Drought tolerance in selected aerobic and upland rice varieties is driven by different metabolic and antioxidative responses

Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding

Upland rice is a distinctive drought-aerobic ecotype of cultivated rice highly resistant to drought stress. However, the genetic and genomic basis for the drought-aerobic adaptation of upland rice remains largely unclear due to the lack of genomic resources. In this study, we identified 25 typical upland rice accessions and assembled a high-quality genome of one of the typical upland rice varieties, IRAT109, comprising 384 Mb with a contig N50 of 19.6 Mb. Phylogenetic analysis revealed upland and lowland rice have distinct ecotype differentiation within the japonica subgroup. Comparative genomic analyses revealed that adaptive differentiation of lowland and upland rice is likely attributable to the natural variation of many genes in promoter regions, formation of specific genes in upland rice, and expansion of gene families. We revealed differentiated gene expression patterns in the leaves and roots of the two ecotypes and found that lignin synthesis mediated by the phenylpropane pathway plays an important role in the adaptive differentiation of upland and lowland rice. We identified 28 selective sweeps that occurred during domestication and validated that the qRT9 gene in selective regions can positively regulate drought resistance in rice. Eighty key genes closely associated with drought resistance were appraised for their appreciable potential in drought resistance breeding. Our study enhances the understanding of the adaptation of upland rice and provides a genome navigation map of drought resistance breeding, which will facilitate the breeding of drought-resistant rice and the "blue revolution" in agriculture.

Uncovering the impact of AM fungi on wheat nutrient uptake, ion homeostasis, oxidative stress, and antioxidant defense under salinity stress

The growth of wheat (Triticum aestivum) is constrained by soil salinity, although some fungal species have been shown to enhance production in saline environments. The yield of grain crops is affected by salt stress, and this study aimed to investigate how arbuscular mycorrhizal fungus (AMF) mitigates salt stress. An experiment was conducted to assess the impact of AMF on wheat growth and yield in conditions of 200 mM salt stress. Wheat seeds were coated with AMF at a rate of 0.1 g (10⁸ spores) during sowing. The results of the experiment demonstrated that AMF inoculation led to a significant improvement in the growth attributes of wheat, including root and shoot length, fresh and dry weight of root and shoot. Furthermore, a significant increase in chlorophyll a, b, total, and carotenoids was observed in the S2 AMF treatment, validating the effectiveness of AMF in enhancing wheat growth under salt stress conditions. Additionally, AMF application reduced the negative effects of salinity stress by increasing the uptake of micronutrients such as Zn, Fe, Cu, and Mn while regulating the uptake of Na (decrease) and K (increase) under salinity stress. In conclusion, this study confirms that AMF is a successful strategy for reducing the negative effects of salt stress on wheat growth and yield. However, further investigations are recommended at the field level under different cereal crops to establish AMF as a more effective amendment for the alleviation of salinity stress in wheat.

Transcriptional Expression of Nitrogen Metabolism Genes and Primary Metabolic Variations in Rice Affected by Different Water Status

The era of climate change strongly requires higher efficiency of energies, such as light, water, nutrients, etc., during crop production. Rice is the world's greatest water-consuming plant, and, thus, water-saving practices such as alternative wetting and drying (AWD) are widely recommended worldwide. However the AWD still has concerns such as lower tillering, shallow rooting, and an unexpected water deficit. The AWD is a possibility to not only save water consumption but also utilize various nitrogen forms from the soil. The current study tried to investigate the transcriptional expression of genes in relation to the acquisition-transportation-assimilation process of nitrogen using qRT-PCR at the tillering and heading stages and to profile tissue-specific primary metabolites. We employed two water supply systems, continuous flooding (CF) and alternative wetting and drying (AWD), during rice growth (seeding to heading). The AWD system is effective at acquiring soil nitrate; however, nitrogen assimilation was predominant in the root during the shift from the vegetative to the reproductive stage. In addition, as a result of the greater amino acids in the shoot, the AWD was likely to rearrange amino acid pools to produce proteins in accordance with phase transition. Accordingly, it is suggested that the AWD 1) actively acquired nitrate from soil and 2) resulted in an abundance of amino acid pools, which are considered a rearrangement under limited N availability. Based on the current study, further steps are necessary to evaluate form-dependent N metabolism and root development under the AWD condition and a possible practice in the rice production system.

Morphological, physiological and biochemical response of Lallemantia species to elevated temperature and light duration during seed development

Seed weight, storability, and germinability can depend on maternal plant's environment. However, there is slight information about the effect of light and temperature on seed quality of Lallemantia species. The purpose of this research was to determine the properties of physio-biochemical of maternal plant, seed quality, and seed chemical composition of Lallemantia species (Lallemantia iberica and Lallemantia royleana) under temperature (15 °C, 25 °C, and 35 °C) and photoperiod (8 hd^-1, 16 hd^-1, and 24 hd^-1) maternal plants environment. Increasing temperature and photoperiod caused a reduction in leaf chlorophyll, stomatal movement, total soluble sugar, superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX) enzymes activities, and an increment in malondialdehyde (MDA) and hydrogen peroxide (H2O2) content of seeds. However, the highest weight, germination, vigor index, and longevity, seed chemical compositions were obtained in offspring which matured under 25 °C for 16 hd^-1. The highest germination, oil, and relative percentage of fatty acids (oleic acid (OA), linoleic acid (LA), and linolenic acid (LNA)) were obtained in L. iberica seeds. On the contrary, longevity, mucilage, and sucrose were more abundant in L. royleana seeds. Overall, this research has clearly shown that temperature and light quality and quantity of maternal plant's environment have an immensely effect on producing of seeds with high-quality. However, it is necessary to investigate the impact of the epigenetic mechanisms of the maternal plant on the offspring in future studies.

Sunlight promoted self-fenton photodegradation and pathway of doxycycline: Interactive effects of nanomaterial on bean plant and its genotoxicity against Allium cepa

Photocatalytic induction of electron/hole recombination, surface property and light response ability effectively enhance the photocatalytic activity of nanomaterial. In this work, the effective charge carrier separating Sn/Mn-ZnFe₂O₄-CdFe₂O₄-Ag₃PO₄ Quantum dots (M/SZFO-CFO-AP QDs) was fabricated for photocatalytic degradation of doxycycline (doxy) antibiotic. The result showed enhanced photocatalytic activity of doxy and the degradation efficiency of doxy was about 98.8% in short span of time. The calculated WH plot and urbach energy of prepared photocatalyst exhibited evidence for the prevalence of point defects and its contribution to efficient charge separation and transferability. The total organic carbon (TOC) removal was found to be 98.9%, which depicts the complete mineralization of doxy. The synergetic charge transfer of n-p-n heterojunction enables the effective removal of doxy under visible light irradiation. Further, the genotoxicity study was determined by interacting the SZFO-CFO-AP QDs with Allium Cepa. The results depict that SZFO-CFO-AP QDs show lower toxicity level and there were no trace of defective mitotic phases and micro nuclei. Further, the progression and development of bean plant was determined after treating with prepared nanomaterials and the result showed the enhanced growth in SZFO-CFO-AP QDs treated bean plant compared to the counterparts. Therefore, the prepared SZFO-CFO-AP QDs was can be used as an environmental friendly photocatalyst for effective treatment of antibiotic present in the water bodies.

Can biochemical traits bridge the gap between genomics and plant performance? A study in rice under drought

The possibility of introducing metabolic/biochemical phenotyping to complement genomics-based predictions in breeding pipelines has been considered for years. Here we examine to what extent and under what environmental conditions metabolic/biochemical traits can effectively contribute to understanding and predicting plant performance. In this study, multivariable statistical models based on flag leaf central metabolism and oxidative stress status were used to predict grain yield (GY) performance for 271 indica rice (Oryza sativa) accessions grown in the field under well-watered and reproductive stage drought conditions. The resulting models displayed significantly higher predictability than multivariable models based on genomic data for the prediction of GY under drought (Q2 = 0.54-0.56 versus 0.35) and for stress-induced GY loss (Q2 = 0.59-0.64 versus 0.03-0.06). Models based on the combined datasets showed predictabilities similar to metabolic/biochemical-based models alone. In contrast to genetic markers, models with enzyme activities and metabolite values also quantitatively integrated the effect of physiological differences such as plant height on GY. The models highlighted antioxidant enzymes of the ascorbate-glutathione cycle and a lipid oxidation stress marker as important predictors of rice GY stability under drought at the reproductive stage, and these stress-related variables were more predictive than leaf central metabolites. These findings provide evidence that metabolic/biochemical traits can integrate dynamic cellular and physiological responses to the environment and can help bridge the gap between the genome and the phenome of crops as predictors of GY performance under drought.

Genome-Wide Expression Analysis of Root Tips in Contrasting Rice Genotypes Revealed Novel Candidate Genes for Water Stress Adaptation

Root system architecture (RSA) is an important agronomic trait with vital roles in plant productivity under water stress conditions. A deep and branched root system may help plants to avoid water stress by enabling them to acquire more water and nutrient resources. Nevertheless, our knowledge of the genetics and molecular control mechanisms of RSA is still relatively limited. In this study, we analyzed the transcriptome response of root tips to water stress in two well-known genotypes of rice: IR64, a high-yielding lowland genotype, which represents a drought-susceptible and shallow-rooting genotype; and Azucena, a traditional, upland, drought-tolerant and deep-rooting genotype. We collected samples from three zones (Z) of root tip: two consecutive 5 mm sections (Z1 and Z2) and the following next 10 mm section (Z3), which mainly includes meristematic and maturation regions. Our results showed that Z1 of Azucena was enriched for genes involved in cell cycle and division and root growth and development whereas in IR64 root, responses to oxidative stress were strongly enriched. While the expansion of the lateral root system was used as a strategy by both genotypes when facing water shortage, it was more pronounced in Azucena. Our results also suggested that by enhancing meristematic cell wall thickening for insulation purposes as a means of confronting stress, the sensitive IR64 genotype may have reduced its capacity for root elongation to extract water from deeper layers of the soil. Furthermore, several members of gene families such as NAC, AP2/ERF, AUX/IAA, EXPANSIN, WRKY, and MYB emerged as main players in RSA and drought adaptation. We also found that HSP and HSF gene families participated in oxidative stress inhibition in IR64 root tip. Meta-quantitative trait loci (QTL) analysis revealed that 288 differentially expressed genes were colocalized with RSA QTLs previously reported under drought and normal conditions. This finding warrants further research into their possible roles in drought adaptation. Overall, our analyses presented several major molecular differences between Azucena and IR64, which may partly explain their differential root growth responses to water stress. It appears that Azucena avoided water stress through enhancing growth and root exploration to access water, whereas IR64 might mainly rely on cell insulation to maintain water and antioxidant system to withstand stress. We identified a large number of novel RSA and drought associated candidate genes, which should encourage further exploration of their potential to enhance drought adaptation in rice.