Drought, a major abiotic stressor affecting global agricultural productivity, significantly reduces crop yields and threatens food security worldwide. As the primary organ for perceiving soil moisture signals and absorbing water, the crop root system architecture plays a pivotal role in plant adaptation to drought conditions. With the development of high-throughput imaging technologies (i.e., 2D/3D image acquisition), high-throughput genotyping platforms, and gene-editing technologies, significant progress has been achieved in the characterization of root traits and the dissection of molecular genetic regulatory networks underlying these traits in crops. This review comprehensively synthesizes recent advances in the phenotypic characterization, underlying molecular regulatory networks, and functional roles of key root architectural traits, including the root length, angle, density, and root hair development, in enhancing drought resilience. Finally, we discuss the existing challenges in the current research and provide an outlook on the future trend of integrating multi-omics, high-throughput phenomics, and genome editing technologies to breed new drought-resistant crop varieties with ideal drought-resistant root architectures.

Drought severely limits global rice production, and the exploitation of heterosis offers a promising route for improving drought resistance. However, the molecular mechanisms that underlie drought resistance in hybrid rice remain largely unknown. Here, we performed integrated multi-omics analyses of flag leaves from the elite hybrid rice Hanyou73 (HY73) and its parental lines, Hanhui3 (HH3) and Huhan7B (HH7B), during grain filling under drought. We discovered that non-additive effect (NAE)-driven carbon metabolic reprogramming is fundamental to HY73's superior drought resistance. Proteomic profiling revealed that HY73 prioritizes carbon metabolism, selectively retaining monosaccharides (MOSs) such as glucose-6-phosphate (G6P) and glucose-1-phosphate (G1P) to bolster stress-buffering processes. Subsequent metabolomic analysis revealed that this carbon retention fuels a hybrid-specific MOS-acetyl-coenzyme A (AcCoA)-fatty acyl/prenol lipid (MOS-AcCoA-FA/PR) shunt that diverts carbon into vital lipid-based hormonal, structural, and energetic processes. Importantly, NAE-driven accumulation of AcCoA is correlated with increased lysine acetylation (Kac) in HY73, indicating a connection between metabolism and post-translational regulation. Acetylomic analyses pinpointed acetylation at lysine 155 (K155ac) on the phosphoglucomutase OsPGM3 as a key regulatory switch in carbon metabolism. OsPGM3 governs the balance between G6P and G1P under drought, coordinating local carbon use for the sugar-lipid shunt with the sugar export vital for yield potential. K155ac precisely fine-tunes OsPGM3 activity, acting as a post-translational checkpoint that is responsive to drought-induced carbon shifts. Together, our findings reveal a hybrid-specific NAE-carbon flux-Kac regulatory axis that precisely balances drought adaptation with yield maintenance, offering new targets for the breeding of climate-resilient hybrid rice.

Deep rooting is an important factor affecting rice drought avoidance. However, few genes that control this trait have been identified in rice. In the present work, we cloned a gene, OsIAA8, associated with a rice quantitative trait locus for deep rooting. Overexpression of OsIAA8 increased deep rooting and yield under drought stress. OsIAA8, which encodes an Aux/IAA protein, interacts with auxin response factor OsARF12, and osarfl2 mutant plants also displayed increased deep rooting. The expression of several auxin transport genes (e.g., OsPIN2 and OsPIN8) was down-regulated in OsIAA8-overexpressing rice plants. OsARF12 promotes the transcription of these genes, whereas OsIAA8 inhibited this transcription activation. Furthermore, the auxin content in the roots of OsIAA8-overexpressing plants was reduced compared with wild type plants. Of five haplotypes at the OsIAA8 locus, accessions carrying Hap 2 had higher deep rooting. This study revealed that OsIAA8-OsARF12 module regulates deep rooting by inhibiting auxin transport, providing the insights into improvement of root architecture and drought resistance in rice breeding.

Drought stress severely impacts crop productivity. As a subclass of plant transcription factors, APETALA2/Ethylene Responsive Factors (AP2/ERFs) play crucial roles in plant development and abiotic stress responses. In rice, the functions of many members of the ERF subfamily of AP2/ERFs in drought resistance remain unclear. Here, we characterized the function of OsERF65, an ERF transcription factor gene from indica rice cultivar ‘Zhenshan97B’(ZS97B), in drought tolerance. Overexpression of OsERF65ZS97B significantly enhanced the drought tolerance of transgenic rice. In contrast, its knockout reduced rice drought tolerance. Transcriptome sequencing analysis revealed that late embryogenesis abundant (LEA) genes were significantly up-regulated in OsERF65-overexpressing rice plants. Further assays verified that OsERF65 binds to the promoters and activates the transcription of LEA genes. Yeast two-hybrid analysis showed that OsERF65 could interact with OsMYB48 and other transcription factors. Additionally, five haplotypes of OsERF65 were identified in rice germplasm, with Hap1 dominant in indica rice and Hap2 dominant in japonica rice. The OsERF65Hap1 encoded protein exhibited stronger transcriptional activation activity than OsERF65Hap2. Collectively, our findings reveal an indica rice-derived ERF transcription factor that positively regulates drought tolerance via upregulation of LEA genes.

Asian cultivated rice is one of the most important cereal crops globally,feeding approximately 50％ of the world's population.Increasing rice nitrogen use efficiency(NUE)is crucial for achieving high yields with low nitrogen inputs(Xu et al.,2012;Hu et al.,2023).However,modern cultivars are typically bred for high yields through excessive nitrogen fertilizer use,leading to the loss of bene-ficial alleles associated with high NUE during the breeding process(Wang and Peng,2017;Hu et al.,2023).

Dissecting the mechanism of drought resistance (DR) and designing drought-resistant rice varieties are promising strategies to address the challenge of climate change. Here, we selected a typical droughtavoidant (DA) variety, IRAT109, and a drought-tolerant (DT) variety, Hanhui15, as parents to develop a stable recombinant inbred line (RIL) population (F8, 1262 lines). The de novo assembled genomes of both parents were released. By resequencing of the RIL population, a set of 1 189 216 reliable SNPs were obtained and used to construct a dense genetic map. Using above- and belowground phenomic platforms and multi- modal cameras, we captured 139 040 image-based traits (i-traits) of whole-plant phenotypes in response to drought stress throughout the entire rice growth period and identified 32 586 drought-responsive quantitative trait loci (QTLs), including 2097 unique QTLs. QTLs associated with panicle i-traits occurred more than 600 times on the middle of chromosome 8, and QTLs associated with leaf i-traits occurred more than 800 times on the 50 end of chromosome 3, indicating the potential effects of these QTLs on plant phenotypes. We selected three candidate genes (OsMADS50, OsGhd8, OsSAUR11) related to leaf, panicle, and root traits, respectively, and verified their functions in DR. OsMADS50 was found to negatively regulate DR by modulating leaf dehydration, grain size, and downward root growth. A total of 18 and 21 composite QTLs significantly related to grain weight and plant biomass were also screened from 597 lines in the RIL population under drought conditions in field experiments, and the composite QTL regions showed substantial overlap (76.9%) with known DR gene regions. Based on three candidate DR genes, we proposed a haplotype design suitable for different environments and breeding objectives. This study provides a valuable reference for multimodal and time-series phenomic analyses, deciphers the genetic mechanisms of DA and DT rice varieties, and offers a molecular navigation map for breeding of DR varieties.

Agricultural production is severely affected by environmental stresses such as drought, and deep rooting is an important factor enhancing crop drought avoidance. H+-ATPases provide a transmembrane proton gradient and are thought to play a crucial role in plant growth and abiotic stress responses. However, their expression under abiotic stress and function on deep rooting is poorly understood in rice. In this study, the conserved domains, potential phosphorylation sites, and three-dimensional structures of ten Oryza sativa PM H+-ATPases (OSAs) were analyzed. Quantitative PCR analysis revealed different expression patterns of these OSA genes under hormone treatment conditions (e.g., abscisic acid) and abiotic stress conditions (e.g., drought and salt stress). Subcellular localization analysis revealed that most OSA proteins were localized to the cell membrane. Phenotype determination of OSA mutants indicated that the ratio of deep rooting (RDR) of both osa7 and osa8 mutants was significantly reduced compared to that of wild-type rice plants. Additionally, OSA haplotypes in 268 rice accessions were analyzed, and the haplotypes associated with RDR were identified. The present results provide valuable information on crucial domains, expression patterns, and functional identification of OSA paralogs to reveal their role in rice responses to abiotic stress.

Background Deep rooting is an important factor affecting rice drought resistance. However, few genes have been identified to control this trait in rice. Previously, we identified several candidate genes by QTL mapping of the ratio of deep rooting and gene expression analysis in rice. Results In the present work, we cloned one of these candidate genes, OsSAUR11, which encodes a small auxin-up RNA (SAUR) protein. Overexpression of OsSAUR11 significantly enhanced the ratio of deep rooting of transgenic rice, but knockout of this gene did not significantly affect deep rooting. The expression of OsSAUR11 in rice root was induced by auxin and drought, and OsSAUR11-GFP was localized both in the plasma membrane and cell nucleus. Through an electrophoretic mobility shift assay and gene expression analysis in transgenic rice, we found that the transcription factor OsbZIP62 can bind to the promoter of OsSAUR11 and promote its expression. A luciferase complementary test showed that OsSAUR11 interacts with the protein phosphatase OsPP36. Additionally, expression of several auxin synthesis and transport genes (e.g., OsYUC5 and OsPIN2) were down-regulated in OsSAUR11-overexpressing rice plants. Conclusions This study revealed a novel gene OsSAUR11 positively regulates deep rooting in rice, which provides an empirical basis for future improvement of rice root architecture and drought resistance.

Mosses are one of the earliest diverging land plants that adapted to living on land. The BURP domain-containing proteins (BURP proteins) are plant-specific proteins that appeared when plants shifted from aquatic environments to land. Phylogenetic analysis revealed that the BURP domain of higher plants is originated from lower land plants and divergent because of motif conversion. To discover the function of BURP protein in moss, rice transgenics with ectopic expression of PpBURP2 were subjected to different abiotic stresses treatments. The results revealed that the ectopic expression of PpBURP2 enhanced the tolerance to osmotic and saline stresses at the seedling stage and drought stress at the adult stage. Further ectopic expression of PpBURP2 improved the cadmium (2+) (Cd2+) tolerance and reduced Cd2+ accumulation in rice leaves. Transcriptomic analysis of the transgenic PpBURP2 plants showed that the differentially expressed genes were involved in the metabolism of secondary metabolites, energy, oxidation-reduction process, and defense-related genes. Further experiments showed that the photosynthetic efficiency and resistance against bacterial leaf blight were obviously improved in transgenic plants. Yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays revealed the physical interaction of BURP domain protein from rice and moss with mitogen-activated protein kinase kinase (MKK) from rice. Therefore, our findings demonstrate that overexpressing PpBURP2 in rice confers resistance to abiotic stresses and bacterial leaf blight. They also suggested that the regulatory role of BURP-like proteins across lower and higher plants was evolutionary conservation of responses of different classes of plants to different environmental challenges.

The Alfin-like (AL) family is a group of small plant-specific transcriptional factors involved in abiotic stresses in dicotyledon. In an early study, we found an AL gene in rice that was associated with grain yield under drought stress. However, little information is known about the AL family in rice. In this study, AL genes in the rice genome were identified, and the OsAL proteins were found to locate in the nucleus and have no transcriptional self-activation activity. The expression of the OsALs was regulated by different environmental stimulations and plant hormones. Association and domestication analysis revealed that natural variation of most OsALs was significantly associated with yield traits, drought resistance and divergence in grain size in indica and japonica rice varieties. Hap1 of OsAL7.1 and Hap7 of OsAL11 were favorable haplotypes of seed weight and germination under osmotic stress. Furthermore, osal7.1 and osal11 mutants have larger seeds and are more sensitive to abscisic acid and mannitol during germination stage. Overexpressing of OsAL7.1 and OsAL11 in rice weakened the tolerance to drought in the adult stage. Thus, our work provides informative knowledge for exploring and harnessing haplotype diversity of OsALs to improve yield stability under drought stress.

Changes in ambient temperature influence crop fertility and production. Understanding of how crops sense and respond to temperature is thus crucial for sustainable agriculture. The thermosensitive genic male-sterile (TGMS) lines are widely used for hybrid rice breeding and also provide a good system to investigate the mechanisms underlying temperature sensing and responses in crops. Here, we show that OsMS1 is a histone binding protein, and its natural allele OsMS1 wenmin1 confers thermosensitive male sterility in rice. OsMS1 is primarily localized in nuclei, while OsMS1 wenmin1 is localized in nuclei and cytoplasm. Temperature regulates the abundances of OsMS1 and OsMS1 wenmin1 proteins. The high temperature causes more reduction of OsMS1 wenmin1 than OsMS1 in nuclei. OsMS1 associates with the transcription factor TDR to regulate expression of downstream genes in a temperature-dependent manner. Thus, our findings uncover a thermosensitive mechanism that could be useful for hybrid crop breeding.

Summary Water is crucial for plant growth and survival. The transcellular water movement is facilitated by aquaporins (AQPs) that rapidly and reversibly modify water permeability. The abundance of AQPs is regulated by its synthesis, redistribution and degradation. However, the molecular mechanism of proteasomal degradation of AQPs remains unclear. Here, we demonstrate that a novel E3 ligase, OsRINGzf1, mediated the degradation of AQPs in rice. OsRINGzf1 is the candidate gene from a drought‐related quantitative trait locus (QTL) on the long arm of chromosome 4 in rice (Oryza sativa) and encodes a Really Interesting New Gene (RING) zinc finger protein 1. OsRINGzf1 possesses the E3 ligase activity, ubiquitinates and mediates OsPIP2;1 degradation, thus reducing its protein abundance. The content of OsPIP2;1 protein was decreased in OsRINGzf1 overexpression (OE) plants. The degradation of OsPIP2;1 was inhibited by MG132. The OsRINGzf1 OE plants, with higher leaf‐related water content (LRWC) and lower leaf water loss rate (LWLR), exhibited enhanced drought resistance, whereas the RNAi and knockout plants of OsRINGzf1 were more sensitive to drought. Together, our data demonstrate that OsRINGzf1 positively regulates drought resistance through promoting the degradation of OsPIP2;1 to enhance water retention capacity in rice.

栽培稻作为主要的粮食作物,消耗了大量的农业用水。解析栽培稻抵抗干旱胁迫的调控机制,培育节水抗旱稻,对于节约淡水资源、保障粮食安全具有重要意义。在长期的进化过程中,栽培稻形成了渗透调节、活性氧有毒物质的清除、气孔调节等多种生理生化机制来适应干旱胁迫,这其中涉及大量基因参与的分子调控途径。笔者结合其研究对近年来在栽培稻响应干旱胁迫的生理生化过程、抗旱基因挖掘及其参与的分子调控机制方面取得的进展进行综述,并对存在的问题和未来的发展趋势进行讨论。

The increasing concentration of greenhousegases(GHGs)in Earth's atmosphere leads to global warming,which further causes a series of climate changes and does great harm to both human society and natural ecosystems.Agricultural GHG emissions,mainly in the form of methane(CH4)and nitrous oxide(N2O),are a significant source of GHGs,accounting for～14％ to-tal global GHGs(Zhang et al.,2022).

为进一步了解MKKs基因的功能,基于CREP数据库芯片数据,分析了MKK家族基因在水稻发育过程中及其对植物激素响应的表达特征。结果表明:除OsMKK10-3基因无生物芯片探针外,其他基因的表达均能在水稻整个生育期中检测到。其中,OsMKK3、OsMKK5和OsMKK10-1基因在生殖器官中表达量较高;OsMKK1、OsMKK4、OsMKK6和OsMKK10-2基因在营养器官中表达量较高。实时定量RT-PCR结果显示:大部分MKKs基因的表达在干旱、盐、高温和冷处理下均上调,且100μmol∕L ABA处理能诱导OsMKK1、OsMKK3和OsMKK5基因表达。不同的表达模式说明MKK家族基因在水稻发育过程和非生物胁迫响应中发挥不同的作用。

Drought stress adversely affects crop growth and productivity worldwide. In response, plants have evolved several strategies in which numerous genes are induced to counter stress. High mobility group (HMG) proteins are the second most abundant family of chromosomal proteins. They play a crucial role in gene transcriptional regulation by modulating the chromatin/DNA structure. In this study, we isolated a novel HMG gene, OsHMGB707 , one of the candidate genes localized in the quantitative trait loci (QTL) interval of rice drought tolerance, and examined its function on rice stress tolerance. The expression of OsHMGB707 was up-regulated by dehydration and high salt treatment. Its overexpression significantly enhanced drought tolerance in transgenic rice plants, whereas its knockdown through RNA interference (RNAi) did not affect the drought tolerance of the transgenic rice plants. Notably, OsHMGB707-GFP is localized in the cell nucleus, and OsHMGB707 is protein-bound to the synthetic four-way junction DNA. Several genes were up-regulated in OsHMGB707-overexpression (OE) rice lines compared to the wild-type rice varieties. Some of the genes encode stress-related proteins (e.g., DREB transcription factors, heat shock protein 20, and heat shock protein DnaJ). In summary, OsHMGB707 encodes a stress-responsive high mobility group protein and regulates rice drought tolerance by promoting the expression of stress-related genes.

Aims Deep root traits are important in rice (Oryza sativa L.) because of their implications for better ability to reach water and nutrients from deep soil. Analysis of gene expression and alternative splicing (AS) will help speed gene identification and understand the role of AS in deep rooting. Methods Rice varieties displaying extreme ratio of deep rooting (RDR) were grown in nutrient solutions. RNA-seq analysis was conducted using StringTie, SUPPA, and 3D RNA-seq pipeline. Functional validation of AS was performed by transgenic overexpression of OsPIN1. Results The reference-based transcriptome assembly transcripts represented an overall portrait of AS in rice roots. A percentage (76.91%) of assembled genes contained at least one predicted intron. Principal component analysis of single-nucleotide polymorphisms from RNA-seq indicated that genetic differentiation generated abundant genetic diversity during adaptive domestication of high RDR varieties. Totals obtained were: 4392 differentially expressed genes, 3053 differentially alternatively spliced genes, 5508 differential transcript usage transcripts, and 1068 differential AS event transcripts. Functional categories of these genes and AS regulation transcripts were involved in DNA metabolic processes, stress responses and cell part. Transgenic overexpression of OsPIN1 containing retained intron events improved RDR in rice. Conclusions AS increased the complexity of gene expression for environmental adaptation while the gene expression level did not change significantly. Our findings provide new perspectives for enhancing drought avoidance.

Water stress is the most important adverse factor limiting rice production. Too much water leads to flood and too little leads to drought. Floods and droughts can severely damage crop at different times of the rice life cycle. So the research on submergence tolerance and drought resistance of rice is particularly urgent. In this study, we reported that OsEBP89 (Oryza sativa Ethylene-responsive element binding protein, clone 89), a member of the AP2/ERF subfamily, is involved in a novel signal transduction associated with the tolerance to drought and submergence stress. OsEBP89 was found to be strongly inhibited by drought stress and promoted by submergence. The OsEBP89 protein was located at the nucleus in the rice protoplast. Loss of OsEBP89 was found to improve the seed germination under submerged conditions and also enhanced the tolerance to drought stress throughout growth stage. Additionally, OsEBP89 knockout rice plants increased the accumulation of proline, improved the ability to scavenge ROS compared to overexpression lines and wild type after PEG treatment. Transcriptome data indicates that knockout of OsEBP89 improved the expression of specific genes in response to adverse factors, such as OsAPX1, OsHsfA3, and OsP5CS. Further results indicate that OsEBP89 can interact with and be phosphorylated by SnRK1α (sucrose non-fermenting-1-related protein kinase-1 gene). These findings provide insight into the mechanism of abiotic stress tolerance, and suggest OsEBP89 as a new genetic engineering resource to improve abiotic stress tolerance in rice.

The resource and environmental challenges faced by rice production call for resource-saving and environment-friendly rice varieties. Water-saving and drought-resistance rice (WDR) is a new type of cultivated rice combining both high yield potential and acceptable grain quality as a current lowland paddy rice, as well as water-saving and drought resistance as a traditional upland rice. The lowland and upland rice are two ecotypes adapted to contrasting soil water status, originating mainly because of their differentiated drought resistance. Upland rice, domesticated in a water–limited environment and experiencing a bidirectional selection process, has better drought resistance and especially better drought avoidance. Though the potential tradeoff between drought resistance and productivity is very common in rice, the bidirectional selection could overcome this tradeoff and accumulate recombination genotypes. It is very important to choose elite parents on the basis of studies on the great genetic diversity of rice yield and drought resistance among the rice germplasm resources and adapt the bidirectional selection strategies to especially integrate drought avoidance, drought tolerance, high water use efficiency, and productivity in WDR breeding. The breeding history and genomic studies indicated that lowland paddy rice and upland rice hybridization breeding with suitable selection in different environments is an effective approach to improving complex traits such as yield potential and drought resistance. Meanwhile, molecular technology shows higher efficiency on value-added breeding such as transferring and pyramiding pest- and disease-resistant genes, which helps WDR obtain other green characters. Twenty-two WDR varieties were registered and distributed to farmers in recent years and could be planted in both irrigated and rainfed ecosystems, thus showing promising application prospects. The major crop management technology of WDR in lowland paddy fields with water-saving cultivation and in rainfed fields by dry seeding with aerobic cultivation were also discussed in this article.

BACKGROUND:Drought is a major abiotic stress factor that influences the yield of crops. Basic leucine zipper motif (bZIP) transcription factors play an important regulatory role in plant drought stress responses. However, the functions of a number of bZIP transcription factors in rice are still unknown.RESULTS:In this study, a novel drought stress-related bZIP transcription factor, OsbZIP62, was identified in rice. This gene was selected from a transcriptome analysis of several typical rice varieties with different drought tolerances. OsbZIP62 expression was induced by drought, hydrogen peroxide, and abscisic acid (ABA) treatment. Overexpression of OsbZIP62-VP64 (OsbZIP62V) enhanced the drought tolerance and oxidative stress tolerance of transgenic rice, while osbzip62 mutants exhibited the opposite phenotype. OsbZIP62-GFP was localized to the nucleus, and the N-terminal sequence (amino acids 1-68) was necessary for the transcriptional activation activity of OsbZIP62. RNA-seq analysis showed that the expression of many stress-related genes (e.g., OsGL1, OsNAC10, and DSM2) was upregulated in OsbZIP62V plants. Moreover, OsbZIP62 could bind to the promoters of several putative target genes and could interact with stress/ABA-activated protein kinases (SAPKs).CONCLUSIONS:OsbZIP62 is involved in ABA signalling pathways and positively regulates rice drought tolerance by regulating the expression of genes associated with stress, and this gene could be used for the genetic modification of crops with improved drought tolerance.