated the gene gain event in Leguminosae RNS evolution through comprehensive phylogenomic analyses.We revealed that Leguminosae-gain genes were acquired by gene duplication and underwent a strong purifying selection.Kyoto Encyclopedia of Genes and Genomes analyses showed that the innovated genes were enriched in flavonoid biosynthesis pathways,particular downstream of chalcone synthase(CHS).Among them,Leguminosae-gain typeⅡchalcone isomerase(CHI)could be further divided into CHI1A and CHI1B clades,which resulted from the products of tandem duplication.Furthermore,the duplicated CHI genes exhibited exon–intron structural divergences evolved through exon/intron gain/loss and insertion/deletion.Knocking down CHI1B significantly reduced nodulation in Glycine max(soybean)and Medicago truncatula;whereas,knocking down its duplication gene CHI1A had no effect on nodulation.Therefore,Leguminosae-gain typeⅡCHI participated in RNS and the duplicated CHI1A and CHI1B genes exhibited RNS functional divergence.This study provides functional insights into Leguminosae-gain genetic innovation and sub-functionalization after gene duplication that contribute to the evolution and adaptation of RNS in Leguminosae.展开更多
Tiller angle of rice （Oryza sativa L.） is an important agronomic trait that contributes to grain production, and has long attracted attentions of breeders for achieving ideal plant architecture to improve grain yiel...Tiller angle of rice （Oryza sativa L.） is an important agronomic trait that contributes to grain production, and has long attracted attentions of breeders for achieving ideal plant architecture to improve grain yield. Although enormous efforts have been made over the past decades to study mutants with extremely spreading or compact tillers, the molecular mechanism underlying the control of tiller angle of cereal crops remains unknown. Here we report the cloning of the LAZY1 （LA1） gene that regulates shoot gravitropism by which the rice tiller angle is controlled. We show that LA1, a novel grass-specific gene, is temporally and spatially expressed, and plays a negative role in polar auxin transport （PAT）. Loss-of-function of LA1 enhances PAT greatly and thus alters the endogenous IAA distribution in shoots, leading to the reduced gravitropism, and therefore the tiller-spreading phenotype of rice plants.展开更多
NAC family genes encode plant-specific transcription factors involved in diverse biological processes. In this study, the Arabidopsis NAC gene ATAF1 was found to be induced by drought, high-salinity, abscisic acid （...NAC family genes encode plant-specific transcription factors involved in diverse biological processes. In this study, the Arabidopsis NAC gene ATAF1 was found to be induced by drought, high-salinity, abscisic acid （ABA）, methyl jasmonate, mechanical wounding, and Botrytis cinerea infection. Significant induction of ATAF1 was found in an ABA-deficient mutant aba2 subjected to drought or high salinity, revealing an ABA-independent mechanism of expression. Arabidopsis ATAFl-overexpression lines displayed many altered phenotypes, including dwarfism and short primary roots. Furthermore, in vivo experiments indicate that ATAF1 is a bonafide regulator modulating plant responses to many abiotic stresses and necrotrophic-pathogen infection. Overexpression of ATAF1 in Arabidopsis increased plant sensitivity to ABA, salt, and oxidative stresses. Especially, ATAF1 overexpression plants, but not mutant lines, showed remarkably enhanced plant tolerance to drought. Additionally, ATAF1 overexpression enhanced plant susceptibility to the necrotrophic pathogen B. cinerea, but did not alter disease symptoms caused by avirulent or virulent strains of P. syringae pv tomato DC3000. Transgenic plants overexpressing ATAF1 were hypersensitive to oxidative stress, suggesting that reactive oxygen intermediates may be related to ATAFl-mediated signaling in response to both pathogen and abiotic stresses.展开更多
During vegetative development, higher plants continuously form new leaves in regular spatial and temporal patterns. Mutants with abnormal leaf developmental patterns not only provide a great insight into understanding...During vegetative development, higher plants continuously form new leaves in regular spatial and temporal patterns. Mutants with abnormal leaf developmental patterns not only provide a great insight into understanding the regulatory mechanism of plant architecture, but also enrich the ways to its modification by which crop yield could be improved. Here, we reported the characterization of the rice leafy-head2 （lhd2） mutant that exhibits shortened plastochron, dwarfism, reduced tiller number, and failure of phase transition from vegetative to reproductive growth. Anatomical and histological study revealed that the rapid emergence of leaves in lhd2 was resulted from the rapid initiation of leaf primordia whereas the reduced tiller number was a consequence of the suppression of the tiller bud outgrowth. The molecular and genetic analysis showed that LHD2 encodes a putative RNA binding protein with 67% similarity to maize TEl. Comparison of genome-scale expression profiles between wild-type and lhd2 plants suggested that LHD2 may regulate rice shoot development through KNOXand hormone-related genes. The similar phenotypes caused by LHD2 mutation and the conserved expression pattern of LHD2 indicated a conserved mechanism in controlling the temporal leaf initiation in grass.展开更多
Gelatinization temperature（GT） is an important parameter in evaluating the cooking and eating quality of rice.Indeed,the phenotype,biochemistry and inheritance of GT have been widely studied in recent times.Previous...Gelatinization temperature（GT） is an important parameter in evaluating the cooking and eating quality of rice.Indeed,the phenotype,biochemistry and inheritance of GT have been widely studied in recent times.Previous map-based cloning revealed that GT was controlled by ALK gene,which encodes a putative soluble starch synthase II-3.Complementation vector and RNAi vector were constructed and transformed into Nipponbare mediated by Agrobacterium.Phenotypic and molecular analyses of transgenic lines provided direct evidence for ALK as a key gene for GT.Meanwhile,amylose content,gel consistency and pasting properties were also affected in transgenic lines.Two of four nonsynonymous single nucleotide polymorphisms in coding sequence of ALK were identified as essential for GT.Based on the single nucleotide polymorphisms（SNPs）,two new sets of SNP markers combined with one cleaved amplified polymorphic sequence marker were developed for application in rice quality breeding.展开更多
Epigenetics refers to the study of heritable changes in gene function that do not involve changes in the DNA sequence. Such effects on cellular and physiological phenotypic traits may result from external or environme...Epigenetics refers to the study of heritable changes in gene function that do not involve changes in the DNA sequence. Such effects on cellular and physiological phenotypic traits may result from external or environmental factors or be part of normal developmental program. In eukaryotes, DNA wraps on a histone octamer(two copies of H2A, H2B, H3 and H4) to form nucleosome, the fundamental unit of chromatin. The structure of chromatin is subjected to a dynamic regulation through multiple epigenetic mechanisms, including DNA methylation, histone posttranslational modifications(PTMs), chromatin remodeling and noncoding RNAs. As conserved regulatory mechanisms in gene expression, epigenetic mechanisms participate in almost all the important biological processes ranging from basal development to environmental response. Importantly, all of the major epigenetic mechanisms in mammalians also occur in plants. Plant studies have provided numerous important contributions to the epigenetic research. For example, gene imprinting, a mechanism of parental allele-specific gene expression, was firstly observed in maize; evidence of paramutation, an epigenetic phenomenon that one allele acts in a single locus to induce a heritable change in the other allele, was firstly reported in maize and tomato.Moreover, some unique epigenetic mechanisms have been evolved in plants. For example, the 24-nt siRNA-involved RNA-directed DNA methylation(RdDM) pathway is plant-specific because of the involvements of two plant-specific DNA-dependent RNA polymerases, Pol IV and Pol V. A thorough study of epigenetic mechanisms is of great significance to improve crop agronomic traits and environmental adaptability. In this review, we make a brief summary of important progress achieved in plant epigenetics field in China over the past several decades and give a brief outlook on future research prospects.We focus our review on DNA methylation and histone PTMs, the two most important aspects of epigenetic mechanisms.展开更多
Epigenetics refers to the study of heritable changes in gene expression or cellular phenotype without changes in DNA sequence. Epigenetic regulation of gene expression is accomplished by DNA methylation, histone modif...Epigenetics refers to the study of heritable changes in gene expression or cellular phenotype without changes in DNA sequence. Epigenetic regulation of gene expression is accomplished by DNA methylation, histone modifications, histone variants, chromatin remodeling, and may involve small RNAs. DNA methylation at cytosine is carried out by enzymes called DNA Methyltransferases and is involved in many cellular processes, such as silencing of transposable elements and pericentromeric repeats, X-chromosome inactivation and genomic imprinting, etc. Histone modifications refer to posttranslational covalent attachment of chemical groups onto histones such as phosphorylation, acetylation, and methylation, etc. Histone variants, the non-canonical histones with amino acid sequences divergent from canonical histones, can have different epigenetic impacts on the genome from canonical histones. Higher-order chromatin structures maintained or modified by chromatin remodeling proteins also play important roles in regulating gene expression. Small non-coding RNAs play various roles in the regulation of gene expression at preas well as posttranscriptional levels. A special issue of Molecular Plant on ＇Epigenetics and Plant Development＇ （Volume 4, Number 2, 2009） published a variety of articles covering many aspects of epigenetic regulation of plant development. We have tried here to present a bird＇s-eye view of these credible efforts towards understanding the mysterious world of epigenetics. The majority of the articles are about the chromatin modifying proteins, including histone modifiers, histone variants, and chromatin remodeling pro- teins that regulate various developmental processes, such as flowering time, vernalization, stem cell maintenance, and response to hormonal and environmental stresses, etc. Regulation of expression of seed transcriptome, involvement of direct tandem repeat elements in the PHE1 imprinting in addition to PcG proteins activity, paramutation, and epigenetic barriers in species hybridization are described well. The last two papers are about the Pol V-mediated heterochromatin formation in- dependent of the 24nt-siRNA and the effect of genome position and tissue type on epigenetic regulation of gene expression. These findings not only further our current understanding of epigenetic mechanisms involved in many biological phenomena, but also pave the path for the future work, by raising many new questions that are discussed in the following lines.展开更多
基金The authors thank ProfMary Lou Guerinot （Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire） for providing IRT1 peptide antibody and for the critical reading of the manuscript. We are also grateful to Drs Zhentao Lin and Yongfu Fu （Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing） for providing the BiFC assay system and technical supporting. This work was supported by the National Natural Science Foundation of China （Grant nos, 30530460 and 30521001） and the Ministry of Science and Technology of China （Grant nos, 2005cb20904 and 2006AA 10A 105） and Chinese Academy of Sciences （Grant no. KSCX2-YW-N- 001） as well as by the Harvest Plus-China Program.
文摘Iron is an essential element for plant growth and development. Iron homeostasis in plants is tightly regulated at both transcriptional and posttranscriptional level. Several bHLH transcription factors involved in iron homeostasis have been identified recently. However, their regulatory mechanisms remain unknown. In this work, we demonstrate that the transcription factor FIT interacted with AtbHLH38 and AtbHLH39 and directly conferred the expression regulation of iron uptake genes for iron homeostasis in Arabidopsis. Yeast two-hybrid analysis and transient expression in Arabidopsis protoplasts showed that AtbHLH38 or AtbHLH39 interacted with FIT, a central transcription factor involved in iron homeostasis in Arabidopsis. Expression of FIT/AtbHLH38 or FIT/AtbHLH39 in yeast cells activated GUS expression driven by ferric chelate reductase （FRO2） and ferrous transporter （IRT1） promoters. Overexpression of FITwith either AtbHLH38 or AtbHLH39 in plants converted the expression of the iron uptake genes FRO2 and IRT1 from induced to constitutive. Further analysis revealed that FRO2 and IRT1 were not regulated at the posttranscriptional level in these plants because IRT1 protein accumulation and high ferric chelate reductase activity were detected in the overexpression plants under both iron deficiency and iron sufficiency. The double overexpression plants accumulated more iron in their shoots than wild type or the plants overexpressing either AtbHLH38, AtbHLH39 or FIT. Our data support that ferric-chelate reductase FRO2 and ferrous-transporter IRT1 are the targets of the three transcription factors and the transcription of FRO2 and IRT1 is directly regulated by a complex of FIT/AtbHLH38 or FIT/AtbHLH39.
基金supported by the National Key R&D Program of China (2022YFD1500503 to X.S.)the Key Projects in Science and Technology of Inner Mongolia (2021ZD0031 to X.C.and S.Z.)+6 种基金the National Key Research and Development Program (2022YFF1002802 to X.D.)the Youth Innovation Promotion Association,CAS (Y2022039 to X.D.)the Youth Innovation Promotion Association,CAS (2022096 to S.Z.)the National Science Foundation of China (NSFC32272692 to J.Z.)Project ZR2022QC054 of the Shandong Provincial Natural Science Foundation (to Y.T.)funding from the State Key Laboratory of Protein and Plant Gene Research (to Q.L.).
文摘The inducible CRISPR activation(CRISPR-a)system offers unparalleled precision and versatility for regu-lating endogenous genes,making it highly sought after in plant research.In this study,we developed a chem-ically inducible CRISPR-a tool for plants called ER-Tag by combining the LexA-VP16-ER inducible system with the SunTag CRISPR-a system.We systematically compared different induction strategies and achieved high efficiency in target gene activation.We demonstrated that guide RNAs can be multiplexed and pooled for large-scale screening of effective morphogenic genes and gene pairs involved in plant regeneration.Further experiments showed that induced activation of these morphogenic genes can accelerate regenera-tion and improve regeneration efficiency in both eudicot and monocot plants,including alfalfa,woodland strawberry,and sheepgrass.Our study expands the CRISPR toolset in plants and provides a powerful new strategy for studying gene function when constitutive expression is not feasible or ideal.
基金This work was supported by the National Key Research and Development Program of China(2019YFD1002701-02)the National Natural Science Foundation of China(32170371)the Strategic Priority Research Program of Chinese Academy of Sciences(XDA24030503).
文摘Natural rubber(NR)is an irreplaceable biopolymer of economic and strategic importance owing to its unique physical and chemical properties.The Parárubber tree(Hevea brasiliensis(Willd.ex A.Juss.)Müll.Arg.)is currently the exclusive commercial source of NR,and it is primarily grown in plantations restricted to the tropical and subtropical areas of Southeast Asia.However,current Parárubber production barely meets the sharply increasing global industrial demand for rubber.Petroleum-based synthetic rubber(SR)has been used to supplement the shortage of NR but its industrial performance is not comparable to that of NR.Thus,there is an urgent need to develop new productive rubber crops with broader environmental adaptability.This review summarizes the current research progress on alternative rubberproducing plants,including horticultural plants(Taraxacum kok-saghyz Rodin and Lactuca L.species),woody plants(Parthenium argentatum A.Gray and Eucommia ulmoides Oliv.),and other plant species with potential for NR production.With an emphasis on the molecular basis of NR biosynthesis revealed by a multi-omics approach,we highlight new integrative strategies and biotechnologies for exploring the mechanism of NR biosynthesis with a broader scope,which may accelerate the breeding and improvement of new rubber crops.
基金This work was supported by the National Key Research and Development Program of China(2019YFD1000300)the National Natural Science Foundation of China(31991183 and 32072582)+3 种基金the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA24020308)the Beijing Municipal Science and Technology Project(Z211100004621001)the Qingdao Science and Technology Bureau(22-3-7-xdny-4-nsh)the Key-Area Research and Development Program of Guangdong Province(2018B020202006).
文摘Fruit color is an important horticultural trait,which greatly affects consumer preferences.In tomato,fruit color is determined by the accumulation of different pigments,such as carotenoids in the pericarp and f lavonoids in the peel,along with the degradation of chlorophyll during fruit ripening.Since fruit color is a multigenic trait,it takes years to introgress all color-related genes in a single genetic background via traditional crossbreeding,and the avoidance of linkage drag during this process is difficult.Here,we proposed a rapid breeding strategy to generate tomato lines with different colored fruits from red-fruited materials by CRISPR/Cas9-mediated multiplex gene editing of three fruit color-related genes(PSY1,MYB12,and SGR1).Using this strategy,the red-fruited cultivar‘Ailsa Craig’has been engineered to a series of tomato genotypes with different fruit colors,including yellow,brown,pink,light-yellow,pink-brown,yellow-green,and light green.Compared with traditional crossbreeding,this strategy requires less time and can obtain transgene-free plants with different colored fruits in less than 1 year.Most importantly,it does not alter other important agronomic traits,like yield and fruit quality.Our strategy has great practical potential for tomato breeding and serves as a reference for improving multigene-controlled traits of horticultural crops.
基金supported by grants from the National Key R&D Program of China (2022YFF1003403)the CAS Project for Young Scientists in Basic Research (YSBR-078)+1 种基金the National Natural Science Foundation of China (31788103,32122064,31801014,31900168)the Chinese Academy of Sciences (XDA24030504).
文摘Dear Editor,Genome editing has revolutionized speed breeding by enabling researchers to alter the genome directly as desired(Gao,2021).The most widely used CRISPR–Cas9 technology has mainly been applied to engineer null mutations in coding sequences,with the goal of creating loss-of-function alleles.Recently,upstream regulatory elements of the promoter region and 50 upstream open reading frame(uORF)have been engineered to generate gain-of-function alleles,producing versatile cis-regulatory effects,usually through changes in gene expression levels(Rodrıguez-Leal et al.,2017;Zhang et al.,2018;Song et al.,2022).
基金Supplementary information is linked to the online version of the paper on the Cell Research website. Acknowledgments We thank Professor Gary Loake （University of Edinburg, UK） for critical reading of this manuscript. This work was supported by grants from Ministry of Agriculture of China （2008ZX08001）, Ministry of Science and Technology of China （2009CB 118506, 2006AA10A101）, and National Natural Science Foundation of China （30671128, 30621001）.
文摘The architecture of the panicle, including grain size and panicle morphology, directly determines grain yield. Panicle erectness, which is selected for achieving ideal plant arehitecture in the northern part of China, has drawn increasing attention of rice breeders. Here, dense and erect panicle 2 （dep2） mutant, which shows a dense and erect panicle phenotype, was identified. DEP2 encodes a plant-specific protein without any known functional domain. Expression profiling of DEP2 revealed that it is highly expressed in young tissues, with most abundance in young panicles. Morphological and expression analysis indicated that mutation in DEP2 mainly affects the rapid elongation of rachis and primary and secondary branches, but does not impair the initiation or formation of panicle primordia. Further analysis suggests that decrease of panicle length in dep2 is caused by a defect in cell proliferation during the exponential elongation of panicle. Despite a more compact plant type in the dep2 mutant, no significant alteration in grain production was found between wild type and dep2 mutant. Therefore, the study of DEP2 not only strengthens our understanding of the molecular genetic basis of panicle architecture but also has important implications for rice breeding.
基金We thank Dr Senya Matsufuji(Jikei University,Japan)for providing the yeast spe2 strain,Dr Guixian Xia(Institute of Microbiology,Chinese Academy of Sciences,China)for yeast expression vector pREP5N and ABRC stock center for BAC clones(F17K4 and T16G12)and T-DNA insertion lines(Salk_007279 and Salk_020185).This work was supported by grants from National Natural Science Foundation of China(30330040)the Ministry of Sciences and Technology of China(J02-A-001).
文摘Polyamines are implicated in regulating various developmental processes in plants, but their exact roles and how they govern these processes still remain elusive. We report here an Arabidopsis bushy and dwarf mutant, bud2, which results from the complete deletion of one member of the small gene family that encodes S-adenosylmethionine decarboxylases （SAMDCs） necessary for the formation of the indispensable intermediate in the polyamine biosynthetic pathway. The bud2 plant has enlarged vascular systems in inflorescences, roots, and petioles, and an altered homeostasis ofpolyamines. The double mutant of bud2 and samdcl, a knockdown mutant of another SAMDC member, is embryo lethal, demonstrating that SAMDCs are essential for plant embryogenesis. Our results suggest that polyamines are required for the normal growth and development of higher plants.
基金We thank Prof Joanne Chory （The Salk Institute for Biological Studies, USA） for providing the Arabidopsis bril-101 mutant seeds. This work was supported by grants from the National Natural Science Foundation of China （grant numbers： 30070074, 30330040 and 30570161）.
文摘Brassinosteroids （BRs） are a major group of plant hormones that regulate plant growth and development. BRI1, a protein localized to the plasma membrane, functions as a BR receptor and it has been proposed that its kinase activity has an essential role in BR-regulated plant growth and development. Here we report the isolation and molecular characterization of a new allele of bril, bril-301, which shows moderate morphological phenotypes and a reduced response to BRs under normal growth conditions. Sequence analysis identified a two-base alteration from GG to AT, resulting in a conversion of 989G to 9891 in the BRI1 kinase domain. An in vitro assay of kinase activity showed that bril-301 has no detectable autophosphorylation activity or phosphorylation activity towards the BRI1 substrates TTL and BAK1. Furthermore, our results suggest that bril-301, even with extremely impaired kinase activity, still retains partial function in regulating plant growth and development, which raises the question of whether BRI1 kinase activity is essential for BR-mediated growth and development in higher plants.
基金Acknowledgments This work was supported Science Foundation of China by the National Natural （grant numbers 30530460 and 30521001）, the Ministry of Science and Technology of China （grant numbers 2005cb20904 and 2006AA10A105） and the Chinese Academy of Sciences （grant number KSCX2-YW-N-001）.
文摘Thiamine （vitamin B1） is an essential compound for organisms. It contains a pyrimidine ring structure and a thiazole ring structure. These two moieties of thiamine are synthesized independently and then coupled together. Here we report the molecular characterization of AtTHIC, which is involved in thiamine biosynthesis in Arabidopsis. AtTHIC is similar to Escherichia coli ThiC, which is involved in pyrimidine biosynthesis in prokaryotes. Heterologous expression of AtTHIC could functionally complement the thiC knock-out mutant of E. coll. Downregulation of AtTHIC expression by T-DNA insertion at its promoter region resulted in a drastic reduction of thiamine content in plants and the knock-down mutant thicl showed albino （white leaves） and lethal phenotypes under the normal culture conditions. The thicl mutant could be rescued by supplementation of thiamine and its defect functions could be complemented by expression ofAtTHIC cDNA. Transient expression analysis revealed that the AtTHIC protein targets plastids and chloroplasts. AtTHIC was strongly expressed in leaves, flowers and siliques and the transcription of AtTHIC was downregulated by extrinsic thiamine. In conclusion, AtTHIC is a gene involved in pyrimidine synthesis in the thiamine biosynthesis pathway of Arabidopsis, and our results provide some new clues for elucidating the pathway of thiamine biosynthesis in plants.
基金We thank Dr Ottoline Leyser （University of York, UK） for providing axrl-3 and Dr Mark Estelle （UC, San Diego, USA） for providing tirlafb2afb3 triple mutant seeds. This work was supported by a grant from the National Natural Science Foundation of China （30830009）.
文摘The ratio of auxin and cytokinin plays a crucial role in regulating aerial architecture by promoting or repressing axillary bud outgrowth. We have previously identified an Arabidopsis mutant bud2 that displays altered root and shoot architecture, which results from the loss-of-function of S-adenosylmethionine decarboxylase 4 （SAMDC4）. In this study, we demonstrate that BUD2 could be induced by auxin, and the induction is dependent on auxin signaling. The mutation of BUD2 results in hyposensitivity to auxin and hypersensitivity to cytokinin, which is confirmed by callus induction assays. Our study suggests that polyamines may play their roles in regulating the plant architecture through affecting the homeostasis of cytokinins and sensitivities to auxin and cytokinin.
基金supported by the National Natural Science Foundation of China(31788103,32170620)the Chinese Academy of Sciences(QYZDY-SSW-SMC022,XDB27030201,XDA24010302)the State Key Laboratory of Plant Genomics。
文摘Phased small interfering RNAs(phasiRNAs) are abundantly expressed in anthers and linked to environment-related male fertility in grasses, yet how they function under different environmental conditions remains unclear. Here, we identified a rice(Oryza sativa) low temperature-induced Argonaute(AGO) protein, OsAGO1d, that is responsible for generating phasiRNAs and preserving male fertility at low temperature. Loss of OsAGO1d function causes low-temperature male sterility associated with delayed programmed cell death of tapetal cells during anther development. OsAGO1d binds miR2118 and miR2275 family members and triggers phasiRNA biogenesis;it also binds 21-nt phasiRNAs with a 5′ terminal U. In total, phasiRNAs from 972loci are OsAGO1d-dependent. OsAGO1d protein moves from anther wall cells into meiocytes, where it loads miR2275 to produce 24-nt phasiRNAs. Together, our results show that OsAGO1d acts as a mobile signal to fine-tune phasiRNA production and this function is important for male fertility at low temperature.
基金the research grants from the Ministry of Sciences and Technology，the Natural Science Foundation of China，the Ministry of Education
文摘Pollen germination and embryogenesis are important to sexual plant reproduction. The processes require a large number of genes to be expressed. Transcription of eukaryotic nuclear genes is accomplished by three conserved RNA polymerases acting in association with a set of auxiliary general transcription factors （GTFs）, including B-type GTFs. The roles of B-type GTFs in plant reproduction remain poorly understood. Here we report functional characterization of a novel plant-specific TFIIB-related gene PTF2 in Arabidopsis. Mutation in PTF2 caused failure of pollen germination. Pollen-rescue revealed that the mutation also disrupted embryogenesis and resulted in seed abortion. PTF2 is expressed prolifically in developing pollen and the other tissues with active cell division and differentiation, including embryo and shoot apical meristem. The PTF2 protein shares a lower amino acid sequence similarity with other known TFIIB and TFIIB-related proteins in Arabidopsis. It can interact with TATA-box binding protein 2 （TBP2） and bind to the double- stranded DNA （dsDNA） as the other known TFIIB and TFIIB-related proteins do. In addition, PTF2 can form a homodimer and interact with the subunits of RNA polymerases （RNAPs）, implying that it may be involved in the RNAPs transcription. These results suggest that PTF2 plays crucial roles in pollen germination and embryogenesis in Arabidopsis, possibly by regulating gene expression through interaction with TBP2 and the subunits of RNAPs.
基金supported by the National Natural Science Foundation of China(31830057)the National Key R&D Program of China(2022YFF1001400)the Foundation of Hubei Hongshan Laboratory(2021hszd014).
文摘E3 ligases are key enzymes required for protein degradation.Here,we identified a C3H2C3 RING domaincontaining E3 ubiquitin ligase gene named GhATL68b.It is preferentially and highly expressed in developing cotton fiber cells and shows greater conservation in plants than in animals or archaea.The four orthologous copies of this gene in various diploid cottons and eight in the allotetraploid G.hirsutum were found to have originated from a single common ancestor that can be traced back to Chlamydomonas reinhardtii at about 992 million years ago.Structural variations in the GhATL68b promoter regions of G.hirsutum,G.herbaceum,G.arboreum,and G.raimondii are correlated with significantly different methylation patterns.Homozygous CRISPR-Cas9 knockout cotton lines exhibit significant reductions in fiber quality traits,including upper-half mean length,elongation at break,uniformity,and mature fiber weight.In vitro ubiquitination and cell-free protein degradation assays revealed that GhATL68b modulates the homeostasis of 2,4-dienoyl-CoA reductase,a rate-limiting enzyme for theβ-oxidation of polyunsaturated fatty acids(PUFAs),via the ubiquitin proteasome pathway.Fiber cells harvested from these knockout mutants contain significantly lower levels of PUFAs important for production of glycerophospholipids and regulation of plasma membrane fluidity.The fiber growth defects of the mutant can be fully rescued by the addition of linolenic acid(C18:3),the most abundant type of PUFA,to the ovule culture medium.This experimentally characterized C3H2C3 type E3 ubiquitin ligase involved in regulating fiber cell elongation may provide us with a new genetic target for improved cotton lint production.
基金The National Natural Science Foundation of China(grant nos.32388201,32300512 and U22A20467)“Strategic Priority Research Program”of the Chinese Academy of Sciences(grant no.XDA24030501)+1 种基金CAS Project for Young Scientists in Basic Research(YSBR-078)the Xplorer Prize。
文摘Gene innovation plays an essential role in trait evolution.Rhizobial symbioses,the most important N2-fixing agent in agricultural systems that exists mainly in Leguminosae,is one of the most attractive evolution events.However,the gene innovations underlying Leguminosae root nodule symbiosis(RNS)remain largely unknown.Here,we investigated the gene gain event in Leguminosae RNS evolution through comprehensive phylogenomic analyses.We revealed that Leguminosae-gain genes were acquired by gene duplication and underwent a strong purifying selection.Kyoto Encyclopedia of Genes and Genomes analyses showed that the innovated genes were enriched in flavonoid biosynthesis pathways,particular downstream of chalcone synthase(CHS).Among them,Leguminosae-gain typeⅡchalcone isomerase(CHI)could be further divided into CHI1A and CHI1B clades,which resulted from the products of tandem duplication.Furthermore,the duplicated CHI genes exhibited exon–intron structural divergences evolved through exon/intron gain/loss and insertion/deletion.Knocking down CHI1B significantly reduced nodulation in Glycine max(soybean)and Medicago truncatula;whereas,knocking down its duplication gene CHI1A had no effect on nodulation.Therefore,Leguminosae-gain typeⅡCHI participated in RNS and the duplicated CHI1A and CHI1B genes exhibited RNS functional divergence.This study provides functional insights into Leguminosae-gain genetic innovation and sub-functionalization after gene duplication that contribute to the evolution and adaptation of RNS in Leguminosae.
基金grants from the Ministry of Science and Technology of China(2005CB 1208)the National Natural Science Foundation of China(30330040 and 30570161).
文摘Tiller angle of rice （Oryza sativa L.） is an important agronomic trait that contributes to grain production, and has long attracted attentions of breeders for achieving ideal plant architecture to improve grain yield. Although enormous efforts have been made over the past decades to study mutants with extremely spreading or compact tillers, the molecular mechanism underlying the control of tiller angle of cereal crops remains unknown. Here we report the cloning of the LAZY1 （LA1） gene that regulates shoot gravitropism by which the rice tiller angle is controlled. We show that LA1, a novel grass-specific gene, is temporally and spatially expressed, and plays a negative role in polar auxin transport （PAT）. Loss-of-function of LA1 enhances PAT greatly and thus alters the endogenous IAA distribution in shoots, leading to the reduced gravitropism, and therefore the tiller-spreading phenotype of rice plants.
基金We would like to thank Dr Nam-Hai Chua （Rockefeller Univer- sity） for kindly providing the pBA002Myc vector and the Arabi- dopsis Biological Resource Center （ABRC）, Ohio State University for providing ToDNA insertion lines. This work was supported by grants from National Natural Science Foundation of China （No. 30530400/90717006/30670195） to Q Xie and Y Wu, the Chinese Academy of Science （KSCX2-YW-N-010 and CXTD-S2005-2）, and the （iuangdong Natural Science Foundation, China （No. 5300648） to Z Deng.
文摘NAC family genes encode plant-specific transcription factors involved in diverse biological processes. In this study, the Arabidopsis NAC gene ATAF1 was found to be induced by drought, high-salinity, abscisic acid （ABA）, methyl jasmonate, mechanical wounding, and Botrytis cinerea infection. Significant induction of ATAF1 was found in an ABA-deficient mutant aba2 subjected to drought or high salinity, revealing an ABA-independent mechanism of expression. Arabidopsis ATAFl-overexpression lines displayed many altered phenotypes, including dwarfism and short primary roots. Furthermore, in vivo experiments indicate that ATAF1 is a bonafide regulator modulating plant responses to many abiotic stresses and necrotrophic-pathogen infection. Overexpression of ATAF1 in Arabidopsis increased plant sensitivity to ABA, salt, and oxidative stresses. Especially, ATAF1 overexpression plants, but not mutant lines, showed remarkably enhanced plant tolerance to drought. Additionally, ATAF1 overexpression enhanced plant susceptibility to the necrotrophic pathogen B. cinerea, but did not alter disease symptoms caused by avirulent or virulent strains of P. syringae pv tomato DC3000. Transgenic plants overexpressing ATAF1 were hypersensitive to oxidative stress, suggesting that reactive oxygen intermediates may be related to ATAFl-mediated signaling in response to both pathogen and abiotic stresses.
文摘During vegetative development, higher plants continuously form new leaves in regular spatial and temporal patterns. Mutants with abnormal leaf developmental patterns not only provide a great insight into understanding the regulatory mechanism of plant architecture, but also enrich the ways to its modification by which crop yield could be improved. Here, we reported the characterization of the rice leafy-head2 （lhd2） mutant that exhibits shortened plastochron, dwarfism, reduced tiller number, and failure of phase transition from vegetative to reproductive growth. Anatomical and histological study revealed that the rapid emergence of leaves in lhd2 was resulted from the rapid initiation of leaf primordia whereas the reduced tiller number was a consequence of the suppression of the tiller bud outgrowth. The molecular and genetic analysis showed that LHD2 encodes a putative RNA binding protein with 67% similarity to maize TEl. Comparison of genome-scale expression profiles between wild-type and lhd2 plants suggested that LHD2 may regulate rice shoot development through KNOXand hormone-related genes. The similar phenotypes caused by LHD2 mutation and the conserved expression pattern of LHD2 indicated a conserved mechanism in controlling the temporal leaf initiation in grass.
基金supported by grants from the Hi-Tech Research and Development (863) Program of China (2006AA10A102)Transform Program (2008ZX08001-006)+1 种基金Science and Technology Project,Zhejiang Province (2009C32047)CNRRI foundation (2009RG002-1)
文摘Gelatinization temperature（GT） is an important parameter in evaluating the cooking and eating quality of rice.Indeed,the phenotype,biochemistry and inheritance of GT have been widely studied in recent times.Previous map-based cloning revealed that GT was controlled by ALK gene,which encodes a putative soluble starch synthase II-3.Complementation vector and RNAi vector were constructed and transformed into Nipponbare mediated by Agrobacterium.Phenotypic and molecular analyses of transgenic lines provided direct evidence for ALK as a key gene for GT.Meanwhile,amylose content,gel consistency and pasting properties were also affected in transgenic lines.Two of four nonsynonymous single nucleotide polymorphisms in coding sequence of ALK were identified as essential for GT.Based on the single nucleotide polymorphisms（SNPs）,two new sets of SNP markers combined with one cleaved amplified polymorphic sequence marker were developed for application in rice quality breeding.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB27040203)the National Natural Science Foundation of China (No.31770155)
文摘Epigenetics refers to the study of heritable changes in gene function that do not involve changes in the DNA sequence. Such effects on cellular and physiological phenotypic traits may result from external or environmental factors or be part of normal developmental program. In eukaryotes, DNA wraps on a histone octamer(two copies of H2A, H2B, H3 and H4) to form nucleosome, the fundamental unit of chromatin. The structure of chromatin is subjected to a dynamic regulation through multiple epigenetic mechanisms, including DNA methylation, histone posttranslational modifications(PTMs), chromatin remodeling and noncoding RNAs. As conserved regulatory mechanisms in gene expression, epigenetic mechanisms participate in almost all the important biological processes ranging from basal development to environmental response. Importantly, all of the major epigenetic mechanisms in mammalians also occur in plants. Plant studies have provided numerous important contributions to the epigenetic research. For example, gene imprinting, a mechanism of parental allele-specific gene expression, was firstly observed in maize; evidence of paramutation, an epigenetic phenomenon that one allele acts in a single locus to induce a heritable change in the other allele, was firstly reported in maize and tomato.Moreover, some unique epigenetic mechanisms have been evolved in plants. For example, the 24-nt siRNA-involved RNA-directed DNA methylation(RdDM) pathway is plant-specific because of the involvements of two plant-specific DNA-dependent RNA polymerases, Pol IV and Pol V. A thorough study of epigenetic mechanisms is of great significance to improve crop agronomic traits and environmental adaptability. In this review, we make a brief summary of important progress achieved in plant epigenetics field in China over the past several decades and give a brief outlook on future research prospects.We focus our review on DNA methylation and histone PTMs, the two most important aspects of epigenetic mechanisms.
文摘Epigenetics refers to the study of heritable changes in gene expression or cellular phenotype without changes in DNA sequence. Epigenetic regulation of gene expression is accomplished by DNA methylation, histone modifications, histone variants, chromatin remodeling, and may involve small RNAs. DNA methylation at cytosine is carried out by enzymes called DNA Methyltransferases and is involved in many cellular processes, such as silencing of transposable elements and pericentromeric repeats, X-chromosome inactivation and genomic imprinting, etc. Histone modifications refer to posttranslational covalent attachment of chemical groups onto histones such as phosphorylation, acetylation, and methylation, etc. Histone variants, the non-canonical histones with amino acid sequences divergent from canonical histones, can have different epigenetic impacts on the genome from canonical histones. Higher-order chromatin structures maintained or modified by chromatin remodeling proteins also play important roles in regulating gene expression. Small non-coding RNAs play various roles in the regulation of gene expression at preas well as posttranscriptional levels. A special issue of Molecular Plant on ＇Epigenetics and Plant Development＇ （Volume 4, Number 2, 2009） published a variety of articles covering many aspects of epigenetic regulation of plant development. We have tried here to present a bird＇s-eye view of these credible efforts towards understanding the mysterious world of epigenetics. The majority of the articles are about the chromatin modifying proteins, including histone modifiers, histone variants, and chromatin remodeling pro- teins that regulate various developmental processes, such as flowering time, vernalization, stem cell maintenance, and response to hormonal and environmental stresses, etc. Regulation of expression of seed transcriptome, involvement of direct tandem repeat elements in the PHE1 imprinting in addition to PcG proteins activity, paramutation, and epigenetic barriers in species hybridization are described well. The last two papers are about the Pol V-mediated heterochromatin formation in- dependent of the 24nt-siRNA and the effect of genome position and tissue type on epigenetic regulation of gene expression. These findings not only further our current understanding of epigenetic mechanisms involved in many biological phenomena, but also pave the path for the future work, by raising many new questions that are discussed in the following lines.
