Heterologous expression of rice 9-cis-epoxycarotenoid dioxygenase 4 (OsNCED4) in Arabidopsis confers sugar oversensitivity and drought tolerance

Transcriptomic and physiological analyses reveal different grape varieties response to high temperature stress

High temperatures affect grape yield and quality. Grapes can develop thermotolerance under extreme temperature stress. However, little is known about the changes in transcription that occur because of high-temperature stress. The heat resistance indices and transcriptome data of five grape cultivars, 'Xinyu' (XY), 'Miguang' (MG), 'Summer Black' (XH), 'Beihong' (BH), and 'Flame seedless' (FL), were compared in this study to evaluate the similarities and differences between the regulatory genes and to understand the mechanisms of heat stress resistance differences. High temperatures caused varying degrees of damage in five grape cultivars, with substantial changes observed in gene expression patterns and enriched pathway responses between natural environmental conditions (35 °C ± 2 °C) and extreme high temperature stress (40 °C ± 2 °C). Genes belonging to the HSPs, HSFs, WRKYs, MYBs, and NACs transcription factor families, and those involved in auxin (IAA) signaling, abscisic acid (ABA) signaling, starch and sucrose pathways, and protein processing in the endoplasmic reticulum pathway, were found to be differentially regulated and may play important roles in the response of grape plants to high-temperature stress. In conclusion, the comparison of transcriptional changes among the five grape cultivars revealed a significant variability in the activation of key pathways that influence grape response to high temperatures. This enhances our understanding of the molecular mechanisms underlying grape response to high-temperature stress.

Molecular Mechanisms and Regulatory Pathways Underlying Drought Stress Response in Rice

Rice is a staple food for 350 million people globally. Its yield thus affects global food security. Drought is a serious environmental factor affecting rice growth. Alleviating the inhibition of drought stress is thus an urgent challenge that should be solved to enhance rice growth and yield. This review details the effects of drought on rice morphology, physiology, biochemistry, and the genes associated with drought stress response, their biological functions, and molecular regulatory pathways. The review further highlights the main future research directions to collectively provide theoretical support and reference for improving drought stress adaptation mechanisms and breeding new drought-resistant rice varieties.

GmWRKY17-mediated transcriptional regulation of GmDREB1D and GmABA2 controls drought tolerance in soybean

Drought affects soybean growth and ultimately led to yield reduction. WRKY transcription factors involve in the regulation of abiotic stress. Few functions of WRKY transcription factors underlying drought tolerance in soybean are clear. Here, we reported a WRKY transcription factor named GmWRKY17 that positively regulates soybean drought tolerance by regulating drought-induced genes and ABA-related genes. Transcriptome sequencing (RNA-Seq) and yeast one hybrid analysis identified downstream genes regulated by GmWRKY17. ChIP-qPCR, EMSA and dual-luciferase reporter assay showed that GmWRKY17 directly bound to the promoters of the GmDREB1D and GmABA2, and activated their expression under drought stress. Overexpression of GmDREB1D gene enhanced drought tolerance of soybean. Taken together, our study revealed a regulatory mechanism that GmWRKY17 transcription factor may improve soybean drought tolerance by mediating ABA synthesis and DREB signaling pathway.

Explicating genetic architecture governing nutritional quality in pigmented rice

Rice is one of the most important staple plant foods that provide a major source of calories and nutrients for tackling the global hunger index especially in developing countries. In terms of nutritional profile, pigmented rice grains are favoured for their nutritional and health benefits. The pigmented rice varieties are rich sources of flavonoids, anthocyanin and proanthocyanidin that can be readily incorporated into diets to help address various lifestyle diseases. However, the cultivation of pigmented rice is limited due to low productivity and unfavourable cooking qualities. With the advances in genome sequencing, molecular breeding, gene expression analysis and multi-omics approaches, various attempts have been made to explore the genetic architecture of rice grain pigmentation. In this review, we have compiled the current state of knowledge of the genetic architecture and nutritional value of pigmentation in rice based upon the available experimental evidence. Future research areas that can help to deepen our understanding and help in harnessing the economic and health benefits of pigmented rice are also explored.

Genome-Wide Identification and Analysis of Collar Region-Preferential Genes in Rice

The collar region plays a crucial role in leaf angle formation and plant architecture, which is important for improving crop yield given the challenges of diminishing arable land and changing environmental conditions. To determine collar region-preferential genes (CRPGs) affecting plant architecture and crop yield, we conducted genome-wide transcriptomic analysis. By integrating our RNA sequencing data with public rice anatomical expression data, we identified 657 CRPGs. Verification involved testing six randomly selected CRPGs, all of which exhibited collar-preferential expression. The functional significance of CRPGs was assessed via Gene Ontology enrichment analysis, utilizing MapMan and KEGG, and literature analysis provided additional information for characterized CRPGs. Our findings revealed links between manipulating leaf angle and phytohormone-related pathways and stress responses. Moreover, based on the CRPGs, five transcription factors downstream of the liguleless 1 (LG1) gene were identified. Overall, the identified CRPGs provide potential targets for further research and breeding applications aimed at improving crop productivity by manipulating leaf architecture.

A mulberry 9-cis-epoxycarotenoid dioxygenase gene MaNCED1 is involved in plant growth regulation and confers salt and drought tolerance in transgenic tobacco

The phytohormone abscisic acid (ABA) is vital in regulating root elongation, seed germination, and abiotic stress responses in plants. Conversely, the mechanisms of ABA in mulberry root growth, seed germination, and abiotic stress responses are poorly understood. Here, we reported that exogenous ABA and drought treatment inhibited the growth of mulberry seedlings but significantly increased the ratio of root/stem. Inhibition of ABA synthesis by fluridone and sodium tungstate resulted in the decrease of root/stem ratio. We also showed that the expression of MaNCED1 in the root was strongly induced by drought and salt stress. Increasing the expression of MaNCED1 in tobacco using overexpression leads to increased root elongation and reduced seed germination. Compared with the wild type, the accumulation of H2O2 and MDA was reduced, while the POD activity and proline content was increased in the transgenic plants after drought and salt treatment. Further studies revealed increased resistance to drought and salt stress in MaNCED1 overexpressed tobaccos. Meanwhile, the auxin and ethylene signal pathway-related gene expression levels increased in MaNCED1 overexpressed tobaccos. This study demonstrated the roles of mulberry MaNCED1 in regulating plant development and abiotic stress responses. It gave further insights into the coordinated regulation of ABA, auxin, and ethylene in seed growth and germination.

An R2R3 MYB transcription factor PsFLP regulates the symmetric division of guard mother cells during stomatal development in Pisum sativum

MYB transcriptional regulators belong to one of the most significant transcription factors families in plants, among which R2R3-MYB transcription factors are involved in plant growth and development, hormone signal transduction, and stress response. Two R2R3-MYB transcription factors, FLP and its paralogous AtMYB88, redundantly regulate the symmetrical division of guard mother cells (GMCs), and abiotic stress response in Arabidopsis thaliana. Only one orthologue gene of FLP was identified in pea (Pisum sativum FLP; PsFLP). In this study, we explored the gene function of PsFLP by virus-induced gene silencing (VIGS) technology. The phenotypic analysis displayed that the silencing of PsFLP expression led to the abnormal development of stomata and the emergence of multiple guard cells tightly united. In addition, the abnormal stomata of flp could be fully rescued by PsFLP driven by the FLP promoter. In conclusion, the results showed that PsFLP plays a conservative negative role in regulating the symmetric division of GMC during stomatal development. Based on real-time quantitative PCR, the relative expressions of AAO3, NCED3, and SnRK2.3 significantly increased in the flp pFLP::PsFLP plants compared to mutant, indicating that PsFLP might be involved in drought stress response. Thus, PsFLP regulates the genes related to cell cycle division during the stomatal development of peas and participates in response to drought stress. The study provides a basis for further research on its function and application in leguminous crop breeding.

ABA biosynthesis gene OsNCED3 contributes to preharvest sprouting resistance and grain development in rice

Preharvest sprouting (PHS) is an unfavorable trait in cereal crops and causes serious yield loss. However, the molecular mechanism underlying PHS remains largely elusive. Here, we identified a member of 9-cis-epoxycarotenoid dioxygenase family, OsNCED3, which regulates PHS and grain development in rice (Oryza sativa L.). OsNCED3 encodes a chloroplast-localized abscisic acid (ABA) biosynthetic enzyme highly expressed in the embryo of developing seeds. Disruption of OsNCED3 by CRISPR/Cas9-mediated mutagenesis led to a lower ABA and higher gibberellic acid (GA) levels (thus a skewed ABA/GA ratio) in the embryo, promoting embryos growth and breaking seed dormancy before seed maturity and harvest, thus decreased seed dormancy and enhanced PHS in rice. However, the overexpression of OsNCED3 enhanced PHS resistance by regulating proper ABA/GA ratio in the embryo. Intriguingly, the overexpression of OsNCED3 resulted in increased grain size and weight, whereas the disruption of OsNCED3 function decreased grain size and weight. Nucleotide diversity analyses suggested that OsNCED3 may be selected during japonica populations adaptation of seed dormancy and germination. Taken together, we have identified a new OsNCED regulator involved rice PHS and grain development, and provide a potential target gene for improving PHS resistance and grain development in rice.

SiNCED1, a 9-cis-epoxycarotenoid dioxygenase gene in Setaria italica, is involved in drought tolerance and seed germination in transgenic Arabidopsis

Foxtail millet (Setaria italica L.) is a vital cereal food crop with promising development and utilization potential because of its outstanding ability to resist drought stress. However, the molecular mechanisms underlying its drought stress resistance remain unclear. In this study, we aimed to elucidate the molecular function of a 9-cis-epoxycarotenoid dioxygenase gene, SiNCED1, in the drought stress response of foxtail millet. Expression pattern analysis showed that SiNCED1 expression was significantly induced by abscisic acid (ABA), osmotic stress, and salt stress. Furthermore, ectopic overexpression of SiNCED1 could enhance drought stress resistance by elevating endogenous ABA levels and promoting stomatal closure. Transcript analysis indicated that SiNCED1 modulated ABA-related stress responsive gene expression. In addition, we found that ectopic expression of SiNCED1 delayed seed germination under normal and abiotic stress conditions. Taken together, our results show that SiNCED1 plays a positive role in the drought tolerance and seed dormancy of foxtail millet by modulating ABA biosynthesis. In conclusion, this study revealed that SiNCED1 is an important candidate gene for the improvement of drought stress tolerance in foxtail millet and could be beneficial in the breeding and investigation of drought tolerance in other agronomic crops.

Modifications of Phytohormone Metabolism Aimed at Stimulation of Plant Growth, Improving Their Productivity and Tolerance to Abiotic and Biotic Stress Factors

Due to the growing human population, the increase in crop yield is an important challenge for modern agriculture. As abiotic and biotic stresses cause severe losses in agriculture, it is also crucial to obtain varieties that are more tolerant to these factors. In the past, traditional breeding methods were used to obtain new varieties displaying demanded traits. Nowadays, genetic engineering is another available tool. An important direction of the research on genetically modified plants concerns the modification of phytohormone metabolism. This review summarizes the state-of-the-art research concerning the modulation of phytohormone content aimed at the stimulation of plant growth and the improvement of stress tolerance. It aims to provide a useful basis for developing new strategies for crop yield improvement by genetic engineering of phytohormone metabolism.

Insights into the Regulation of Rice Seed Storability by Seed Tissue-Specific Transcriptomic and Metabolic Profiling

Non-dormant seeds are continuously aging and deteriorating during storage, leading to declining seed vigor, which is a challenge for the rice seed industry. Improving the storability of seeds is of great significance to ensure the quality of rice and national food security. Through a set of chromosome segment substitution lines population constructed using japonica rice NIP as donor parent and indica rice ZS97 as recurrent parent, we performed seed storability QTL analysis and selected four non-storable NILs to further investigate the storability regulatory mechanisms underlying it. The seeds were divided into four tissues, which were the embryo, endosperm, aleurone layer, and hull, and tissue-specific transcriptome and metabolome analyses were performed on them. By exploring the common differentially expressed genes and differentially accumulated metabolites, as well as the KEGG pathway of the four non-storable NILs, we revealed that the phenylpropanoid biosynthesis pathway and diterpenoid biosynthesis pathway played a central role in regulating seed storability. Integrated analysis pinpointed 12 candidate genes that may take part in seed storability. The comprehensive analysis disclosed the divergent and synergistic effect of different seed tissues in the regulation of rice storability.

miR2105 and the kinase OsSAPK10 co-regulate OsbZIP86 to mediate drought-induced ABA biosynthesis in rice

Mediating induced abscisic acid (ABA) biosynthesis is important for enhancing plant stress tolerance. Here, we found that rice (Oryza sativa L.) osa-miR2105 (miR2105) and the Stress/ABA-activated protein kinase (OsSAPK10) coordinately regulate the rice basic region-leucine zipper transcription factor (bZIP TF; OsbZIP86) at the posttranscriptional and posttranslational levels to control drought-induced ABA biosynthesis via modulation of rice 9-cis-epoxycarotenoid dioxygenase (OsNCED3) expression. OsbZIP86 expression is regulated by miR2105-directed cleavage of the OsbZIP86 mRNA. OsbZIP86 encodes a nuclear TF that binds to the promoter of the ABA biosynthetic gene OsNCED3. OsSAPK10 can phosphorylate and activate OsbZIP86 to enhance the expression of OsNCED3. Under normal growth conditions, altered expression of miR2105 and OsbZIP86 displayed no substantial effect on rice growth. However, under drought conditions, miR2105 knockdown or OsbZIP86 overexpression transgenic rice plants showed higher ABA content, enhanced tolerance to drought, lower rates of water loss, and more stomatal closure of seedlings, compared with wild-type rice Zhonghua 11; in contrast, miR2105 overexpression, OsbZIP86 downregulation, and OsbZIP86 knockout plants displayed opposite phenotypes. Collectively, our results show that the "miR2105-(OsSAPK10)-OsbZIP86-OsNCED3" module regulates the drought-induced ABA biosynthesis without penalty on rice growth under normal conditions, suggesting candidates for improving drought tolerance in rice.

Comparative Analysis of Heat-Tolerant and Heat-Susceptible Rice Highlights the Role of OsNCED1 Gene in Heat Stress Tolerance

To elucidate the mechanism underlying the response of rice to heat stress (HS), the transcriptome profile of panicles was comparatively analyzed between the heat-tolerant line 252 (HTL252) and heat-susceptible line 082 (HSL082), two rice recombinant inbred lines (RILs). Our differentially expressed gene (DEG) analysis revealed that the DEGs are mainly associated with protein binding, catalysis, stress response, and cellular process. The MapMan analysis demonstrated that the heat-responsive (HR) genes for heat shock proteins, transcription factors, development, and phytohormones are specifically induced in HTL252 under HS. Based on the DEG analysis, the key gene OsNCED1 (Os02g0704000), which was induced under HS, was selected for further functional validation. Moreover, 9-cis-epoxycarotenoid dioxygenase (NCED) is a key rate-limiting enzyme in the ABA biosynthetic pathway. Overexpression of OsNCED1 improved the HS tolerance of rice at the heading and flowering stage. OsNCED1-overexpression plants exhibited significant increases in pollen viability, seed setting rate, superoxide dismutase (SOD) and peroxidase (POD) activities, while significantly lower electrolyte leakage and malondialdehyde (MDA) content relative to the wild type (WT). These results suggested that OsNCED1 overexpression can improve the heat tolerance of rice by enhancing the antioxidant capacity. Overall, this study lays a foundation for revealing the molecular regulatory mechanism underlying the response of rice to prolonged HS.

Cellulose synthase-like protein OsCSLD4 plays an important role in the response of rice to salt stress by mediating abscisic acid biosynthesis to regulate osmotic stress tolerance

Cell wall polysaccharide biosynthesis enzymes play important roles in plant growth, development and stress responses. The functions of cell wall polysaccharide synthesis enzymes in plant growth and development have been well studied. In contrast, their roles in plant responses to environmental stress are poorly understood. Previous studies have demonstrated that the rice cell wall cellulose synthase-like D4 protein (OsCSLD4) is involved in cell wall polysaccharide synthesis and is important for rice growth and development. This study demonstrated that the OsCSLD4 function-disrupted mutant nd1 was sensitive to salt stress, but insensitive to abscisic acid (ABA). The expression of some ABA synthesis and response genes was repressed in nd1 under both normal and salt stress conditions. Exogenous ABA can restore nd1-impaired salt stress tolerance. Moreover, overexpression of OsCSLD4 can enhance rice ABA synthesis gene expression, increase ABA content and improve rice salt tolerance, thus implying that OsCSLD4-regulated rice salt stress tolerance is mediated by ABA synthesis. Additionally, nd1 decreased rice tolerance to osmotic stress, but not ion toxic tolerance. The results from the transcriptome analysis showed that more osmotic stress-responsive genes were impaired in nd1 than salt stress-responsive genes, thus indicating that OsCSLD4 is involved in rice salt stress response through an ABA-induced osmotic response pathway. Intriguingly, the disruption of OsCSLD4 function decreased grain width and weight, while overexpression of OsCSLD4 increased grain width and weight. Taken together, this study demonstrates a novel plant salt stress adaptation mechanism by which crops can coordinate salt stress tolerance and yield.

Global N6-Methyladenosine Profiling Revealed the Tissue-Specific Epitranscriptomic Regulation of Rice Responses to Salt Stress

N⁶-methyladenosine (m⁶A) methylation represents a new layer of the epitranscriptomic regulation of plant development and growth. However, the effects of m⁶A on rice responses to environmental stimuli remain unclear. In this study, we performed a methylated-RNA immunoprecipitation sequencing analysis and compared the changes in m⁶A methylation and gene expression in rice under salt stress conditions. Salt stress significantly increased the m⁶A methylation in the shoots (p value < 0.05). Additionally, 2537 and 2304 differential m⁶A sites within 2134 and 1997 genes were identified in the shoots and roots, respectively, under salt stress and control conditions. These differential m⁶A sites were largely regulated in a tissue-specific manner. A unique set of genes encoding transcription factors, antioxidants, and auxin-responsive proteins had increased or decreased m⁶A methylation levels only in the shoots or roots under salt stress, implying m⁶A may mediate salt tolerance by regulating transcription, ROS homeostasis, and auxin signaling in a tissue-specific manner. Integrating analyses of m⁶A modifications and gene expression changes revealed that m⁶A changes regulate the expression of genes controlling plant growth, stress responses, and ion transport under saline conditions. These findings may help clarify the regulatory effects of m⁶A modifications on rice salt tolerance.

Evolutionary Origin of the Carotenoid Cleavage Oxygenase Family in Plants and Expression of Pepper Genes in Response to Abiotic Stresses

Plant carotenoid cleavage oxygenase (CCO) is an enzyme that catalyzes the synthesis of carotenoids and participates in many important physiological functions. The plant CCOs exist in two forms, namely carotenoid cleavage dioxygenase (CCD) and nine-cis epoxide carotenoid dioxygenase (NCED). Although studies have shown that this gene family has been identified in many species, such as Arabidopsis, grape, and tomato, the evolutionary origin of the CCO family and the expression pattern of pepper genes in response to H₂O₂ and other abiotic stresses are still unclear. In this study, we used the bioinformatics method to identify and analyze the members of the CCO gene family from pepper and other 13 plants from lower to higher plant species based on the whole genome sequence. A total of 158 CCO genes were identified in different plant species and further divided into two groups (e.g., groups I and II). The former was subdivided into CCD7 and CCD8 and have independent evolutionary origins, respectively, while the latter was subdivided into CCD1, CCD4, CCD-like, and NCED, which may have come from a common ancestor. In addition, the results of RNA-seq showed that the expression patterns of pepper CaCCO genes were different in the tissues tested, and only few genes were expressed at high levels such as CaCCD1a, CaCCD4a, CaNCED3, and CaCCD1b. For hydrogen peroxide (H₂O₂) and other abiotic stresses, such as plant hormones, heat, cold, drought, and NaCl treatments, induction of about half of the CaCCO genes was observed. Moreover, the expression patterns of CaCCOs were further investigated under heat, cold, drought, and NaCl treatments using quantitative real-time PCR (qRT-PCR), and most members were responsive to these stresses, especially some CaCCOs with significant expression changes were identified, such as CaCCD4c, CaCCD-like1, CaCCD8, and CaCCD1b, suggesting the important roles of CaCCOs in abiotic stress responses. All these results will provide a valuable analytical basis for understanding the evolution and functions of the CCO family in plants.

ONAC066, A Stress-Responsive NAC Transcription Activator, Positively Contributes to Rice Immunity Against Magnaprothe oryzae Through Modulating Expression of OsWRKY62 and Three Cytochrome P450 Genes

NAC transcriptional factors constitute a large family in rice and some of them have been demonstrated to play crucial roles in rice immunity. The present study investigated the function and mechanism of ONAC066 in rice immunity. ONAC066 shows transcription activator activity that depends on its C-terminal region in rice cells. ONAC066-OE plants exhibited enhanced resistance while ONAC066-Ri and onac066-1 plants showed attenuated resistance to Magnaporthe oryzae. A total of 81 genes were found to be up-regulated in ONAC066-OE plants, and 26 of them were predicted to be induced by M. oryzae. Four OsWRKY genes, including OsWRKY45 and OsWRKY62, were up-regulated in ONAC066-OE plants but down-regulated in ONAC066-Ri plants. ONAC066 bound to NAC core-binding site in OsWRKY62 promoter and activated OsWRKY62 expression, indicating that OsWRKY62 is a ONAC066 target. A set of cytochrome P450 genes were found to be co-expressed with ONAC066 and 5 of them were up-regulated in ONAC066-OE plants but down-regulated in ONAC066-Ri plants. ONAC066 bound to promoters of cytochrome P450 genes LOC_Os02g30110, LOC_Os06g37300, and LOC_Os02g36150 and activated their transcription, indicating that these three cytochrome P450 genes are ONAC066 targets. These results suggest that ONAC066, as a transcription activator, positively contributes to rice immunity through modulating the expression of OsWRKY62 and a set of cytochrome P450 genes to activate defense response.

OsMADS23 phosphorylated by SAPK9 confers drought and salt tolerance by regulating ABA biosynthesis in rice

Some of MADS-box transcription factors (TFs) have been shown to play essential roles in the adaptation of plant to abiotic stress. Still, the mechanisms that MADS-box proteins regulate plant stress response are not fully understood. Here, a stress-responsive MADS-box TF OsMADS23 from rice conferring the osmotic stress tolerance in plants is reported. Overexpression of OsMADS23 remarkably enhanced, but knockout of the gene greatly reduced the drought and salt tolerance in rice plants. Further, OsMADS23 was shown to promote the biosynthesis of endogenous ABA and proline by activating the transcription of target genes OsNCED2, OsNCED3, OsNCED4 and OsP5CR that are key components for ABA and proline biosynthesis, respectively. Then, the convincing evidence showed that the OsNCED2-knockout mutants had lower ABA levels and exhibited higher sensitivity to drought and oxidative stress than wild type, which is similar to osmads23 mutant. Interestingly, the SnRK2-type protein kinase SAPK9 was found to physically interact with and phosphorylate OsMADS23, and thus increase its stability and transcriptional activity. Furthermore, the activation of OsMADS23 by SAPK9-mediated phosphorylation is dependent on ABA in plants. Collectively, these findings establish a mechanism that OsMADS23 functions as a positive regulator in response to osmotic stress by regulating ABA biosynthesis, and provide a new strategy for improving drought and salt tolerance in rice.

Genome-wide characterization of carotenoid oxygenase gene family in three cotton species and functional identification of GaNCED3 in drought and salt stress

Cotton that serves natural fiber for the textile industry is an important industrial crop. However, abiotic stress imposed a significant negative impact on yield and quality of cotton fiber. Carotenoid cleavage oxygenases (CCOs) that specifically catalyze the cleavage of carotenoid are essential for plant growth and development and abiotic stress response. While information of cotton CCOs and their potential functions in abiotic stress is still far from satisfactory, which imposes restrictions on application in genetic breeding for stress resistance. In this study, 15, 15, and 30 CCOs were identified from Gossypium arboreum, Gossypium raimondii, and Gossypium hirsutum, respectively. Phylogenetic relationship indicated that CCO genes could be classified into two groups (NCEDs and CCDs). Cis-elements prediction showed that there were 18 types of stress-related cis-elements in promoter regions. Analysis with transcriptome data revealed tissue-specific expression pattern of cotton CCOs. qRT-PCR analysis revealed only that GhNCED3a_A/D and GhNCED3c_A/D had strong response to drought, salt, and cold stress, while GhCCD1_A/D and GhCCD4_A showed relatively slight expression changes. Virus-induced gene silencing of GaNCED3a, the ortholog gene of GhNCED3a_A/D, suggested that silenced plants exhibited decreased resistance not only to drought but also to salt, with significantly reduced proline content, and high malondialdehyde content and water loss rate. In addition, stress response genes RD29A, DREB1A, and SOS1 significantly downregulated under drought and salt stress in silenced plants compared to control plants, indicating that GaNCED3a played an important role in drought and salt response. The results provided valuable insights into function analysis of cotton CCOs in abiotic stress response, and suggested potential benefit genes for stress-resistant breeding.

Crosstalk between phytohormones and secondary metabolites in the drought stress tolerance of crop plants: A review

Drought stress negatively affects crop performance and weakens global food security. It triggers the activation of downstream pathways, mainly through phytohormones homeostasis and their signaling networks, which further initiate the biosynthesis of secondary metabolites (SMs). Roots sense drought stress, the signal travels to the above-ground tissues to induce systemic phytohormones signaling. The systemic signals further trigger the biosynthesis of SMs and stomatal closure to prevent water loss. SMs primarily scavenge reactive oxygen species (ROS) to protect plants from lipid peroxidation and also perform additional defense-related functions. Moreover, drought-induced volatile SMs can alert the plant tissues to perform drought stress mitigating functions in plants. Other phytohormone-induced stress responses include cell wall and cuticle thickening, root and leaf morphology alteration, and anatomical changes of roots, stems, and leaves, which in turn minimize the oxidative stress, water loss, and other adverse effects of drought. Exogenous applications of phytohormones and genetic engineering of phytohormones signaling and biosynthesis pathways mitigate the drought stress effects. Direct modulation of the SMs biosynthetic pathway genes or indirect via phytohormones' regulation provides drought tolerance. Thus, phytohormones and SMs play key roles in plant development under the drought stress environment in crop plants.

Overexpression of DBF-Interactor Protein 6 Containing an R3H Domain Enhances Drought Tolerance in Populus L. (Populus tomentosa)

Drought is the primary disaster that endangers agricultural production, including animal husbandry, and affects the distribution, growth, yield, and quality of crops. Previous study had revealed that DIP, as a potential regulator of DBF activity, played an important role in response to drought stress in maize. In this study, a total of 67 DIPs were identified from seventeen land plants, including six tobacco DIPs (NtDIPs). NtDIP6 gene was further selected as a candidate gene for subsequent experiments based on the phylogenetic analysis and structural analysis. The transgenic tobacco and poplar plants over-expressing NtDIP6 gene were generated using the Agrobacterium- mediated method. Although there was not phenotypic difference between transgenic plants and wild-type plants under normal conditions, overexpression of the NtDIP6 gene in transgenic tobacco and poplar plants enhanced the drought tolerance under drought treatments in comparison with the wild type. The content of antioxidant defense enzymes peroxidase (POD), catalase (CAT), and the photosynthetic rate increased in NtDIP6-Ox transgenic tobacco and poplar plants, while the content of malondialdehyde decreased, suggesting that the overexpression of NtDIP6 enhances the antioxidant capacity of transgenic poplar. Furthermore, the results of qRT-PCR showed that the level of expression of drought-related response genes significantly increased in the NtDIP6-Ox transgenic plants. These results indicated that NtDIP6, as a positive response regulator, improves drought stress tolerance by scavenging superoxide via the accumulation of antioxidant defense enzymes.

Comparative transcriptome analysis of two rice genotypes differing in their tolerance to saline-alkaline stress

Saline-alkaline stress is an abiotic stress that suppresses rice plant growth and reduces yield. However, few studies have investigated the mechanism by which rice plants respond to saline-alkaline stress at a global transcriptional level. Dongdao-4 and Jigeng-88, which differ in their tolerance to saline-alkaline stress, were used to explore gene expression differences under saline-alkaline stress by RNA-seq technology. In seedlings of Dongdao-4 and Jigeng-88, 3523 and 4066 genes with differential levels of expression were detected, respectively. A total of 799 genes were upregulated in the shoots of both Dongdao-4 and Jigeng-88, while 411 genes were upregulated in the roots of both genotypes. Among the downregulated genes in Dongdao-4 and Jigeng-88, a total of 453 and 372 genes were found in shoots and roots, respectively. Gene ontology (GO) analysis showed that upregulated genes were enriched in several GO terms such as response to stress, response to jasmonic acid, organic acid metabolic process, nicotianamine biosynthetic process, and iron homeostasis. The downregulated genes were enriched in several GO terms, such as photosynthesis and response to reactive oxygen species. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that Dongdao-4 seedlings were specifically enriched in the biosynthesis of secondary metabolites such as diterpenoids and phenylpropanoids. The upregulated genes that were involved in secondary metabolite biosynthesis, amino acid biosynthesis, betalain biosynthesis, organic acid metabolic process, and iron homeostasis pathways may be central to saline-alkaline tolerance in both rice genotypes. In contrast, the genes involved in the diterpenoid and phenylpropanoid biosynthesis pathways may contribute to the greater tolerance to saline-alkaline stress in Dongdao-4 seedlings than in Jigeng-88. These results suggest that Dongdao-4 was equipped with a more efficient mechanism involved in multiple biological processes to adapt to saline-alkaline stress.

Production and roles of IAA and ABA during development of superior and inferior rice grains

Current understanding of the role of plant hormones during cereal grain filling is confounded by contradictory reports on hormone production that is based on poor methodology. We report here on the accurate measurement of indole-3-acetic acid (IAA) and abscisic acid (ABA) by combined liquid chromatography-tandem mass spectrometry in multiple reaction-monitoring mode with heavy isotope labelled internal standards. ABA and IAA contents of superior versus inferior rice grains (ABA maxima 159 ng g-1 FW and 109 ng g-1 FW, IAA maxima 2 µg g-1 FW and 1.7 µg g-1 FW respectively) correlated with the expression of biosynthetic genes and with grain fill. Results confirm that grain ABA is produced primarily by OsNCED2(5), but suggest that ABA import and metabolism also play important roles in ABA regulation. The IAA content of grains is primarily influenced by OsYUC9 and OsYUC11. However, the distinct expression profile of OsYUC12 suggests a specific role for IAA produced by this enzyme. Co-expression of OsYUC12 with OsIAA29 indicates their involvement in a common signalling pathway. Co-expression and cis-element analysis identified several aleurone-specific transcriptional regulators as well as glutelin as strong candidates for detailed investigation for direct regulation by the auxin-signalling pathway.

Nucleotide variations of 9-cis-epoxycarotenoid dioxygenase 2 (NCED2) and pericarp coloration genes (Rc and Rd) from upland rice varieties

In this study, we analyzed the Rc and Rd genes that are responsible for the coloration of rice pericarps from six upland rice varieties. We also examined the association of pericarp coloration to the single nucleotide polymorphism in 9-cis-epoxycarotenoid dioxygenase 2 (NCED2), a key gene involved in abscisic acid (ABA) biosynthesis. Our findings demonstrated that all the upland rice varieties analyzed have a Rd gene which encodes a complete dihydroflavonol-4-reductase without early translational termination codon irrespective of their pericarp colors. However, the upland rice varieties with white pericarps were found to have a defective Rc gene with a 14-base deletion at exon 7 which could disrupt the function of a positive regulator of proanthocyanidin biosynthesis. In addition, the NCED2 genes from the upland rice varieties with white pericarps in this study have a C-allele while the NCED2 genes from Pandasan Red, Tomou and Taragang varieties that bear red pericarps were found to have a T-allele which was reported to be associated with a higher ABA level in upland rice. A better understanding of the gene sequences of upland rice varieties with red pericarp may provide important information for rice breeding programs.

Abscisic acid induced cellular responses of sub1A QTL to aluminium toxicity in rice (Oryza sativa L.)

Involvement of abscisic acid (ABA) was studied for aluminium (Al) sensitivity through functioning of sub1A quantitative trait loci in rice cultivars. sub1A quantitative trait loci bearing cv. Swarna Sub1 was found almost compatible with non sub1A quantitative trait loci bearing cv. Swarna for abscisic acid accumulation all through the aluminium concentrations. However, abscisic acid was self inductive by over expression of its biosynthetic gene in nine-cis-epoxycarotenoid dioxygenase 3 (NCED3) more in cv. Swarna than other. The effect of abscisic acid pretreatment was variable for specific leaf weight, leaf mass ratio and others for the cultivars. Bio-accumulation of aluminium had revealed the sensitivity of toxicity more in cv. Swarna than other. In connection to oxidative stress generation of reactive oxygen species was detected by both histochemical and in vitro assays through hematoxylin, Evans blue and schiff's reactions. Abscisic acid pretreatment had significantly reversed the effects of aluminium toxicity for reactive oxygen species generation. Regardless of varieties sensitivity of aluminium was more prone in shoot than root as detected by nitro blue tetrazolium and 3,3'-diaminobenzidine mediated signalling. Activity in metal chelation in extra cellular spaces monitored through esterase activity and that also established independence of abscisic acid pretreatment for cv. Swarna Sub1. The specific polymorphism of esterase at protein level strengthened the bio-monitoring of aluminium through the rice varieties as well its modulation with abscisic acid. Abscisic acid has been discussed an important effectors to modulate the tolerance pathway of rice cultivars through intrusion of sub1A quantitative trait loci.

CRISPR-associated nucleases: the Dawn of a new age of efficient crop improvement

The world stands at a new threshold today. As a planet, we face various challenges, and the key one is how to continue to produce enough food, feed, fiber, and fuel to support the burgeoning population. In the past, plant breeding and the ability to genetically engineer crops contributed to increasing food production. However, both approaches rely on random mixing or integration of genes, and the process can be unpredictable and time-consuming. Given the challenge of limited availability of natural resources and changing environmental conditions, the need to rapidly and precisely improve crops has become urgent. The discovery of CRISPR-associated endonucleases offers a precise yet versatile platform for rapid crop improvement. This review summarizes a brief history of the discovery of CRISPR-associated nucleases and their application in genome editing of various plant species. Also provided is an overview of several new endonucleases reported recently, which can be utilized for editing of specific genes in plants through various forms of DNA sequence alteration. Genome editing, with its ever-expanding toolset, increased efficiency, and its potential integration with the emerging synthetic biology approaches hold promise for efficient crop improvement to meet the challenge of supporting the needs of future generations.

OsNCED5, a 9-cis-epoxycarotenoid dioxygenase gene, regulates salt and water stress tolerance and leaf senescence in rice

9-cis-epoxycarotenoid dioxygenase (NCED) is a rate-limiting enzyme for abscisic acid (ABA) biosynthesis. However, the molecular mechanisms of NCED5 that modulate plant development and abiotic stress tolerance are still unclear, particular in rice. Here, we demonstrate that a rice NCED gene, OsNCED5, was expressed in all tissues we tested, and was induced by exposure to salt stress, water stress, and darkness. Mutational analysis showed that nced5 mutants reduced ABA level and decreased tolerance to salt and water stress and delayed leaf senescence. However, OsNCED5 overexpression increased ABA level, enhanced tolerance to the stresses, and accelerated leaf senescence. Transcript analysis showed that OsNCED5 regulated ABA-dependent abiotic stress and senescence-related gene expression. Additionally, ectopic expression of OsNCED5 tested in Arabidopsis thaliana altered plant size and leaf morphology and delayed seed germination and flowering time. Thus, OsNCED5 may regulate plant development and stress resistance through control of ABA biosynthesis. These findings contribute to our understanding of the molecular mechanisms by which NCED regulates plant development and responses to abiotic stress in different crop species.