The impact of high-temperature stress on rice: Challenges and solutions

Heat stress (HS) caused by rapidly warming climate has become a serious threat to global food security.Rice (Oryza sativa L.) is a staple food crop for over half of the world’s population,and its yield and quality are often reduced by HS.There is an urgent need for breeding heat-tolerant rice cultivars.Rice plants show various morphological and physiological symptoms under HS.Precise analysis of the symptoms(phenotyping) is essential for the selection of elite germplasm and the identification of thermotolerance genes.In response to HS,rice plants trigger a cascade of events and activate complex transcriptional regulatory networks.Protein homeostasis under HS is especially important for rice thermotolerance,which is affected by protein quality control,effective elimination of toxic proteins,and translational regulation.Although some agronomic and genetic approaches for improving heat tolerance have been adopted in rice,the molecular mechanisms underlying rice response to HS are still elusive,and success in engineering rice thermotolerance in breeding has been limited.In this review,we summarize HS-caused symptoms in rice and progress in heat-stress sensing and signal cascade research,and propose approaches for improving rice thermotolerance in future.

Elite sd1 alleles in japonica rice and their breeding applications in northeast China

The Green Revolution gene sd1 has been used extensively in modern rice breeding,especially in indica cultivars.However,elite sd1 alleles and related germplasm resources used for japonica rice breeding have not been identified,and extensive efforts are needed for japonica rice breeding to obtain new dwarfing sources.Data from MBKbase-Rice revealed seven sd1 haplotypes in indica and four in japonica rice.Two new sd1 alleles were identified in indica rice.In 295 japonica accessions from northeast Asia,except for the weak functional allele SD1-EQ,sd1-r was the major allele,reducing plant height in comparison with SD1-EQ.Japonica germplasm resources carrying reported sd1 alleles were identified by genotype searching and further verified by literature search,genealogical analysis,and d Caps markers.Pedigrees and geographic distribution showed that sd1-r is an excellent allele widely used in northern China and Tohoku in Japan,and sd1-j is commonly used in east China and Kyushu in Japan.Dongnong-and Xiushui-series cultivars carrying sd1-r and sd1-j,respectively,are essential branches of the backbone parents of Chinese japonica rice,Akihikari and Ce21,with the largest number of descendants and derived generations.In semi-dwarf japonica rice breeding,sd1-d was introgressed into Daohuaxiang 2(DHX2).Dwarf and semi-dwarf lines carrying sd1-d were selected and designated as 1279 and 1280,respectively,after withstanding typhoon-induced strong winds and heavy rains in 2020,and are anticipated to become useful intermediate materials for future genetic research and breeding.This work will facilitate the introduction,parental selection,and marker-assisted breeding,and provide a material basis for the next step in identifying favorable genes that selected together with the sd1 alleles in japonica backbone parents.

Salt tolerance in rice:Physiological responses and molecular mechanisms

Crop yield loss due to soil salinization is an increasing threat to agriculture worldwide.Salt stress drastically affects the growth,development,and grain productivity of rice(Oryza sativa L.),and the improvement of rice tolerance to salt stress is a desirable approach for meeting increasing food demand.The main contributors to salt toxicity at a global scale are Na^(+)and Cl^(-)ions,which affect up to 50%of irrigated soils.Plant responses to salt stress occur at the organismic,cellular,and molecular levels and are pleiotropic,involving(1)maintenance of ionic homeostasis,(2)osmotic adjustment,(3)ROS scavenging,and(4)nutritional balance.In this review,we discuss recent research progress on these four aspects of plant physiological response,with particular attention to hormonal and gene expression regulation and salt tolerance signaling pathways in rice.The information summarized here will be useful for accelerating the breeding of salt-tolerant rice.

Exploration of rice yield potential: Decoding agronomic and physiological traits

Rice grain yield is determined by three major"visible"morphological traits:grain weight,grain number per panicle,and effective tiller number,which are affected by a series of"invisible"physiological factors including nutrient use efficiency and photosynthetic efficiency.In the past few decades,substantial progress has been made on elucidating the molecular mechanisms underlying grain yield formation,laying a solid foundation for improving rice yield by molecular breeding.This review outlines our current understanding of the three morphological yield-determining components and summarizes major progress in decoding physiological traits such as nutrient use efficiency and photosynthetic efficiency.It also discusses the integration of current knowledge about yield formation and crop improvement strategies including genome editing with conventional and molecular breeding.

Successful Production of an All-Female Common Carp (Cyprinus carpio L.) Population Using cyp17a1-Deficient Neomale Carp

Due to sexual dimorphism in the growth of certain cultured fish species,the production of monosex fishes is desirable for the aquaculture industry.Nowadays,the most widely practiced technique available for the mass production of monosex fish populations is sex steroid-induced sex reversal.Here,a novel strategy for the successful production of all-female(AF)common carp(Cyprinus carpio L.),to take advantage of the sexual dimorphism in growth documented in this species,has been developed using genetic engineering via single gene-targeting manipulation without any exogenous hormone treatments.Male and female heterozygous cyp17a1-deficient common carp were first obtained using the clustered regularly interspaced short palindromic repeats/CRISPR-associated endonuclease 9(CRISPR/Cas9)technique.An all-male phenotype for homozygous cyp17a1-deficient carp,regardless of the individuals’sexdetermination genotypes(XY or XX),has been observed.A male-specific DNA marker newly identified in our laboratory was used to screen the neomale carp population with the XX genotype from the cyp17a1-deficient carp.These neomale carp develop a normal testis structure with normal spermatogenesis and sperm capacity.The neomale common carp were then mated with wild-type(WT)females(cyp17a1^(+/+)XX genotype)using artificial fertilization.All the AF offspring sample fish from the neomale-WT female mating were confirmed as having the cyp17a^(1+/-)XX genotype,and normal development of gonads to ovaries was observed in 100.00%of this group at eight months post-fertilization(mpf).A total of 1000 carp fingerlings,500 from the WT male and female and 500 from the neomale and WT female mating,were mixed and reared in the same pond.The average body weight of cyp17a1^(+/-)XX females was higher by 6.60%(8 mpf)and 32.66%(12 mpf)than that of the control common carp.Our study demonstrates the first successful production of a monosex teleost population with the advantages of sexual dimorphism in growth using genetic manipulation targeting a single locus.

The U-box ubiquitin ligase TUD1 promotes brassinosteroid-induced GSK2 degradation in rice

Brassinosteroids(BRs)are a class of steroid hormones with great potential for use in crop improvement.De-repression is usually one of the key events in hormone signaling.However,how the stability of GSK2,the central negative regulator of BR signaling in rice(Oryza sativa),is regulated by BRs remains elusive.Here,we identify the U-box ubiquitin ligase TUD1 as a GSK2-interacting protein by yeast two-hybrid screening.We show that TUD1 is able to directly interact with GSK2 and ubiquitinate the protein.Phenotypes of the tud1 mutant are highly similar to those of plants with constitutively activated GSK2.Consistent with this finding,GSK2 protein accumulates in the tud1 mutant compared with the wild type.In addition,inhibition of BR synthesis promotes GSK2 accumulation and suppresses TUD1 stability.By contrast,BRs can induce GSK2 degradation but promote TUD1 accumulation.Furthermore,the GSK2 degradation process is largely impaired in tud1 in response to BR.In conclusion,our study demonstrates the role of TUD1 in BR-induced GSK2 degradation,thereby advancing our understanding of a critical step in the BR signaling pathway of rice.

The INO80 chromatin remodeling complex promotes thermo-morphogenesis by connecting H2A.Z eviction and active transcription in Arabidopsis.

Global warming imposes a major threat to plant growth and crop production. In some plants including Arabidopsis thaliana, elevated temperatures induce a series of morphological and developmental adjustments, termed thermomorphogenesis to facilitate plant cooling under high-temperature conditions. Plant thermal response is suppressed by histone variant H2A.Z. At warm temperatures, H2A.Z is evicted from nucleosomes at thermo-responsive genes, resulting in their expression changes. However, the mechanisms that regulate H2A.Z eviction and subsequent transcription changes are largely unknown. Here, we show that the INO80 chromatin remodeling complex (INO80-C) promotes thermomorphogenesis and activates the expression of thermo-responsive and auxin-related genes. INO80-C associates with PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), a potent regulator in thermomorphogenesis, and mediates temperature-induced H2A.Z eviction at PIF4 targets. Moreover, INO80-C directly interacts with COMPASS-like and transcription elongation factors to promote active histone modification Histone H3 lysine 4 trimethylation (H3K4me3) and RNA Polymerase II (RNA Pol II) elongation, leading to the thermal induction of transcription. Notably, transcription elongation factors SPT4 and SPT5 are required for the H2A.Z eviction at PIF4 targets, suggesting the cooperation of INO80-C and transcription elongation in H2A.Z removal. Our results demonstrate that the (PIF4)-(INO80-C)-(COMPASS-like)-(transcription elongator) module controls plant thermal response, and establish a link between H2A.Z eviction and active transcription.

Modulation of nitrate-induced phosphate response by the MYB transcription factor RLI1/HINGE1 in the nucleus

The coordinated utilization of nitrogen(N)and phosphorus(P)is vital for plants to maintain nutrient balance and achieve optimal growth.Previously,we revealed a mechanism by which nitrate induces genes for phosphate utilization;this mechanism depends on NRT1.1B-facilitated degradation of cytoplasmic SPX4,which in turn promotes cytoplasmic-nuclear shuttling of PHR2,the central transcription factor of phosphate signaling,and triggers the nitrate-induced phosphate response(NIPR)and N-P coordinated utilization in rice.In this study,we unveiled a fine-tuning mechanism of NIPR in the nucleus regulated by Highly Induced by Nitrate Gene 1(HINGE1,also known as RLI1),a MYB-transcription factor closely related to PHR2.RLI1/HINGE1,which is transcriptionally activated by PHR2 under nitrate induction,can directly activate the expression of phosphate starvation-induced genes.More importantly,RLI1/HINGE1 competes with PHR2 for binding to its repressor proteins in the nucleus(SPX proteins),and consequently releases PHR2 to further enhance phosphate response.Therefore,RLI1/HINGE1 amplifies the phosphate response in the nucleus downstream of the cytoplasmic SPX4-PHR2 cascade,thereby enabling fine-tuning of N-P balance when nitrate supply is sufficient.

From Green Super Rice to green agriculture:Reaping the promise of functional genomics research

Producing sufficient food with finite resources to feed the growing global population while having a smaller impact on the environment has always been a great challenge.Here,we review the concept and practices of Green Super Rice(GSR)that have led to a paradigm shift in goals for crop genetic improvement and models of food production for promoting sustainable agriculture.The momentous achievements and global deliveries of GSR have been fueled by the integration of abundant genetic resources,functional gene discoveries,and innovative breeding techniques with precise gene and whole-genome selection and efficient agronomic management to promote resource-saving,environmentally friendly crop production systems.We also provide perspectives on new horizons in genomic breeding technologies geared toward delivering green and nutritious crop varieties to further enhance the development of green agricul-ture and better nourish the world population.

An engineered platform for reconstituting functional multisubunit SCF E3 ligase in vitro

Multisubunit SKP1/Cullin1/F-box(SCF)E3 ligases play essential roles in regulating the stability of crucial regulatory factors and controlling growth and development in eukaryotes.Detecting E3 ligase activity in vitro is important forexploring the molecular mechanism of protein ubiquitination.However,in vitro ubiquitination assay systems for multisubunit E3 ligases remain difficult to achieve,especially in plants,mainly owing to difficulties in achieving active components of multisubunit E3 ligases with high purity and characterizing specific E2 and E3 pairs.In this study,we characterized components of the rice ScFDiwARF3(SCFDs)E3 ligase,screened the coordinated E2,and reconstituted active ScFD3 E3 ligase in vitro.We further engineered SCFD3 E3 ligase using a fused SKP1-Cullin1-RBX1(eSCR)protein and found that both the wild-type SCFD3 E3 ligase and the engineered SCFD3 E3 ligase catalyzed ubiquitination of the substrate D53,which is the key transcriptional repressor in strigolactone signaling.Finally,we replaced D3 with other F-box proteins from rice and humans and reconstituted active escF E3 ligases,including escFaID2,escFBxL1s,and escFcDC4 E3 ligases.Our work reconstitutes functional SCF E3 ligases in vitro and generates an engineered system with interchangeable F-box proteins,providing a powerful platform for studying the mechanisms of multisubunit SCF E3 ligases in eukaryotes.

The divergence of brassinosteroid sensitivity between rice subspecies involves natural variation conferring altered internal auto-binding of OsBSK2

Japonica/geng and indica/xian are two major rice(Oryza sativa)subspecies with multiple divergent traits,but how these traits are related and interact within each subspecies remains elusive.Brassinosteroids(BRs)are a class of steroid phytohormones that modulate many important agronomic traits in rice.Here,using different physiological assays,we revealed that japonica rice exhibits an overall lower BR sensitivity than indica.Extensive screening of BR signaling genes led to the identification of a set of genes distributed throughout the primary BR signaling pathway with divergent polymorphisms.Among these,we demonstrate that the C38/T variant in BR Signaling Kinase2(OsBSK2),causing the amino acid change P13L,plays a central role in mediating differential BR signaling in japonica and indica rice.OsBSK2in indica plays a greater role in BR signaling than OsB SK2in japonica by affecting the auto-binding and protein accumulation of OsBSK2.Finally,we determined that OsBSK2 is involved in a number of divergent traits in japonica relative to indica rice,including grain shape,tiller number,cold adaptation,and nitrogen-use efficiency.Our study suggests that the natural variation in OsB SK2 plays a key role in the divergence of BR signaling,which underlies multiple divergent traits between japonica and indica.

POLLEN STERILITY,a novel suppressor of cell division,is required for timely tapetal programmed cell death in rice

Timely programmed cell death(PCD) of the tapetum supplying nutrients to microspores is a prerequisite for normal pollen development.Here we identified a unique mutant of rice(Oryza sativa L.),pollen sterility(post),which showed aborted pollens accompanied with extra-large husks.Due to failure of timely PCD of tapetal cells,post exhibited abnormal pollen wall patterning and defective pollen grains.By map-based cloning,we identified a causal gene,POST,encoding a novel protein which is ubiquitously localized in cells.RNA in situ hybridization showed that POST is highly detected in the tapetum and microspores at stages 8 and 9.Transcriptome analysis indicated that POST could function as an important regulator of the metabolic process involved in tapetal PCD.Compared with wild-type rice,post mutant has an increased cell number resulting from elevated expression of cell cycle associated genes in grain husks.Overexpression of POST inhibits grain size in wild type,while appropriate expression of POST in post mutant can recover the seed fertility but has little effect on the large grains,illustrating that fine-tuning of POST expression could be a potential strategy for rice yield improvement.The connection between cell division and cell death conferred by POST provides novel insights into the understanding of the tapetal PCD process.

Rice geographic adaption to poor soil: novel insights for sustainable agriculture

Rice is one of the most important staple crops, feeding more than half of the population on Earth. How to steadily increase yield has been a major challenge in the context of an ever-growing population and climate change. Over the past decades, breeding practices have greatly increased cereal grain yield mainly owing to the adoption of semidwarf alleles and the development of hybrid crop varieties.

A REF6-dependent H3K27me3-depleted state facilitates gene activation during germination in Arabidopsis

Seed germination is a critical developmental switch from a quiescent state to active growth,which involves extensive changes in metabolism,gene expression,and cellular identity.However,our understanding of epigenetic and transcriptional reprogramming during this process is limited.The histone H3 lysine 27 trimethylation(H3K27me3)plays a key role in regulating gene repression and cell fate specification.Here,we profile H3K27me3 dynamics and dissect the function of H3K27 demethylation during germination in Arabidopsis.Our temporal genome-wide profiling of H3K27me3 and transcription reveals delayed H3K27me3reprogramming compared with transcriptomic changes during germination,with H3K27me3 changes mainly occurring when the embryo is entering into vegetative development.RELATIVE OF EARLY FLOWERING 6(REF6)-mediated H3K27 demethylation is necessary for robust germination but does not significantly contribute to H3K27me3 dynamics during germination,but rather stably establishes an H3K27me3-depleted state that facilitates the activation of hormone-related and expansin-coding genes important for germination.We also show that the REF6 chromatin occupancy is gradually established during germination to counteract increased Polycomb repressive complex 2(PRC2).Our study provides key insights into the H3K27me3 dynamics during germination and suggests the function of H3K27me3 in facilitating cell fate switch.Furthermore,we reveal the importance of H3K27 demethylation-established transcriptional competence in gene activation during germination and likely other developmental processes.

Nitrogen assimilation in plants:current status and future prospects

Nitrogen(N)is the driving force for crop yields;however,excessive N application in agriculture not only increases production cost,but also causes severe environmental problems.Therefore,comprehensively understanding the molecular mechanisms of N use efficiency(NUE)and breeding crops with higher NUE is essential to tackle these problems.NUE of crops is determined by N uptake,transport,assimilation,and remobilization.In the process of N assimilation,nitrate reductase(NR),nitrite reductase(Ni R),glutamine synthetase(GS),and glutamine-2-oxoglutarate aminotransferase(GOGAT,also known as glutamate synthase)are the major enzymes.NR and Ni R mediate the initiation of inorganic N utilization,and GS/GOGAT cycle converts inorganic N to organic N,playing a vital role in N assimilation and the final NUE of crops.Besides,asparagine synthetase(ASN),glutamate dehydrogenase(GDH),and carbamoyl phosphate synthetase(CPSase)are also involved.In this review,we summarize the function and regulation of these enzymes reported in three major crops—rice,maize,and wheat,also in the model plant Arabidopsis,and we highlight their application in improving NUE of crops via manipulating N assimilation.Anticipated challenges and prospects toward fully understanding the function of N assimilation and further exploring the potential for NUE improvement are discussed.

A transceptor-channel complex couples nitrate sensing to calcium signaling in Ambidopsis

Nitrate-induced Ca^(2+) signaling is crucial for the primary nitrate response in plants.However,the molecular mechanism underlying the generation of the nitrate-specific calcium signature remains unknown.We report here that a cyclic nucleotide-gated channel(CNGC)protein,CNGC15,and the nitrate transceptor(NRT1.1)constitute a molecular switch that controls calcium influx depending on nitrate levels.The expression of CNGC15 is induced by nitrate,and its protein is localized at the plasma membrane after establishment of young seedlings.We found that disruption of CNGC15 results in the loss of the nitrate-induced Ca^(2+) signature(primary nitrate response)and retards root growth,reminiscent of the phenotype observed in the nrt1.1 mutant.We further showed that CNGC15 is an active Ca^(2+)-permeable channel that physically interacts with the NRT1.1 protein in the plasma membrane.Importantly,we discovered that CNGC15-NRT1.1 interaction silences the channel activity of the heterocomplex,which dissociates upon a rise in nitrate levels,leading to reactivation of the CNGC15 channel.The dynamic interactions between CNGC15 and NRT1.1 therefore control the channel activity and Ca^(2+) influx in a nitrate-dependent manner.Our study reveals a new nutrient-sensing mechanism that utilizes a nutrient transceptor-channel complex assembly to couple nutrient status to a specific Ca^(2+) signature.

A cryptic inhibitor of cytokinin phosphorelay controls rice grain size

Plant hormone cytokinin signals through histidine-aspartic acid(H-D)phosphorelay to regulate plant growth and development.While it is well known that the phosphorelay involves histidine kinases,histidine phosphotransfer proteins(HPs),and response regulators(RRs),how this process is regulated by external components remains unknown.Here we demonstrate that protein phosphatase with kelch-like domains(PPKL1),known as a signaling component of steroid hormone brassinosteroid,is actually a cryptic inhibitor of cytokinin phosphorelay in rice(Oryza sativa).Mutation at a specific amino acid D364 of PPKL1 activates cytokinin response and thus enlarges grain size in a semi-dominant mutant named s48.Overexpression of PPKL1 containing D364,either with the deletion of the phosphatase domain or not,rescues the s48 mutant phenotype.PPKL1 interacts with OsAHP2,one of authentic HPs,and D364 resides in a region resembling the receiver domain of RRs.Accordingly,PPKL1 can utilize D364 to suppress OsAHP2-to-RR phosphorelay,whereas mutation of D364 abolishes the effect.This function of PPKL1 is independent of the phosphatase domain that is required for brassinosteroid signaling.Importantly,editing of the D364-residential region produces a diversity of semi-dominant mutations associated with variously increased grain sizes.Further screening of the edited plants enables the identification of two genotypes that confer significantly improved grain yield.Collectively,our study uncovers a noncanonical cytokinin signaling suppressor and provides a robust tool for seed rational design.

OsCPL3 is involved in brassinosteroid signaling by regulating OsGSK2 stability

Glycogen synthase kinase 3(GSK3)proteins play key roles in brassinosteroid(BR)signaling during plant growth and development by phosphorylating various substrates.However,how GSK3 protein stability and activity are themselves modulated is not well understood.Here,we demonstrate in vitro and in vivo that C-TERMINAL DOMAIN PHOSPHATASELIKE 3(Os CPL3),a member of the RNA Pol II CTD phosphatase-like family,physically interacts with Os GSK2 in rice(Oryza sativa).Os CPL3 expression was widely detected in various tissues and organs including roots,leaves and lamina joints,and was induced by exogenous BR treatment.Os CPL3 localized to the nucleus,where it dephosphorylated Os GSK2 at the Ser-222 and Thr-284 residues to modulate its protein turnover and kinase activity,in turn affecting the degradation of BRASSINAZOLERESISTANT 1(BZR1)and BR signaling.Loss of Os CPL3 function resulted in higher Os GSK2 abundance and lower Os BZR1 levels,leading to decreased BR responsiveness and alterations in plant morphology including semi-dwarfism,leaf erectness and grain size,which are of fundamental importance to crop productivity.These results reveal a previously unrecognized role for Os CPL3 and add another layer of complexity to the tightly controlled BR signaling pathway in plants.

An unprecedented one-arrow-two-hawks strategy achieves high yield with early flowering in rice

By 2021,nearly 9%of the global population was still suffering from hunger.It has estimated that the world population will reach 9.7 billion in 2050(United Nations,2019;Tian et al.,2021),which requires a 2.4%increase per year for the yields of major crops.However,current growth rates are only half of this,imposing serious challenges in increasing grain yield by crop breeding.Plant growth and development mainly require energy and nutrients,and thus it is generally considered that the crop yield could be increased by elevating photosynthetic efficiency and higher nitrogen-use efficiency.Moreover,the uptake and transport of nitrogen must be coordinated with carbon fixation and production of carbohydrates by photosynthesis.However,effective strategies for optimizing the carbon/nitrogen status in crops are still relatively limited and therefore require new promising targets.