Drought Resistance in Rice from Conventional to Molecular Breeding: A Review

Dynamic proteome and acetylome profiling reveals key regulators of sucrose accumulation in sugarcane

KEY MESSAGE

Lysine acetylation and protein abundance both play crucial roles in regulating sucrose accumulation in sugarcane, with 73 dual-function proteins identified as potential targets for molecular breeding to enhance sucrose levels. Lysine acetylation plays a crucial role in regulating various biological processes in plants, but its role in sucrose accumulation in sugarcane remains unexplored In this study, we conducted a comprehensive quantitative proteome and acetylated proteome analysis on the leaves of two sugarcane genotypes with high and low sucrose levels at early, middle, and late stages of sucrose accumulation. Quantitative proteome analysis identified 2363 differentially abundant proteins (DAPs), of which 165 were associated with sugar metabolism pathways, providing more targets for improving sucrose content in sugarcane. The acetylated proteome analysis identified 1397 differentially acetylated proteins (DAcPs) with 2377 acetylation sites. Many DAcPs were also involved in sugar metabolism, demonstrating that lysine acetylation is associated with sucrose accumulation. A comparison of the DAPs and DAcPs identified 650 overlapping proteins, with 73 of them related to sugar metabolism, confirming dual regulatory roles of protein abundance and acetylation in sucrose accumulation in sugarcane. These 73 proteins serve as targets for sucrose improvement with dual regulatory effects. Our data also suggest that histone acetylation and nitrogen metabolism may be related to sucrose accumulation. This work enhances our understanding of the mechanisms regulating sucrose accumulation and proposes targets for improving sucrose content in sugarcane through molecular breeding.

Phenotypic Physiological and Metabolomic Analyses Reveal Crucial Metabolic Pathways in Quinoa (Chenopodium quinoa Willd.) in Response to PEG-6000 Induced Drought Stress

Drought stress seriously threatens human food security, and enhancing crops' drought tolerance is an urgent problem to be solved in breeding. Quinoa is known for its high nutritional value and strong drought tolerance, but its molecular mechanism in response to drought stress is still unclear. In this study, we used drought-tolerant (D2) and drought-sensitive (ZK1) quinoa varieties, and PEG-6000 was used to simulate drought stress in quinoa seedlings. Phenotypic and physiological biochemical indicators were measured during the seedling stage, and LC-MS was used for a metabolite analysis of drought stress to explore the drought tolerance mechanism of quinoa under drought stress. With the intensification of drought stress, chlorophyll content gradually increased, and D2 reached its maximum at W4, an increase of 49.85% compared with W1. The total chlorophyll content, photosynthesis rate, and stomatal conductance of ZK1 were significantly lower than D2 under moderate and severe drought stress. Metabolomic results showed that a total of 1295 positive ion mode (pos) metabolites and 914 negative ion mode (neg) metabolites were identified. Of these, 12(R)-HETE, phosphatidylcholine, monogalactose diester (MGDG), and stachyose up-regulated expression under drought stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that unsaturated fatty acid biosynthesis and glycerophospholipid metabolism pathways were significantly enriched. In summary, our results elucidate that quinoa responds to drought stress by accumulating chlorophyll and sugars, activating unsaturated fatty acid metabolism, and protecting the photosynthetic system. These findings provide new insights for the breeding of drought-tolerant quinoa varieties and the study of drought tolerance mechanisms.

Phenomics-assisted genetic dissection and molecular design of drought resistance in rice

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 drought-avoidant (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 multimodal 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 5' 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.

Synergistic Effects of Microbial Biostimulants and Calcium in Alleviating Drought Stress in Oilseed Rape

The study aimed to examine the changes in winter oilseed rape (Brassica napus L.) under simulated prolonged drought and to assess the effects of a microbial biostimulant ProbioHumus and calcium, individually and in combination, in order to improve the plant's drought resistance and to identify the biochemical processes occurring in the plant tissues. The oilseed rape cv. 'Visby' was grown under controlled laboratory conditions. CaCO3 (hereafter, Ca) (3.71 g) was added to the soil of one pot at 70 g m-2. Seedlings at the 3-4 leaf stage were sprayed with ProbioHumus 2 mL 100 mL-1 and exposed to drought for 8 days to achieve a high water deficit. Irrigation was then resumed, and recovery was assessed after 4 days. The data showed that the microbial biostimulant alleviated the physiological and biochemical response of oilseed rape to drought stress. ProbioHumus + Ca reduced plant wilting by increasing leaf relative water content (RWC) by 87% and induced drought tolerance by increasing endogenous proline content 4-fold, increasing photosynthetic pigment content in leaves by 10-28%, reducing H2O2 by 53% and malondialdehyde (MDA) by 45%, and stimulating stomata opening (by 2-fold on the upper and 1.4-fold in the lower leaf surface), vs. drought control. The most effective measure to increase plant survival and/or resume growth after drought was the application of a microbial biostimulant with additional calcium to the soil. The practical implications of this research point to the potential benefits of applying these ecological measures under field conditions.

Genome-wide association study revealed candidate genes associated with leaf size in alfalfa (Medicago sativa L.)

BACKGROUND

Alfalfa (Medicago sativa L.) is one of the most widely cultivated perennial leguminous forages globally, known for its high yield and quality. Leaf size plays a crucial role in influencing its photosynthetic capacity, forage yield, and quality. Therefore, understanding the genetic factors regulating leaf size is of great importance for breeding new alfalfa varieties with improved yield and quality. In this study, we performed a genome-wide association study on four leaf size-related traits in 176 alfalfa germplasm resources to identify candidate genes associated with leaf size.

RESULTS

Phenotypic analysis revealed varying degrees of variation among the four traits, with coefficients of variation ranging from 3.43 to 36.84%. The broad sense heritability of these traits was found to be between 38.30% and 53.23%. Correlation analysis showed a significant positive correlation among the four traits (P < 0.01). The GWAS identified 39 SNPs associated with leaf size, distributed across eight chromosomes, of which 9 SNPs were linked to multiple traits. Haplotype analysis further confirmed that the number of superior alleles in each material was positively correlated with leaf area. Finally, we identified five genes near these 39 significant SNPs that are associated with leaf size or development.

CONCLUSION

Our findings provide new molecular markers for marker-assisted selection in alfalfa breeding programs. Moreover, this study provides a solid foundation for subsequent functional verification and genetic improvement in alfalfa.

Impact of water stress to plant epigenetic mechanisms in stress and adaptation

Water is the basic molecule in living beings, and it has a major impact on vital processes. Plants are sessile organisms with a sophisticated regulatory network that regulates how resources are distributed between developmental and adaptation processes. Drought-stressed plants can change their survival strategies to adapt to this unfavorable situation. Indeed, plants modify, change, and modulate gene expression when grown in a low-water environment. This adaptation occurs through several mechanisms that affect the expression of genes, allowing these plants to resist in dry regions. Epigenetic modulation has emerged as a major factor in the transcription regulation of drought stress-related genes. Moreover, specific molecular and epigenetic modifications in the expression of certain genetic networks lead to adapted responses that aid a plant's acclimatization and survival during repeated stress. Indeed, understanding plant responses to severe environmental stresses, including drought, is critical for biotechnological applications. Here, we first focused on drought stress in plants and their general adaptation mechanisms to this stress. We also discussed plant epigenetic regulation when exposed to water stress and how this adaptation can be passed down through generations.

Editorial for the Special Issue 'Molecular Breeding and Genetics Research in Plants'

Despite significant advancements in plant breeding research, the challenges posed by a growing global population, the impact of abiotic and biotic stresses, and the uncertainties of climate change necessitate continued focus and innovation in plant breeding and genetic studies [...].

Nei 6 You 7075, a hybrid rice cultivar, exhibits enhanced disease resistance and drought tolerance traits

BACKGROUND

Rice is the main food crop for much of the population in China. Therefore, selecting and breeding new disease resistance and drought tolerance in rice is essential to ensure national food security. The utilization of heterosis has significantly enhanced rice productivity, yet many of the molecular mechanisms underlying this phenomenon remain largely unexplored. 'Nei 6 You 7075' ('N6Y7075') is a novel hybrid rice cultivar with exceptional quality, developed through the crossbreeding of 'Fuhui 7075' ('FH7075') and 'Neixiang 6 A' ('NX6A'). However, the precise mechanisms underlying the disease resistance and drought tolerance in 'N6Y7075' are poorly understood. In this study, we investigated the resistance of hybrid rice 'N6Y7075' to bacterial blight (Xanthomonas oryzae pv. oryzae), rice blast (Magnaporthe oryzae), and drought and identified differentially expressed genes between hybrid rice 'N6Y7075' and its parents through RNA-seq analysis.

RESULTS

Our research found that the hybrid 'N6Y7075' and its female parent 'NX6A' were less susceptible to bacterial blight and rice blast than the male parent 'FH7075', while 'FH7075' showed better drought tolerance than 'NX6A'. The hybrid 'N6Y7075' exhibited heterosis. Clustering results revealed that the expression profiles of the F1 hybrid closely resembled those of its parental lines rather than exhibiting an intermediate profile between the two parental lines. The disease resistance of hybrid rice 'N6Y7075' may be attributed to the plant-pathogen interaction pathways involving Xa21, CDPK, and RPM1-mediated hypersensitive response and WRKY1-induced defense-related gene expression and programmed cell death. The MAPK signaling pathway PR1 could also be associated with plant defense responses. Hybrid rice 'N6Y7075' may enhance drought tolerance by regulating MAPKKK17 and WAK60 in the MAPK signaling pathway. These proteins affect ABA stress adaptation and stomatal development in plants, respectively.

CONCLUSIONS

Our results provide a preliminary exploration of 'N6Y7075' disease resistance and drought tolerance and provide a relevant theoretical basis for its further study and use. This study provides insights into the molecular mechanisms of heterosis in hybrid rice and identifies potential associated genes.

Sweet corn (Zea mays L.) seed performance enhanced under drought stress by chitosan and minerals coating

Sweet corn (Zea mays L.) var. Saccharata is a tropical and semitropical annual cereal with low germination, poor vigor, and weak seedling establishment in the soil. In order to enhance the physical properties of sweet corn and examine the effects of seed coating on the morphological, biochemical, and physiological characteristics of sweet corn seedlings under drought stress conditions, we conducted a factorial experiment in greenhouse conditions. Seed coating was carried out using a mixture of vermiculite (V), kaolin (K), and perlite (P) in a ratio of 3:1.5:2. The main factors of the greenhouse experiment comprised three levels of coating treatment (chitosan 0.5% + V10K2.5P5 (gr), NaAlg 1% + V10K2.5P5 (gr), and non-coated seeds as a control) along with drought stress at four levels (0, -0.3, -0.6, and -0.9 bar). In greenhouse conditions, the growth indexes of sweet corn seedlings were studied under increasing levels of drought stress. The results showed that as drought stress levels increased, certain growth indicators such as seedling emergence and seedling emergence rate, soluble protein, chlorophyll total content, nitrogen, and phosphorus content decreased. On the other hand, mean emergence, proline, potassium, soluble sugars, malondialdehyde, and hydrogen peroxide were increased. The study found that the highest seedling emergence percentage occurred in the coating treatment of chitosan 0.5% + V10K2.5P5 (gr) at all levels of drought stress. Overall, seed coating with the Chitosan 0.5% + V10K2.5P5 (gr) treatment improved the performance of sweet corn seeds and reduced the negative effects of drought stress by increasing seedling emergence and establishment.

Drought stress mitigation through bioengineering of microbes and crop varieties for sustainable agriculture and food security

Climate change and agriculture are intrinsically connected and sudden changes in climatic conditions adversely impact global food production and security. The climate change-linked abiotic stressors like drought and high temperatures are resulting in crop failure. The most severe abiotic stress drought significantly affect the stomatal closure, production of reactive oxygen species, transpiration, photosynthesis or other physiological processes and plant morphology, and adversely affect plant growth and crop yield. Therefore, there is an exigent need for cost effective and eco-friendly modern technologies to induce drought tolerance in crop plants leading to climate-adapted sustainable agricultural practices for sustained food production. Among many options being pursued in this regard, the use of plant growth promoting microbes (PGPMs) is the most sustainable approach to promote drought stress resilience in crop plants leading to better plant growth and crop productivity. These PGPMs confer drought resistance via various direct or indirect mechanisms including production of antioxidants, enzymes, exopolysaccharides, modulation of phytohormones level, osmotic adjustment by inducing the accumulation of sugars, along with increases in nutrients, water uptake and photosynthetic pigments. However, several technological and ecological challenges limit their use in agriculture and sometimes treatment with plant beneficial microbes fails to produce desired results under field conditions. Thus, development of synthetic microbial communities or host mediated microbiome engineering or development of transgenic plants with the capacity to express desired traits may promote plant survival and growth under drought stress conditions. The present review critically assesses research evidence on the plant growth and stress resilience promoting potentials of PGPMs and their genes as an approach to develop drought resilient plants leading to increased crop productivity. Effective collaboration among scientific communities, policymakers and regulatory agencies is needed to create strong frameworks that both promote and regulate the utilization of synthetic microbial communities and transgenic plants in agriculture.

Impact of Abiotic Stress on Rice and the Role of DNA Methylation in Stress Response Mechanisms

With the intensification of global climate change and the increasing complexity of agricultural environments, the improvement of rice stress tolerance is an important focus of current breeding research. This review summarizes the current knowledge on the impact of various abiotic stresses on rice and the associated epigenetic responses (DNA methylation). Abiotic stress factors, including high temperature, drought, cold, heavy metal pollution, and high salinity, have a negative impact on crop productivity. Epigenetic changes are key regulatory factors in plant stress responses, and DNA methylation is one of the earliest discovered and thoroughly studied mechanisms in these epigenetic regulatory mechanisms. The normal growth of rice is highly dependent on the environment, and changes in the environment can lead to rice sterility and severe yield loss. Changes in the regulation of the DNA methylation pathway are involved in rice's response to stress. Various DNA methylation-regulating protein complexes that function during rice development have been identified. Significant changes in DNA methylation occur in numerous stress-responsive genes, particularly those in the abscisic acid signaling pathway. These findings underscore the complex mechanisms of the abiotic stress response in rice. We propose the effective improvement of tolerance traits by regulating the epigenetic status of rice and emphasize the role of DNA methylation in abiotic stress tolerance, thereby addressing global climate change and ensuring food security.

Modern Plant Breeding Techniques in Crop Improvement and Genetic Diversity: From Molecular Markers and Gene Editing to Artificial Intelligence-A Critical Review

With the development of new technologies in recent years, researchers have made significant progress in crop breeding. Modern breeding differs from traditional breeding because of great changes in technical means and breeding concepts. Whereas traditional breeding initially focused on high yields, modern breeding focuses on breeding orientations based on different crops' audiences or by-products. The process of modern breeding starts from the creation of material populations, which can be constructed by natural mutagenesis, chemical mutagenesis, physical mutagenesis transfer DNA (T-DNA), Tos17 (endogenous retrotransposon), etc. Then, gene function can be mined through QTL mapping, Bulked-segregant analysis (BSA), Genome-wide association studies (GWASs), RNA interference (RNAi), and gene editing. Then, at the transcriptional, post-transcriptional, and translational levels, the functions of genes are described in terms of post-translational aspects. This article mainly discusses the application of the above modern scientific and technological methods of breeding and the advantages and limitations of crop breeding and diversity. In particular, the development of gene editing technology has contributed to modern breeding research.

Transcriptome Regulation Mechanisms Difference between Female and Male Buchloe dactyloides in Response to Drought Stress and Rehydration

Drought, a pervasive global challenge, significantly hampers plant growth and crop yields, with drought stress being a primary inhibitor. Among resilient species, Buchloe dactyloides, a warm-season and dioecious turfgrass, stands out for its strong drought resistance and minimal maintenance requirements, making it a favored choice in ecological management and landscaping. However, there is limited research on the physiological and molecular differences in drought resistance between male and female B. dactyloides. To decipher the transcriptional regulation dynamics of these sexes in response to drought, RNA-sequencing analysis was conducted using the 'Texoka' cultivar as a model. A 14-day natural drought treatment, followed by a 7-day rewatering period, was applied. Notably, distinct physiological responses emerged between genders during and post-drought, accompanied by a more pronounced differential expression of genes (DEGs) in females compared to males. Further, KEGG and GO enrichment analysis revealed different DEGs enrichment pathways of B. dactyloides in response to drought stress. Analysis of the biosynthesis and signaling transduction pathways showed that drought stress significantly enhanced the biosynthesis and signaling pathway of ABA in both female and male B. dactyloides plants, contrasting with the suppression of IAA and JA pathways. Also, we discovered BdMPK8-like as a potential enhancer of drought tolerance in yeast, highlighting novel mechanisms. This study demonstrated the physiological and molecular mechanisms differences between male and female B. dactyloides in response to drought stress, providing a theoretical basis for the corresponding application of female and male B. dactyloides. Additionally, it enriches our understanding of drought resistance mechanisms in dioecious plants, opening avenues for future research and genetic improvement.

Mutation of a RING E3 ligase, OsDIRH2, enhances drought tolerance in rice with low stomata density

Drought is a major environmental stress factor that negatively affects rice growth and yield. From a forward genetic perspective, we selected a drought-insensitive TILLING line (ditl4) from a gamma-ray-induced core mutant population (M10). Under drought conditions, ditl4 exhibited greater fresh weight, survival rate, chlorophyll, proline, and soluble sugar contents, and lower H2O2 and MDA levels than wild-type (WT). In addition, the activities of antioxidant enzymes, such as superoxide dismutase, catalase, and peroxidase, were higher in ditl4 than in the WT. In the relative water loss assay, dilt4 showed significantly decreased leaf curling and water loss compared to WT. Also, the ratio of "closed" stomata aperture was increased in ditl4 under drought stress, suggesting reduced transpiration to prevent water loss. The ditl4 mutant showed decreased stomatal conductance, transpiration, and CO2 assimilation and increased water use efficiency due to the low density of stomata. Whole-genome resequencing analysis of dilt4 identified a single nucleotide polymorphism (SNP) in OsDIRH2 (LOC_Os11g39640), annotated as a RING-H2 type E3 ligase, resulting in a premature stop codon. CRISPR/Cas9-mediated knock-out mutants (OsDIRH2a and OsDIRH2b) enhanced drought tolerance by lowering stomatal density compared to empty vector control plants. These findings suggested that ditl4 with low stomatal density would be useful as a genetic resource for a drought-tolerant breeding program to improve water-use efficiency.

Isolation and Characterization of Plant-Growth-Promoting, Drought-Tolerant Rhizobacteria for Improved Maize Productivity

Drought is one of the main abiotic factors affecting global agricultural productivity. However, the application of bioinocula containing plant-growth-promoting rhizobacteria (PGPR) has been seen as a potential environmentally friendly technology for increasing plants' resistance to water stress. In this study, rhizobacteria strains were isolated from maize (Zea mays L.) and subjected to drought tolerance tests at varying concentrations using polyethylene glycol (PEG)-8000 and screened for plant-growth-promoting activities. From this study, 11 bacterial isolates were characterized and identified molecularly, which include Bacillus licheniformis A5-1, Aeromonas caviae A1-2, A. veronii C7_8, B. cereus B8-3, P. endophytica A10-11, B. halotolerans A9-10, B. licheniformis B9-5, B. simplex B15-6, Priestia flexa B12-4, Priestia flexa C6-7, and Priestia aryabhattai C1-9. All isolates were positive for indole-3-acetic acid (IAA), siderophore, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, ammonia production, nitrogen fixation, and phosphate solubilization, but negative for hydrogen cyanide production. Aeromonas strains A1-2 and C7_8, showing the highest drought tolerance of 0.71 and 0.77, respectively, were selected for bioinoculation, singularly and combined. An increase in the above- and below-ground biomass of the maize plants at 100, 50, and 25% water-holding capacity (WHC) was recorded. Bacterial inoculants, which showed an increase in the aerial biomass of plants subjected to moderate water deficiency by up to 89%, suggested that they can be suitable candidates to enhance drought tolerance and nutrient acquisition and mitigate the impacts of water stress on plants.

Overexpression of OsNAR2.1 by OsNAR2.1 promoter increases drought resistance by increasing the expression of OsPLDα1 in rice

BACKGROUND

pOsNAR2.1:OsNAR2.1 expression could significantly increase nitrogen uptake efficiency and grain yield of rice.

RESULT

This study reported the effects of overexpression of OsNAR2.1 by OsNAR2.1 promoter on physiological and agronomic traits associated with drought tolerance. In comparison to the wild-type (WT), the pOsNAR2.1:OsNAR2.1 transgenic lines exhibited a significant improvement in survival rate when subjected to drought stress and then irrigation. Under limited water supply conditions, compared with WT, the photosynthesis and water use efficiency (WUE) of transgenic lines were increased by 39.2% and 28.8%, respectively. Finally, the transgenic lines had 25.5% and 66.4% higher grain yield than the WT under full watering and limited water supply conditions, respectively. Compared with the WT, the agronomic nitrogen use efficiency (NUE) of transgenic lines increased by 25.5% and 66.4% under full watering and limited water supply conditions, and the N recovery efficiency of transgenic lines increased by 29.3% and 50.2%, respectively. The interaction between OsNAR2.1 protein and OsPLDα1 protein was verified by yeast hybrids. After drought treatment, PLDα activity on the plasma membrane of the transgenic line increased 85.0% compared with WT.

CONCLUSION

These results indicated that pOsNAR2.1:OsNAR2.1 expression could improve the drought resistance of rice by increasing nitrogen uptake and regulating the expression of OsPLDα1.

Genome-Wide Association Study of Rice Diversity Panel Reveals New QTLs for Tolerance to Water Deficit Under the Egyptian Conditions

Drought has a significant impact on rice yield by restricting the crop's ability to grow and develop. Producing rice cultivars adapted to water deficit conditions is still the main interest of rice breeders and geneticists. To address this challenge, a set of 413 highly diverse rice populations were evaluated under normal and water deficit conditions for two growing seasons of 2021 and 2022. High genetic variation was found among genotypes for all studied traits. The heritability estimates ranged from 0.82 (panicle length) to 0.95 (plant height). Sterility percentage (SET%) was the most trait affected by water deficit in two growing seasons. 22 Rice genotypes were classified as drought tolerant in both years. Genome-wide association mapping was performed for all traits in the two growing seasons under both conditions using a total of 700,000 SNPs. The GWAS results revealed important and major SNPs associated with all traits. 26 Significant SNPs with stable allele effects were found to be associated with yield traits under water deficit conditions in both years. The results of this study provided rice genotypes that can be adapted under water deficit conditions and important stable SNP markers that can be used for marker-assisted selection after validation in different genetic backgrounds.

Comparative miRNome and transcriptome analyses reveal the expression of novel miRNAs in the panicle of rice implicated in sustained agronomic performance under terminal drought stress

MAIN CONCLUSION

Differential expression of 128 known and 111 novel miRNAs in the panicle of Nagina 22 under terminal drought stress targeting transcription factors, stress-associated genes, etc., enhances drought tolerance and helps sustain agronomic performance under terminal drought stress. Drought tolerance is a complex multigenic trait, wherein the genes are fine-tuned by coding and non-coding components in mitigating deleterious effects. MicroRNA (miRNA) controls gene expression at post-transcriptional level either by cleaving mRNA (transcript) or by suppressing its translation. miRNAs are known to control developmental processes and abiotic stress tolerance in plants. To identify terminal drought-responsive novel miRNA in contrasting rice cultivars, we constructed small RNA (sRNA) libraries from immature panicles of drought-tolerant rice [Nagina 22 (N 22)] and drought-sensitive (IR 64) cultivars grown under control and terminal drought stress. Our analysis of sRNA-seq data resulted in the identification of 169 known and 148 novel miRNAs in the rice cultivars. Among the novel miRNAs, 68 were up-regulated while 43 were down-regulated in the panicle of N 22 under stress. Interestingly, 31 novel miRNAs up-regulated in N 22 were down-regulated in IR 64, whereas 4 miRNAs down-regulated in N 22 were up-regulated in IR 64 under stress. To detect the effects of miRNA on mRNA expression level, transcriptome analysis was performed, while differential expression of miRNAs and their target genes was validated by RT-qPCR. Targets of the differentially expressed miRNAs include transcription factors and stress-associated genes involved in cellular/metabolic/developmental processes, response to abiotic stress, programmed cell death, photosynthesis, panicle/seed development, and grain yield. Differential expression of the miRNAs could be validated in an independent set of the samples. The findings might be useful in genetic improvement of drought-tolerant rice.

Genome-Wide Identification and Expression Analysis of the DMP and MTL Genes in Sweetpotato (Ipomoea batatas L.)

Sweetpotato (Ipomoea batatas L.) is a strategic crop with both economic and energy value. However, improving sweetpotato varieties through traditional breeding approaches can be a time-consuming and labor-intensive process due to the complex genetic nature of sweetpotato as a hexaploid species (2n = 6x = 90). Double haploid (DH) breeding, based on in vivo haploid induction, provides a new approach for rapid breeding of crops. The success of haploid induction can be achieved by manipulating specific genes. Two of the most critical genes, DMP (DUF679 membrane proteins) and MTL (MATRILINEAL), have been shown to induce haploid production in several species. Here, we identified and characterized DMP and MTL genes in sweetpotato using gene family analysis. In this study, we identified 5 IbDMPs and 25 IbpPLAs. IbDMP5 and IbPLAIIs (IbPLAIIκ, IbPLAIIλ, and IbPLAIIμ) were identified as potential haploid induction (HI) genes in sweetpotato. These results provide valuable information for the identification and potential function of HI genes in sweetpotato and provide ideas for the breeding of DH lines.

OsNAC120 balances plant growth and drought tolerance by integrating GA and ABA signaling in rice

The crosstalk between gibberellin (GA) and abscisic acid (ABA) signaling is crucial for balancing plant growth and adaption to environmental stress. Nevertheless, the molecular mechanism of their mutual antagonism still remains to be fully clarified. In this study, we found that knockout of the rice NAC (NAM, ATAF1/2, CUC2) transcription factor gene OsNAC120 inhibits plant growth but enhances drought tolerance, whereas OsNAC120 overexpression produces the opposite results. Exogenous GA can rescue the semi-dwarf phenotype of osnac120 mutants, and further study showed that OsNAC120 promotes GA biosynthesis by transcriptionally activating the GA biosynthetic genes OsGA20ox1 and OsGA20ox3. The DELLA protein SLENDER RICE1 (SLR1) interacts with OsNAC120 and impedes its transactivation ability, and GA treatment can remove the inhibition of transactivation activity caused by SLR1. On the other hand, OsNAC120 negatively regulates rice drought tolerance by repressing ABA-induced stomatal closure. Mechanistic investigation revealed that OsNAC120 inhibits ABA biosynthesis via transcriptional repression of the ABA biosynthetic genes OsNCED3 and OsNCED4. Rice OSMOTIC STRESS/ABA-ACTIVATED PROTEIN KINASE 9 (OsSAPK9) physically interacts with OsNAC120 and mediates its phosphorylation, which results in OsNAC120 degradation. ABA treatment accelerates OsNAC120 degradation and reduces its transactivation activity. Together, our findings provide evidence that OsNAC120 plays critical roles in balancing GA-mediated growth and ABA-induced drought tolerance in rice. This research will help us to understand the mechanisms underlying the trade-off between plant growth and stress tolerance and to engineer stress-resistant, high-yielding crops.

Advanced Biotechnological Interventions in Mitigating Drought Stress in Plants

This comprehensive article critically analyzes the advanced biotechnological strategies to mitigate plant drought stress. It encompasses an in-depth exploration of the latest developments in plant genomics, proteomics, and metabolomics, shedding light on the complex molecular mechanisms that plants employ to combat drought stress. The study also emphasizes the significant advancements in genetic engineering techniques, particularly CRISPR-Cas9 genome editing, which have revolutionized the creation of drought-resistant crop varieties. Furthermore, the article explores microbial biotechnology's pivotal role, such as plant growth-promoting rhizobacteria (PGPR) and mycorrhizae, in enhancing plant resilience against drought conditions. The integration of these cutting-edge biotechnological interventions with traditional breeding methods is presented as a holistic approach for fortifying crops against drought stress. This integration addresses immediate agricultural needs and contributes significantly to sustainable agriculture, ensuring food security in the face of escalating climate change challenges.

Genotype-specific germination behavior induced by sustainable priming techniques in response to water deprivation stress in rice

Water stress brought about by climate change is among the major global concerns threatening food security. Rice is an important staple food which requires high water resources. Being a semi-aquatic plant, rice is particularly susceptible to drought. The aim of this work was to develop techniques directed to promote rice resilience to water deprivation stress during germination by implementing specific seed priming treatments. Five popular Italian rice varieties were subjected to priming treatments using novel, sustainable solutions, like poly-gamma-glutamic acid (γ-PGA), denatured γ-PGA (dPGA), and iron (Fe) pulsing, alone or in combination. The effect of the developed priming methods was tested under optimal conditions as well as under water deprivation stress imposed by polyethylene glycol (PEG) treatments. The priming efficacy was phenotypically determined in terms of germination behavior by measuring a series of parameters (germinability, germination index, mean germination time, seed vigor index, root and shoot length, germination stress tolerance index). Biochemical analyses were carried out to measure the levels of iron uptake and accumulation of reactive oxygen species (ROS). Integrative data analyses revealed that the rice varieties exhibited a strong genotype- and treatment-specific germination behavior. PEG strongly inhibited germination while most of the priming treatments were able to rescue it in all varieties tested except for Unico, which can be defined as highly stress sensitive. Molecular events (DNA repair, antioxidant response, iron homeostasis) associated with the transition from seed to seedling were monitored in terms of changes in gene expression profiles in two varieties sensitive to water deprivation stress with different responses to priming. The investigated genes appeared to be differentially expressed in a genotype-, priming treatment-, stress- and stage-dependent manner. The proposed seed priming treatments can be envisioned as sustainable and versatile agricultural practices that could help in addressing the impact of climate challenges on the agri-food system.

Screening of Sugarcane Proteins Associated with Defense against Leifsonia xyli subsp. xyli, Agent of Ratoon Stunting Disease

Sugarcane is the most important sugar crop and one of the leading energy-producing crops in the world. Ratoon stunting disease (RSD), caused by the bacterium Leifsonia xyli subsp. xyli, poses a huge threat to ratoon crops, causing a significant yield loss in sugarcane. Breeding resistant varieties is considered the most effective and fundamental approach to control RSD in sugarcane. The exploration of resistance genes forms the foundation for breeding resistant varieties through molecular technology. The pglA gene is a pathogenicity gene in L. xyli subsp. xyli, encoding an endopolygalacturonase. In this study, the pglA gene from L. xyli subsp. xyli and related microorganisms was analyzed. Then, a non-toxic, non-autoactivating pglA bait was successfully expressed in yeast cells. Simultaneously the yeast two-hybrid library was generated using RNA from the L. xyli subsp. xyli-infected sugarcane. Screening the library with the pglA bait uncovered proteins that interacted with pglA, primarily associated with ABA pathways and the plant immune system, suggesting that sugarcane employs these pathways to respond to L. xyli subsp. xyli, triggering pathogenicity or resistance. The expression of genes encoding these proteins was also investigated in L. xyli subsp. xyli-infected sugarcane, suggesting multiple layers of regulatory mechanisms in the interaction between sugarcane and L. xyli subsp. xyli. This work promotes the understanding of plant-pathogen interaction and provides target proteins/genes for molecular breeding to improve sugarcane resistance to L. xyli subsp. xyli.

A Multi-Omics Analysis Revealed the Diversity of the MYB Transcription Factor Family's Evolution and Drought Resistance Pathways

The MYB transcription factor family can regulate biological processes such as ABA signal transduction to cope with drought stress, but its evolutionary mechanism and the diverse pathways of response to drought stress in different species are rarely reported. In this study, a total of 4791 MYB family members were identified in 908,757 amino acid sequences from 12 model plants or crops using bioinformatics methods. It was observed that the number of MYB family members had a linear relationship with the chromosome ploidy of species. A phylogenetic analysis showed that the MYB family members evolved in subfamily clusters. In response to drought stress, the pathways of MYB transcription factor families exhibited species-specific diversity, with closely related species demonstrating a higher resemblance. This study provides abundant references for drought resistance research and the breeding of wheat, soybean, and other plants.

Study on medicinal food plants in the Gaoligongshan Biosphere Reserve, the richest biocultural diversity center in China

BACKGROUND

Traditional knowledge associated with medicinal food plants (MFPs) plays a vital role in fighting hidden hunger and safeguarding the health of local people. MFPs resources are abundant in the Gaoligongshan area, a biosphere reserve with the richest biocultural diversity in China. Local people of different linguistic groups also have rich traditional botanical knowledge. However, there are still few comprehensive and systematic studies on MFPs there.

METHODS

Ethnobotanical investigation including market survey, semi-structured interviews, free listing and key informant interviews was conducted in the Gaoligongshan area, Western Yunnan, Southwest China. A total of 13 local farmers' markets were selected and information about medicinal food plants, including food categories, medicinal and edible parts, modes of consumption, medicinal effects, and distribution were collected. The relative occurrence frequency (RFO) and cultural food significance index (CFSI) were calculated to identify the culturally significant MFPs.

RESULTS

A total of 184 species of MFPs, belonging to 83 families, were collected in the Gaoligongshan area, including vegetables (77), medicinal diets (26), fruits (25), spices (18), herbal tea (13), tea substitutes (11), substitutes for staple food (8), nuts (5), oils and fats (4), and dye material (1). The most frequently used families were Fabaceae, Asteraceae and Apiaceae, with 11, 10, and 9 species, respectively. The most frequently used plant parts were the stems, followed by fruits and leaves. Based on the evaluation results of the CFSI and RFO indices, 18 species of MFPs with magnificent local cultural importance have been screened out, such as Houttuynia cordata, Eryngium foetidum, Sechium edule, Centella asiatica and Pseudocydonia sinensis.

CONCLUSION

These findings have guiding significance for conservation of traditional knowledge associated with MFPs and facilitation of scientific utilization of MFPs to meet local people's needs for a healthy life.

Genome-Wide Association Study Unravels Quantitative Trait Loci and Genes Associated with Yield-Related Traits in Sugarcane

Sugarcane, a major sugar and energy crop worldwide faces an increasing demand for higher yields. Identifying yield-related markers and candidate genes is valuable for breeding high-yield varieties using molecular techniques. In this work, seven yield-related traits were evaluated in a diversity panel of 159 genotypes, derived from Tripidium arundinaceum, Saccharum spontaneum, and modern sugarcane genotypes. All traits exhibited significant genetic variance with high heritability and high correlations. Genetic diversity analysis reveals a genomic decay of 23 kb and an average single nucleotide polymorphism (SNP) number of 25,429 per genotype. These 159 genotypes were divided into 4 subgroups. Genome-wide association analysis identified 47 SNPs associated with brix, spanning 36 quantitative trait loci (QTLs), and 138 SNPs for other traits across 104 QTLs, covering all 32 chromosomes. Interestingly, 12 stable QTLs associated with yield-related traits were identified, which contained 35 candidate genes. This work provides markers and candidate genes for marker-assisted breeding to improve sugarcane yields.

Dissecting the genetic basis of drought responses in common bean using natural variation

The common bean (Phaseolus vulgaris L) is the most important legume for human consumption, contributing 30% of the total daily protein intake in developing countries. A major limitation for its cultivation is drought, which causes more than 60% of the annual losses. Among physiological adaptations to drought, delaying senescence and extending the photosynthetic capacity can improve crop productivity. This strategy is known as functional "stay-green" (SG) and has been discussed as a goal in plant breeding to alleviate the loss of yield under water scarcity conditions. The genetic components behind SG traits have been explored specially in cereals, but they are to date poorly studied in the common bean. For this, we screened 71 common bean cultivars belonging to the three most important gene-pools, Mesoamerica, Andes and Europe, selected to cover the natural variation of the species. Phenotyping experiments under terminal drought during long-days in greenhouse conditions, identified six photoperiod insensitive cultivars of European origin with a clear SG phenotype. Using SNP data produced from whole genome re-sequencing data, we obtained 10 variants significantly associated to the SG phenotype on chromosomes 1, 3, 7, 8, 9 and 10 that are in close proximity to gene models with functional annotations related to hormone signaling and anti-oxidant production. Calculating pairwise FST between subgroups of cultivars divided according to their drought response (susceptibility, escape, recovery or SG), we identified up to 29 genomic windows accounting for 1,45Mb that differentiate SG cultivars; these signals were especially strong on chromosomes 1, 5 and 10. Within these windows, we found genes directly involved in photosynthetic processes and trehalose synthesis. Altogether, these signals represent good targets for further characterization and highlight the multigenic nature of the SG response in legumes.

Phenotyping and metabolome analysis reveal the role of AdoMetDC and Di19 genes in determining acquired tolerance to drought in rice

Water-saving attempts for rice cultivation often reduce yields. Maintaining productivity under drought is possible when rice genotypes are bred with improved metabolism and spikelet fertility. Although attempts have been made to introgress water mining and water use efficiency traits, combining acquired tolerance traits (ATTs), that is, specific traits induced or upregulated to better tolerate severe stress, appears equally important. In our study, we screened 90 rice germplasm accessions that represented the molecular and phenotypic variations of 851 lines of the 3 K rice panel. Utilising phenomics, we identified markers linked to ATTs through association analysis of over 0.2 million SNPs derived from whole-genome sequences. Propensity to respond to 'induction' stress varied significantly among genotypes, reflecting differences in cellular protection against oxidative stress. Among the ATTs, the hydroxyl radical and proline contents exhibited the highest variability. Furthermore, these significant variations in ATTs were strongly correlated with spikelet fertility. The 43 significant markers associated with ATTs were further validated using a different subset of contrasting genotypes. Gene expression studies and metabolomic profiling of two well-known contrasting genotypes, APO (tolerant) and IR64 (sensitive), identified two ATT genes: AdoMetDC and Di19. Our study highlights the relevance of polyamine biosynthesis in modulating ATTs in rice. Genotypes with superior ATTs and the associated markers can be effectively employed in breeding rice varieties with sustained spikelet fertility and grain yield under drought.

Impacts of kinetin implementation on leaves, floral and root-related traits during seed production in hybrid rice under water deficiency

BACKGROUND

Water deficit is one of the most significant abiotic factors affecting rice and agricultural production worldwide. In hybrid rice, cytoplasmic male sterility (CMS) is an important technique for creating high-yielding crop based on heterosis. The phytohormone kinetin (Kin) regulates cell division in plant during the early stages of grain formation, as well as flow assimilation and osmotic regulation under water stress. The present study performed to estimate the effects of irrigation intervals (irrigation each six days (I6), nine days (I9), twelve days (I12) and fifteen days (I15) against continuous flooding (CF, each three days)) and kinetin exogenously application (control, 15 mg L-1 and 30 mg L-1) on hybrid rice (L1, IR69625A; L2, G46A and R, Giza 178 R) seed production.

RESULTS

Leaves traits (Chlorophyll content (CHC), relative water content (RWC), stomatal conductance (SC), Leaf temperature (LT) and transpiration rate (TR)), floral traits such as style length (SL) and total stigma length (TSL), in addition to root traits (i.e., root length (RL), root volume (RV), root: shoot ratio (RSR), root thickness (RT), root xylem vessels number (RXVN) and root xylem vessel area (RXVA) were evaluated and a significant enhancement in most traits was observed. Applying 30 mg L-1 kinetin significantly and positively enhanced all growth, floral and roots traits (RV and RXVA recorded the most increased values by 14.8% and 23.9%, respectively) under prolonging irrigation intervals, in comparison to non-treated plants.

CONCLUSIONS

Subsequently, spraying kinetin exogenously on foliar could be an alternative method to reduce the harmful influences of water deficiency during seed production in hybrid rice.

Drought and salinity stresses induced physio-biochemical changes in sugarcane: an overview of tolerance mechanism and mitigating approaches

Sugarcane productivity is being hampered globally under changing environmental scenarios like drought and salinity. The highly complex nature of the plant responses against these stresses is determined by a variety of factors such as genotype, developmental phase of the plant, progression rate and stress, intensity, and duration. These factors influence plant responses and can determine whether mitigation approaches associated with acclimation are implemented. In this review, we attempt to summarize the effects of drought and salinity on sugarcane growth, specifically on the plant's responses at various levels, viz., physiological, biochemical, and metabolic responses, to these stresses. Furthermore, mitigation strategies for dealing with these stresses have been discussed. Despite sugarcane's complex genomes, conventional breeding approaches can be utilized in conjunction with molecular breeding and omics technologies to develop drought- and salinity-tolerant cultivars. The significant role of plant growth-promoting bacteria in sustaining sugarcane productivity under drought and salinity cannot be overlooked.

Interaction of iron and zinc fortification and late-season water deficit on yield and fatty acid composition of Dragon's Head (Lallemantia iberica L.)

Dragon's head (Lallemantia iberica) is a rich source of alpha-linolenic acid, linoleic acid, essential oil, protein, and mucilage. Therefore, the aim of this study was to evaluate the effects of foliar application of three different concentrations of Fe and Zn (control, 4, and 8 g lit-1) at two different developmental stages (vegetative stage (VS) and reproductive stage (RS)) on the quantity and quality of dragon's head seed yield and fatty acid composition in two crop seasons (2018 and 2019) under two environments (normal irrigation as control (NI) and post-anthesis water deficit (WD). In NI, average yields of seed, oil, and protein were 1155, 340, and 183 kg ha-1, respectively, and in the WD, they were 879, 283, and 148 kg ha-1, respectively. By applying Zn and Fe, the mean values of seed, oil, and protein yields in the NI were 1425, 478, and 264 kg ha-1, while in the WD, they were 1011, 354, and 200 kg ha-1, respectively. Furthermore, the application of WD resulted in a significant increase in zinc concentration, protein percentage, and saturated fatty acid percentage in seeds. Unlike WD, iron and zinc treatments decreased the percentage of saturated fatty acids and increased the percentage of unsaturated fatty acids. The number of capsules per plant had the most positive indirect effect on grain yield. The results showed that foliar spraying of Fe and Zn could effectively mitigate the adverse effects of WD on the quality and quantity of seed and oil yield dragon's head.

QTL mapping and analysis for drought tolerance in rice by genome-wide association study

Rice drought resistance is a complicated quantitative feature involving a range of biological and agronomic variables, but little is known about the underlying genetics and regulatory mechanisms that regulate drought tolerance. This study used 120 recombinant inbred lines (RILs), derived from a cross between drought tolerant Lvhan 1 and susceptible Aixian 1. The RILs were subjected to drought stress at the first ear stage, and phenotypic data of 16 agronomic and physiological traits under varying conditions were investigated. Genome-wide association study (GWAS) on the drought resistance index of traits was carried out. A total of 9 quantitative trait loci (QTLs) associated with drought-related traits were identified on chromosomes 2, 6, 7, 8, 9, and 10, which includes QTLs for plant height (PH) qPH10.1, effective panicles number (EPN) qEPN6.1, panicle length (PL) qPL9.1, thousand-grain weight (TGW) qTGW2.1, qTGW6.1, qTGW8.1, leaf length (LL) qLL7.1, leaf width (LW) qLW7.1, and leaf area (LA) qLA7.1. The fraction of phenotypic variation explained by individual QTL varied from 10.6% to 13.9%. Except for days to flowering (DTF), the mean values of all traits under normal water management conditions were considerably higher than those under drought conditions. Except for the DTF, the drought resistance index of all rice traits was less than 1, indicating that drought treatment reduced the EPN, FGPP, SSR, PH, and LA, which affected the growth and development of rice. The drought resistance index of DTF was 1.02, indicating that drought prolonged the heading time of rice and diminish the yield parameters. Along with identifying QTLs, the results also predicted ten candidate genes, which are directly or indirectly involved in various metabolic functioning related to drought stress. The identification of these genomic sites or QTLs that effectively respond to water scarcity will aid in the quest of understanding the drought tolerance mechanisms. This study will facilitate the marker-assisted rice breeding and handy in the breeding of drought-tolerant rice varieties.

Rhizosphere microbiomes of resurrection plants Ramonda serbica and R. nathaliae: comparative analysis and search for bacteria mitigating drought stress in wheat (Triticum aestivum L.)

Rhizosphere microbial communities play an important role in maintaining the health and productivity of the plant host. The rhizobacteria Pseudomonas putida P2 of Ramonda serbica and Bacillus cereus P5 of R. nathaliae were selected for treatment of the Belija wheat cultivar because of their plant growth-promoting (PGP) properties. Compared to the non-treated drought-stressed plants, the plants treated with rhizobacteria showed increased activity of the two major antioxidant enzymes, superoxide dismutase, and ascorbate peroxidase. Plants treated with the B. cereus P5 strain exhibited higher proline content under drought stress, suggesting that proline accumulation depends on the relative water content (RWC) status of the plants studied. Inoculation of wheat seeds with the P. putida P2 strain improved water status by increasing RWC and alleviating oxidative stress by reducing H2O2 and malondialdehyde concentrations in plants exposed to severe drought, possibly also helping plants to overcome drought through its 1-aminocyclopropane-1-carboxylic acid deaminase activity. Analysis of data from Next Generation sequencing (NGS) revealed that the dominant bacterial taxa in the rhizosphere of resurrection plants R. serbica and R. nathaliae were extremophilic, thermotolerant, Vicinamibacter silvestris, Chthoniobacter flavus, and Gaiella occulta. From the fungi detected Penicillium was the most abundant in both samples, while Fusarium and Mucor were present only in the rhizosphere of R. serbica and the entomopathogenic fungi Metarhizium, and Tolypocladiumu only in the rhizosphere of R. nathaliae. The fungal communities varied among plants, suggesting a stronger environmental influence than plant species. Our study demonstrates the importance of in vivo experiments to confirm the properties of PGP bacteria and indicates that the rhizosphere of resurrection plants is a valuable source of unique microorganisms that can be used to improve the drought stress tolerance of crops.

Genetic diversity Analysis using molecular markers of some rice varieties for Physiological, biochemical and yield Traits under water deficit condition.. [DOI: 10.21203/rs.3.rs-3111398/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Rice is a major staple food crop all over the world. Recent climate change trends forecast an increase in drought severity, necessitating the creation of novel drought-tolerant rice cultivars in order to continue rice production in this ecosystem. This study was carried out at the experimental farm of the rice research and training center (RRTC) using the randomized complete block design (RCBD) to assess the impact of water scarcity on eight rice varieties by identifying differences in physiological and biochemical responses among drought-sensitive and resistant rice varieties, in addition applying two PCR-based molecular marker systems ISSR and SCoT to assess the genetic diversity among the studied rice varieties. The results revealed that, Water shortage stress significantly reduced relative water content, total chlorophyll content, grain yield, and yield characteristics. while, it significantly raised proline content and antioxidant enzyme activity (CAT, APX, and SOD). The combined analysis of variance demonstrated that the mean squares for environments, varieties, and their interaction were highly significant for all investigated traits, suggesting that the germplasm used in the study had significant genetic diversity from one environment (normal irrigation) to another (water deficit) and could rank differently in both of them. Mean performance data showed that, Puebla and Hispagran varieties were selected as the most favourable varieties for most physiological and biochemical parameters studied, as well as yield traits which recorded the highest desirable values under both irrigation treatments. They were recommended for use in rice hybrid breeding programmes for water scarcity tolerance. Genetic Similarity and Cluster Analysis revealed that, the both molecular markers exhibited comparable genetic diversity values but a higher level of polymorphism was represented by ISSR. This indicates the high efficiency of both markers in discriminating the tested varieties. The dendrogram generated by ISSR and SCoT markers combined data divided the varieties into two major clusters. Cluster I consisted of the genotype Sakha 106. Cluster II retained seven varieties, which were further divided into two sub-clusters; Sakha 101, Sakha 105, Sakha 106, Sakha 107 constituted the first subgroup, while Giza 177, Hispagran, and Puebla formed the second one.

Drought stress in rice: morpho-physiological and molecular responses and marker-assisted breeding

Rice (Oryza Sativa L.) is an essential constituent of the global food chain. Drought stress significantly diminished its productivity and threatened global food security. This review concisely discussed how drought stress negatively influenced the rice's optimal growth cycle and altered its morpho-physiological, biochemical, and molecular responses. To withstand adverse drought conditions, plants activate their inherent drought resistance mechanism (escape, avoidance, tolerance, and recovery). Drought acclimation response is characterized by many notable responses, including redox homeostasis, osmotic modifications, balanced water relations, and restored metabolic activity. Drought tolerance is a complicated phenomenon, and conventional breeding strategies have only shown limited success. The application of molecular markers is a pragmatic technique to accelerate the ongoing breeding process, known as marker-assisted breeding. This review study compiled information about quantitative trait loci (QTLs) and genes associated with agronomic yield-related traits (grain size, grain yield, harvest index, etc.) under drought stress. It emphasized the significance of modern breeding techniques and marker-assisted selection (MAS) tools for introgressing the known QTLs/genes into elite rice lines to develop drought-tolerant rice varieties. Hence, this study will provide a solid foundation for understanding the complex phenomenon of drought stress and its utilization in future crop development programs. Though modern genetic markers are expensive, future crop development programs combined with conventional and MAS tools will help the breeders produce high-yielding and drought-tolerant rice varieties.

A Personalized and Smart Flowerpot Enabled by 3D Printing and Cloud Technology for Ornamental Horticulture

This paper presents a personalized and smart flowerpot for ornamental horticulture, integrating 3D printing and cloud technology to address existing design limitations and enable real-time monitoring of environmental parameters in plant cultivation. While 3D printing and cloud technology have seen widespread adoption across industries, their combined application in agriculture, particularly in ornamental horticulture, remains relatively unexplored. To bridge this gap, we developed a flowerpot that maximizes space utilization, simplicity, personalization, and aesthetic appeal. The shell was fabricated using fused deposition modeling (FDM) in 3D printing, and an Arduino-based control framework with sensors was implemented to monitor critical growth factors such as soil moisture, temperature, humidity, and light intensity. Real-time data are transmitted to the Bamfa Cloud through Wi-Fi, and a mobile application provides users with instant access to data and control over watering and lighting adjustments. Our results demonstrate the effectiveness of the smart flowerpot in enabling automated monitoring of plant growth and environmental control. This innovation holds significant promise for advancing smart device development in ornamental horticulture and other related fields, enhancing efficiency, plant health, and overall user experience. Future research in this area has the potential to revolutionize horticultural practices and contribute to the advancement of smart agriculture.

The Era of Plant Breeding: Conventional Breeding to Genomics-assisted Breeding for Crop Improvement

Plant breeding has made a significant contribution to increasing agricultural production. Conventional breeding based on phenotypic selection is not effective for crop improvement. Because phenotype is considerably influenced by environmental factors, which will affect the selection of breeding materials for crop improvement. The past two decades have seen tremendous progress in plant breeding research. Especially the availability of high-throughput molecular markers followed by genomic-assisted approaches significantly contributed to advancing plant breeding. Integration of speed breeding with genomic and phenomic facilities allowed rapid quantitative trait loci (QTL)/gene identifications and ultimately accelerated crop improvement programs. The advances in sequencing technology helps to understand the genome organization of many crops and helped with genomic selection in crop breeding. Plant breeding has gradually changed from phenotype-to-genotype-based to genotype-to-phenotype-based selection. High-throughput phenomic platforms have played a significant role in the modern breeding program and are considered an essential part of precision breeding. In this review, we discuss the rapid advance in plant breeding technology for efficient crop improvements and provide details on various approaches/platforms that are helpful for crop improvement. This review will help researchers understand the recent developments in crop breeding and improvements.

Isolation of three MiDi19-4 genes from mango, the ectopic expression of which confers early flowering and enhances stress tolerance in transgenic Arabidopsis

MAIN CONCLUSION

Three Di19-4 genes were identified in mango. Overexpression of MiDi19-4B in A. thaliana promoted earlier flowering and enhanced drought, salt, and ABA resistance. Drought-induced protein 19 (Di19) is a drought-induced protein that is mainly involved in multiple stress responses. Here, three Di19-4 genes (MiDi19-4A/B/C) in mango (Mangifera indica L.) were identified, and the coding sequences (CDS) had lengths of 684, 666, and 672 bp and encoded proteins with 228, 222, and 224 amino acids, respectively. The promoters of the MiDi19-4 genes contained phytohormone-, light-, and abiotic stress-responsive elements. The MiDi19-4 genes were expressed in every tissue and highly expressed in leaves. Moreover, MiDi19-4 genes were highly correlated with the vegetative growth period and induced by polyethylene glycol (PEG) or salt stress. MiDi19-4B displayed the highest expression during the vegetative growth period and then showed decreased expression, and MiDi19-4B was highly expressed at both the late stage of the vegetative growth period and the initial stage of the flowering induction period. The 35S::GFP-MiDi19-4B fusion protein was located in the cell nucleus. The transgenic plants ectopically expressing MiDi19-4B exhibited earlier flowering and increased expression patterns of FRUITFULL (AtFUL), APETALA1 (AtAP1), and FLOWERING LOCUS T (AtFT). The drought and salt tolerance of MiDi19-4B transgenic plants was significantly increased, and these plants showed decreased sensitivity to abscisic acid (ABA) and considerably increased expression levels of drought- and salt-related genes and ABA signalling pathway genes. Additionally, bimolecular fluorescence complementation (BiFC) experiments revealed that the MiDi19-4B protein interacted with CAULIFLOWER (MiCAL1), MiCAL2, MiAP1-1, and MiAP1-2. Taken together, these results highlighted the important regulatory roles of MiDi19-4B in tolerance to multiple abiotic stresses and in flowering.

Physicochemical Properties and Tissue Structure of High Kernel Elongation Rice (Oryza sativa L.) Varieties as Affected by Heat Treatment

Heat treatment could affect the structure and properties of rice varieties. The present study was conducted in order to determine the effects of heat treatment on the physicochemical properties and tissue structure of Mahsuri Mutan, Basmati 370 and MR219 rice varieties. The three rice varieties were subjected to heat treatment (ageing) at 90 °C, using an oven, for 3 h. After the heat treatment, the samples were cooled at room temperature (25 °C) for 1 h. Physicochemical properties, such as alkali digestion value, water uptake ratio, solids in cooking water, high kernel elongation ratio and amylose contents, were determined. The procedure used in determining both apparent and absolute amylose involved measuring the iodine affinity of defatted whole starch. Ahigh-performance anion-exchange chromatograph was used to analyse branch chain length distribution of amylopectin quantitatively. The starch structure of the rice samples was observed under a scanning electron microscope. Data collected on physicochemical traits, heat treatment and control (ageing and non-ageing) were subjected to an analysis of variance using SAS software version 9.4. In this study, Mahsuri Mutan and Basmati 370 showed superior high kernel elongation as compared to their respective rice progenies. This study also found that heat treatment directly affected the increasingly high kernel elongation for both populations. The phenotypic correlation co-efficient indicated that there was a high positive correlation between high kernel elongation and water uptake ratio, implying that selection for water uptake ratio would increase the high kernel elongation characteristic. The heat treatment showed significant difference in all the physicochemical traits of the varieties studied. Heat treatment also affected the very long branch chains of starch, such as amylose. Observation under an electron microscope showed that the samples subjected to heat treatment had more cracks on the tissue structure compared to normal rice samples. The hexagon structure in Mahsuri Mutan produced a greater elongation effect on its kernel. The findings from this study could be useful to breeders in the selection and development of a new high kernel elongation rice variety.

geneHapR: an R package for gene haplotypic statistics and visualization

BACKGROUND

Together with application of next-generation sequencing technologies and increased accumulation of genomic variation data in different organism species, an opportunity for effectively identification of superior alleles of functional genes to facilitate marker-assisted selection is emerging, and the clarification of haplotypes of functional genes is becoming an essential target in recent study works.

RESULTS

In this paper, we describe an R package 'geneHapR' developed for haplotypes identification, statistics and visualization analysis of candidate genes. This package could integrate genotype data, genomic annotating information and phenotypic variation data to clarify genotype variations, evolutionary-ship, and morphological effects among haplotypes through variants visualization, network construction and phenotypic comparison. 'geneHapR' also provides functions for Linkage Disequilibrium block analysis and visualizing of haplotypes geo-distribution.

CONCLUSIONS

The R package 'geneHapR' provided an easy-to-use tool for haplotype identification, statistic and visualization for candidate gene and will provide useful clues for gene functional dissection and molecular-assistant pyramiding of beneficial alleles of functional locus in future breeding programs.

Biochemical and Epigenetic Modulations under Drought: Remembering the Stress Tolerance Mechanism in Rice

A plant, being a sessile organism, needs to modulate biochemical, physiological, and molecular responses to the environment in a quick and efficient manner to be protected. Drought stress is a frequently occurring abiotic stress that severely affects plant growth, development, and productivity. Short- and long-term memories are well-known phenomena in animals; however, the existence of such remembrance in plants is still being discovered. In this investigation, different rice genotypes were imposed with drought stress just before flowering and the plants were re-watered for recovery from the stress. Seeds collected from the stress-treated (stress-primed) plants were used to raise plants for the subsequent two generations under a similar experimental setup. Modulations in physio-biochemical (chlorophyll, total phenolics and proline contents, antioxidant potential, lipid peroxidation) and epigenetic [5-methylcytosine (5-mC)] parameters were analyzed in the leaves of the plants grown under stress as well as after recovery. There was an increase in proline (>25%) and total phenolic (>19%) contents, antioxidant activity (>7%), and genome-wide 5-mC level (>56%), while a decrease (>9%) in chlorophyll content was recorded to be significant under the stress. Interestingly, a part of the increased proline content, total phenolics content, antioxidant activity, and 5-mC level was retained even after the withdrawal of the stress. Moreover, the increased levels of biochemical and epigenetic parameters were observed to be transmitted/inherited to the subsequent generations. These might help in developing stress-tolerant crops and improving crop productivity under the changing global climate for sustainable food production and global food security.

Morpho-physiological and biochemical response of rice (Oryza sativa L.) to drought stress: A review

Global food shortages are caused mainly by drought, the primary driver of yield loss in agriculture worldwide. Drought stress negatively impacts the physiological and morphological characteristics of rice (Oryza sativa L.), limiting the plant productivity and hence the economy of global rice production. Physiological changes due to drought stress in rice include constrained cell division and elongation, stomatal closure, loss of turgor adjustment, reduced photosynthesis, and lower yields. Morphological changes include inhibition of seed germination, reduced tillers, early maturity, and reduced biomass. In addition, drought stress leads to a metabolic alteration by increasing the buildup of reactive oxygen species, reactive stress metabolites, antioxidative enzymes, and abscisic acid. Rice tends to combat drought through three major phenomena; tolerance, avoidance, and escape. Several mitigation techniques are introduced and adapted to combat drought stress which includes choosing drought-tolerant cultivars, planting early types, maintaining adequate moisture levels, conventional breeding, molecular maintenance, and creating variants with high-yielding characteristics. This review attempts to evaluate the various morpho-physiological responses of the rice plant to drought, along with drought stress reduction techniques.

Molecular characterization reveals that OsSAPK3 improves drought tolerance and grain yield in rice

BACKGROUND

Many data suggest that the sucrose non-fermenting 1-related kinases 2 (SnRK2s) are very important to abiotic stress for plants. In rice, these kinases are known as osmotic stress/ABA-activated protein kinases (SAPKs). Osmotic stress/ABA-activated protein kinase 3 (OsSAPK3) is a member of SnRK2II in rice, but its function is still unclear.

RESULTS

The expression of OsSAPK3 was up regulated by drought, NaCl, PEG and ABA. OsSAPK3 mutated seedings (sapk3-1 and sapk3-2) showed reduced hypersensitivity to exogenous ABA. In addition, under drought conditions, sapk3-1 and sapk3-2 showed more intolerance to drought, including decreased survival rate, increased water loss rate, increased stomatal conductance and significantly decreased expression levels of SLAC1 and SLAC7. Physiological and metabolic analyses showed that OsSAPK3 might play an important role in drought stress signaling pathway by affecting osmotic adjustment and osmolytes, ROS detoxification and expression of ABA dependent and independent dehydration-responsive genes. All gronomic traits analyses demonstrated that OsSAPK3 could improve rice yield by affecting the regulation of tiller numbers and grain size.

CONCLUSION

OsSAPK3 plays an important role in both ABA-dependent and ABA-independent drought stress responses. More interestingly, OsSAPK3 could improve rice yield by indirectly regulating tiller number and grain size. These findings provide new insight for the development of drought-resistant rice.

Evolutionary Analysis of StSnRK2 Family Genes and Their Overexpression in Transgenic Tobacco Improve Drought Tolerance

Sucrose non-ferment 1-related protein kinase 2 (SnRK2) is a highly conserved protein kinase in plants that plays an important role in regulating plant response to drought stress. Although it has been reported in some plants, the evolutionary relationship of potato SnRK2s and their function in drought resistance have not been systematically analyzed. In this study, molecular characteristic analysis showed that 8 StSnRK2s were distributed on six chromosomes, coding proteins were divided into three subgroups, and StSnRK2s clustered in the same subgroup had similar conserved motifs and domains. In addition, StSnRK2 has a wide range of replication events in some species, making it closer to dicots in the process of evolution. In addition, the average nonsynonymous substitution rate/synonymous substitution rate (Ka/Ks) value of SnRK2s in monocots was higher than that of dicots. The codon usage index showed that SnRK2s prefer to use cytosine 3 (C3s), guanine 3 (G3s) and GC content (GC3s) in monocots, whereas thymine 3 (T3s) and adenine 3 (A3s) are preferred in dicots. Furthermore, stress response analysis showed that the expression of StSnRK2s under different degrees of drought stress significantly correlated with one or more stress-related physiological indices, such as proline and malondialdehyde (MDA) content, superoxide dismutase (SOD) and catalase (CAT) activity, ion leakage (IL) etc. The drought resistance of StSnRK2 transgenic plants was determined to occur in the order of StSnRK2.1/2.8 > StSnRK2.2/2.5 > StSnRK2.4/2.6 > StSnRK2.3 > StSnRK2.7, was attributed to not only lower IL but also higher proline, soluble sugar contents and stress-related genes in transgenic plants compared to wild type (WT). In conclusion, this study provides useful insights into the evolution and function of StSnRK2s and lays a foundation for further study on the molecular mechanism of StSnRK2s regulating potato drought resistance.

Transcriptome-based analyses of adaptive divergence between two closely related spruce species on the Qinghai-Tibet plateau and adjacent regions

Speciation among populations connected by gene flow is driven by adaptation to different environments, but underlying gene-environment associations remain largely unknown. Here, 162 individuals from 32 populations were sampled to obtain 191,648 independent single nucleotide polymorphisms (SNPs) across the genomes of two closely related spruce species, Picea asperata and Picea crassifolia, which occur on the Qinghai-Tibet Plateau and in surrounding regions. Using the SNP data set, genotype-environment associations and demographic modelling were used to examine local adaptation and genetic divergence between these two species. While morphologically similar, the two Picea species were genetically differentiated in multiple analyses. These species diverged despite continuous gene flow, and their initial divergence was dated back to the late Quaternary. The effective population sizes of both species have expanded since their divergence, as confirmed by niche distribution simulations. A total of 6365 genes were associated with the tested environmental variables; of these, 41 were positively selected in P. asperata and were mainly associated with temperature, while 83 were positively selected in P. crassifolia and were primarily associated with precipitation. These results deepen our understanding of the adaptive divergence and demographic histories of these two spruce species and highlight the importance of genomic data in deciphering the environmental selection underlying Quaternary interspecific divergence.

QTL and Candidate Genes: Techniques and Advancement in Abiotic Stress Resistance Breeding of Major Cereals

At least 75% of the world's grain production comes from the three most important cereal crops: rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays). However, abiotic stressors such as heavy metal toxicity, salinity, low temperatures, and drought are all significant hazards to the growth and development of these grains. Quantitative trait locus (QTL) discovery and mapping have enhanced agricultural production and output by enabling plant breeders to better comprehend abiotic stress tolerance processes in cereals. Molecular markers and stable QTL are important for molecular breeding and candidate gene discovery, which may be utilized in transgenic or molecular introgression. Researchers can now study synteny between rice, maize, and wheat to gain a better understanding of the relationships between the QTL or genes that are important for a particular stress adaptation and phenotypic improvement in these cereals from analyzing reports on QTL and candidate genes. An overview of constitutive QTL, adaptive QTL, and significant stable multi-environment and multi-trait QTL is provided in this article as a solid framework for use and knowledge in genetic enhancement. Several QTL, such as DRO1 and Saltol, and other significant success cases are discussed in this review. We have highlighted techniques and advancements for abiotic stress tolerance breeding programs in cereals, the challenges encountered in introgressing beneficial QTL using traditional breeding techniques such as mutation breeding and marker-assisted selection (MAS), and the in roads made by new breeding methods such as genome-wide association studies (GWASs), the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system, and meta-QTL (MQTL) analysis. A combination of these conventional and modern breeding approaches can be used to apply the QTL and candidate gene information in genetic improvement of cereals against abiotic stresses.

The coordinated regulation mechanism of rice plant architecture and its tolerance to stress

Rice plant architecture and stress tolerance have historically been primary concerns for rice breeders. The "Green Revolution" and super-rice breeding practices have demonstrated that ideal plant architecture can effectively improve both stress tolerance and yield. The synergistic selection and breeding of rice varieties with ideal architecture and stress tolerance can increase and stabilize yield. While rice plant plant architecture and stress tolerance are separately regulated by complicated genetic networks, the molecular mechanisms underlying their relationships and synergism have not yet been explored. In this paper, we review the regulatory mechanism between plant architecture, stress tolerance, and biological defense at the different level to provide a theoretical basis for the genetic network of the synergistic regulation and improvement of multiple traits.