Genome-Wide Analysis of Invertase Gene Family, and Expression Profiling under Abiotic Stress Conditions in Potato

Characterization and Identification of Drought-Responsive ABA-Aldehyde Oxidase (AAO) Genes in Potato (Solanum tuberosum L.)

Abscisic acid (ABA) is an important stress hormone that affects plants' tolerance to stress. Changes in the content of abscisic can have an impact on plant responses to abiotic stress. The abscisic acid aldehyde oxidase (AAO) plays a crucial role in the final step in the synthesis of abscisic acid; therefore, understanding the function of the AAO gene family is of great significance for insight into plants' response to abiotic stresses. In this study, Solanum tuberosum AAO (StAAO) members were exhaustively explored using genome databases, and nine StAAOs were identified. Chromosomal location analysis indicated that StAAO genes mapped to 4 of the 14 potato chromosomes. Further analyses of gene structure and motif composition showed that members of the specific StAAO subfamily showed relatively conserved characteristics. Phylogenetic relationship analysis indicated that StAAOs proteins were divided into three major clades. Promoter analysis showed that most StAAO promoters contained cis-elements related to abiotic stress response and plant hormones. The results of tissue-specific expression analysis indicated that StAAO4 was predominantly expressed in the roots. Analysis of transcriptome data revealed that StAAO2/4/6 genes responded significantly to drought treatments. Moreover, further qRT-PCR analysis results indicated that StAAO2/4/6 not only significantly responded to drought stress but also to various phytohormone (ABA, SA, and MeJA) and abiotic stresses (salt and low temperature), albeit with different expression patterns. In summary, our study provides comprehensive insights into the sequence characteristics, structural properties, evolutionary relationships, and expression patterns of the StAAO gene family. These findings lay the foundation for a deeper understanding of the StAAO gene family and offer a potential genetic resource for breeding drought-resistant potato varieties.

Comprehensive and evolutionary analysis of Spodoptera litura-inducible Cytochrome P450 monooxygenase gene family in Glycine max elucidate their role in defense

Plants being sessile organisms and lacking both circulating phagocytic cells and somatic adaptive immune response, have thrived on various defense mechanisms to fend off insect pests and invasion of pathogens. CYP450s are the versatile enzymes, which thwart plants against insect pests by ubiquitous biosynthesis of phytohormones, antioxidants, and secondary metabolites, utilizing them as feeding deterrents and direct toxins. Therefore, a comprehensive analysis of biotic stress-responsive CYPs from Glycine max was performed to ascertain their function against S. litura-infestation. Phylogenetic analysis and evolutionary studies on conserved domains and motifs disclosed the evolutionary correspondence of these GmCYPs with already characterized members of the CYP450 superfamily and close relatedness to Medicago truncatula. These GmCYPs were mapped on 13 chromosomes; they possess 1-8 exons; they have evolved due to duplication and are localized in endoplasmic reticulumn. Further, identification of methyl-jasmonate, salicylic acid, defense responsive and flavonoid biosynthesis regulating cis-acting elements, their interaction with biotic stress regulating proteins and their differential expression in diverse types of tissues, and during herbivory, depicted their responsiveness to biotic stress. Three-dimensional homology modelling of GmCYPs, docking with heme cofactor required for their catalytic activity and enzyme-substrate interactions were performed to understand the functional mechanism of their action. Moreover, to gain insight into their involvement in plant defense, gene expression analysis was evaluated, which revealed differential expression of 11 GmCYPs upon S. litura-infestation, 12 GmCYPs on wounding while foliar spray of ethylene, methyl-jasmonate and salicylic acid differentially regulated 11 GmCYPs, 6 GmCYPs, and 10 GmCYPs respectively. Our study comprehensively analysed the underlying mechanism of GmCYPs function during S. litura-infestation, which can be further utilized for functional characterization to develop new strategies for enhancing soybean resistance to insect pests.

Comprehensive Analysis of GH3 Gene Family in Potato and Functional Characterization of StGH3.3 under Drought Stress

As an important hormone response gene, Gretchen Hagen 3 (GH3) maintains hormonal homeostasis by conjugating excess auxin with amino acids during plant stress-related signaling pathways. GH3 genes have been characterized in many plant species, but they are rarely reported in potato. Here, 19 StGH3 genes were isolated and characterized. Phylogenetic analysis indicated that StGH3s were divided into two categories (group I and group III). Analyses of gene structure and motif composition showed that the members of a specific StGH3 subfamily are relatively conserved. Collinearity analysis of StGH3 genes in potato and other plants laid a foundation for further exploring the evolutionary characteristics of the StGH3 genes. Promoter analysis showed that most StGH3 promoters contained hormone and abiotic stress response elements. Multiple transcriptome studies indicated that some StGH3 genes were responsive to ABA, water deficits, and salt treatments. Moreover, qRT-PCR analysis indicated that StGH3 genes could be induced by phytohormones (ABA, SA, and MeJA) and abiotic stresses (water deficit, high salt, and low temperature), although with different patterns. Furthermore, transgenic tobacco with transient overexpression of the StGH3.3 gene showed positive regulation in response to water deficits by increasing proline accumulation and reducing the leaf water loss rate. These results suggested that StGH3 genes may be involved in the response to abiotic stress through hormonal signal pathways. Overall, this study provides useful insights into the evolution and function of StGH3s and lays a foundation for further study on the molecular mechanisms of StGH3s in the regulation of potato drought resistance.

Editorial to the Special Issue "Eco-Physiological and Molecular Basis of Stress Tolerance in Plants"

Farmers are currently facing the challenge of producing sufficient crop yield [...].

Transcriptome and Metabolome Profiling Provide Insights into Flavonoid Synthesis in Acanthus ilicifolius Linn

Acanthus ilicifolius is an important medicinal plant in mangrove forests, which is rich in secondary metabolites with various biological activities. In this study, we used transcriptomic analysis to obtain differentially expressed genes in the flavonoid metabolic pathway and metabolomic methods to detect changes in the types and content in the flavonoid metabolic synthesis pathway. The results showed that DEGs were identified in the mature roots vs. leaves comparison (9001 up-regulated and 8910 down-regulated), mature roots vs. stems comparison (5861 up-regulated and 7374 down-regulated), and mature stems vs. leaves comparison (10,837 up-regulated and 11,903 down-regulated). Furthermore, two AiCHS genes and four AiCHI genes were up-regulated in the mature roots vs. stems of mature A. ilicifolius, and were down-regulated in mature stems vs. leaves, which were highly expressed in the A. ilicifolius stems. A total of 215 differential metabolites were found in the roots vs. leaves of mature A. ilicifolius, 173 differential metabolites in the roots vs. stems, and 228 differential metabolites in the stems vs. leaves. The metabolomic results showed that some flavonoids in A. ilicifolius stems were higher than in the roots. A total of 18 flavonoid differential metabolites were detected in the roots, stems, and leaves of mature A. ilicifolius. In mature leaves, quercetin-3-O-glucoside-7-O-rhamnoside, gossypitrin, isoquercitrin, quercetin 3,7-bis-O-β-D-glucoside, and isorhamnetin 3-O-β-(2″-O-acetyl-β-D-glucuronide) were found in a high content, while in mature roots, di-O-methylquercetin and isorhamnetin were the major compounds. The combined analysis of the metabolome and transcriptome revealed that DEGs and differential metabolites were related to flavonoid biosynthesis. This study provides a theoretical basis for analyzing the molecular mechanism of flavonoid synthesis in A. ilicifolius and provides a reference for further research and exploitation of its medicinal value.

Estimating the combining ability and genetic parameters for growth habit, yield, and fiber quality traits in some Egyptian cotton crosses

It is crucial to understand how targeted traits in a hybrid breeding program are influenced by gene activity and combining ability. During the three growing seasons of 2015, 2016, and 2017, a field study was conducted with twelve cotton genotypes, comprised of four testers and eight lines. Thirty-two F1 crosses were produced in the 2015 breeding season using the line x tester mating design. The twelve genotypes and their thirty-two F1 crosses were then evaluated in 2016 and 2017. The results demonstrated highly significant differences among cotton genotypes for all the studied traits, showing a wide range of genetic diversity in the parent genotypes. Additionally, the line-x-tester interaction was highly significant for all traits, suggesting the impact of both additive and non-additive variations in gene expression. Furthermore, the thirty-two cotton crosses showed high seed cotton output, lint cotton yield, and fiber quality, such as fiber length values exceeding 31 mm and a fiber strength above 10 g/tex. Accordingly, selecting lines and testers with high GCA effects and crosses with high SCA effects would be an effective approach to improve the desired traits in cotton and develop new varieties with excellent yield and fiber quality.

A quantitative and qualitative assessment of sugar beet genotype resistance to root-knot nematode, Meloidogyne incognita

Sugar beet productivity is highly constrained by the root-knot nematode (RKN) Meloidogyne incognita. Eight sugar beet genotypes were screened under greenhouse conditions for their susceptibility to M. incognita according to an adapted quantitative scheme for assignment Canto-Saenz's host suitability (resistance) designations (AQSCS). Besides, the degree of susceptibility or tolerance of the examined genotypes was recorded by the modified host-parasite index (MHPI) scale based on yield performance. In addition, single nucleotide polymorphism (SNP) was also determined. Sugar beet genotypes have been classified into four categories for their susceptibility or tolerance according to the AQSCS scale. The first category, the moderately resistant (MR) group implies only one variety named SVH 2015, which did not support nematode reproduction (RF≤1), and had less root damage (GI≈2). Second, the tolerant group (T) involving Lilly and Halawa KWS supported fairly high nematode reproduction (RF>1) with relatively plant damage (GI≤2). Whereas the susceptible (S) category involved four varieties, FARIDA, Lammia KWS, Polat, and Capella, which supported nematode reproduction factor (RF>1) with high plant damage (GI>2). The fourth category refers to the highly susceptible (HYS) varieties such as Natura KWS that showed (RF≤1) and very high plant damage (GI>2). However, the MHPI scale showed that Lammia KWS variety was shifted from the (S) category to the (T) category. Results revealed significant differences among genotypes regarding disease severity, yield production, and quality traits. The SVH 2015 variety exhibited the lowest disease index values concerning population density with 800/250 cm³ soils, RF=2, root damage/gall index (GI=1.8), gall size (GS=2.3), gall area (GA=3.7), damage index (DI=3.4), susceptibility rate (SR=2.4), and MHP index (MHPI=2.5). However, Lammia KWS showed the highest disease index values regarding population density with 8890/250 cm³ soils, RF= 22.2, GI= 4.8, and SR= 14.1. Meanwhile, Natura KWS the highest GS, GA and MHPI with 7.1, 8 and 20.9, respectively. The lowest DI was achieved by Capella (DI= 6) followed by Lammia KWS (DI= 5.9). For yield production, and quality traits, SVH 2015 exhibited the lowest reductions of sugar yields/beet's root with 11.1%. While Natura KWS had the highest reduction with 79.3%, as well as it showed the highest reduction in quality traits; including sucrose, T.S.S, and purity with 65, 27.3, and 51.9%, respectively. The amino acid alignment and prediction of the DNA sequences revealed the presence of five SNPs among all sugar beet verities.

Characteristics and Expression Analysis of Invertase Gene Family in Common Wheat (Triticum aestivum L.)

Invertase (INV) irreversibly catalyzes the conversion of sucrose into glucose and fructose, playing important role in plant development and stress tolerance. However, the functions of INV genes in wheat have been less studied. In this study, a total of 126 TaINV genes were identified using a genome-wide search method, which could be classified into five classes (TaCWI-α, TaCWI-β, TaCI-α, TaCI-β, and TaVI) based on phylogenetic relationship. A total of 101 TaINVs were collinear with their ancestors in the synteny analysis, and we speculated that polyploidy events were the main force in the expansion of the TaINV gene family. Compared with TaCI, TaCWI and TaVI are more similar in gene structure and protein properties. Transcriptome sequencing analysis showed that TaINVs expressed in multiple tissues with different expression levels. Among 19 tissue-specific expressed TaINVs, 12 TaINVs showed grain-specific expression pattern and might play an important role in wheat grain development. In addition, qRT-PCR results further confirmed that TaCWI50 and TaVI27 show different expression in grain weight NILs. Our results demonstrated that the high expression of TaCWI50 and TaVI27 may be associated with a larger TGW phenotype. This work provides the foundations for understanding the grain development mechanism.

Genetic analysis of yield traits in Egyptian cotton crosses (Gossypium barbdense L.) under normal conditions

To generate high-yielding cultivars with favorable fiber quality traits, cotton breeders can use information about combining ability and gene activity within a population to locate elite parents and potential F1 crosses. To this end, in the current study, twelve cotton parents (eight genotypes as female parents and four testers) and their F1 crosses obtained utilizing the linex tester mating design were evaluated for their general and specialized combining abilities (GCA and SCA, respectively) of yield traits. The findings showed that for all the investigated variables, variances owing to genotypes, parents, crosses, and parent vs cross showed extremely significant (P ≤ 0.01) differences. Additionally, throughout the course of two growing seasons, the mean squares for genotypes (parents and crosses) showed strong significance for all the variables under study. The greatest and most desired means for all the examined qualities were in the parent G.94, Pima S6, and tester G.86. The best crossings for the qualities examined were G.86 (G.89 × G.86), G.93 × Suvin, and G.86 × Suvin. The parents' Suvin, G89x G86 and TNB were shown to have the most desired general combining ability effects for seed cotton yield/plant, lint yield/plant, boll weight, number of bolls/plants, and lint index, while Suvin, G.96 and pima S6 were preferred for favored lint percentage. For seed cotton yield, lint percentage, boll weight, and number of bolls per plant per year, the cross-G.86 x (G.89 × G.86) displayed highly significant specific combining ability impacts. The crosses G.86 × Suvin, Kar x TNB, G.93 × Suvin, and G.93 × TNB for all the studied traits for each year and their combined were found to have highly significant positive heterotic effects relative to better parent, and they could be used in future cotton breeding programs for improving the studied traits.

Comparative Effect of Commercially Available Nanoparticles on Soil Bacterial Community and “Botrytis fabae” Caused Brown Spot: In vitro and in vivo Experiment

This study revealed the possible effects of various levels of silver nanoparticle (AgNP) application on plant diseases and soil microbial diversity. It investigated the comparison between the application of AgNPs and two commercial nanoproducts (Zn and FeNPs) on the rhizobacterial population and Botrytis fabae. Two experiments were conducted. The first studied the influence of 13 AgNP concentration on soil bacterial diversity besides two other commercial nanoparticles, ZnNPs (2,000 ppm) and FeNPs (2,500 ppm), used for comparison and application on onion seedlings. The second experiment was designed to determine the antifungal activity of previous AgNP concentrations (150, 200, 250, 300, 400, and 500 ppm) against B. fabae, tested using commercial fungicide as control. The results obtained from both experiments revealed the positive impact of AgNPs on the microbial community, representing a decrease in both the soil microbial biomass and the growth of brown spot disease, affecting microbial community composition, including bacteria, fungi, and biological varieties. In contrast, the two commercial products displayed lower effects compared to AgNPs. This result clearly showed that the AgNPs strongly inhibited the plant pathogen B. fabae growth and development, decreasing the number of bacteria (cfu/ml) and reducing the rhizosphere. Using AgNPs as an antimicrobial agent in the agricultural domain is recommended.

Impact of Silver Nanoparticles on Lemon Growth Performance: Insecticidal and Antifungal Activities of Essential Oils From Peels and Leaves

Ten-year-old lemon (Citrus limon L. cv. Eureka) was used during the 2019 and 2020 seasons to investigate the effect of AgNPs at control, 5, 7.5, and 10 mg/L as a foliar application on vegetative growth, yield, and fruit quality. The selected trees were subjected to agricultural practices applied in the field during the study. The results indicated that the foliar application of AgNPs positively improved the shoot length, total chlorophyll, flower, and fruit set percentage, fruit yield, physical and chemical characteristics of fruits, and leaf mineral composition from macro and micronutrients compared to control in both seasons. The foliar application of AgNPs at 10 mg/L showed the highest mean values followed by 7.5 and 5 mg/L, respectively, for the previous characteristics. The treated leaves and fruit peels were hydrodistillated to extract the essential oils (EOs), and GC-MS analysis of leaf EOs. The analysis of leaves EOs showed the presence of neral, geranial, neryl acetate, and limonene as the main abundant bioactive compounds. While in peel the main compounds were neral, geranial, neryl acetate, D-limonene, geraniol acetate, linalool, and citronellal. Toxin effect of both EOs from leaves and peels were evaluated on the rice weevils (Sitophilus oryzae) and the results indicated a higher effect of lemon peel EOs than leaves based on mortality percentage and the values of LC50 and LC95 mg/L. Melia azedarach wood samples loaded with the produced lemon EOs were evaluated for their antifungal activity against the molecularly identified fungus, Fusarium solani (acc # OL410542). The reduction in mycelial growth was increased gradually with the applied treatments. The most potent activity was found in lemon leaf EOs, while peel EOs showed the lowest reduction values. The mycelial growth reduction percentages reached 72.96 and 52.59%, by 0.1% leaf and peel EOs, respectively, compared with control.

Impact of Plant Spacing and Nitrogen Rates on Growth Characteristics and Yield Attributes of Egyptian Cotton (Gossypium barbadense L.)

This current study was performed to determine the influences of plant spacing, Nitrogen (N) fertilization rate and their effect, on growth traits, yield, and yield components of cotton (Gossypium barbadense L.) cv. Giza 97 during the 2019 and 2020 seasons. A split plot experiment in three replicates was utilized whereas the cotton seeds were planted at 20, 30, and 40 cm, as main plots and nitrogen at 75, 100, and 125%, was in subplots. The results revealed that the planting spacing at 40 cm significantly (p ≤ 0.01) increased plant height, number of fruiting branches per plant, number of bolls per plant, boll weight (BW), lint percentage (L%), seed cotton yield (SCY), lint cotton yield (LCY), seed index and lint index by 165.68 cm, 20.92, 23.93, 3.75 g, 42.01%, 4.24 ton/ha, 5.16 ton/ha, 12.05, 7.86, respectively, as average in both seasons. The application of N fertilizer rate at 125% caused a maximum increase in growth and yield parameters i.e., plant height (169.08 cm), number of vegetative branches (2.67), number of fruiting branches per plant (20.82), number bolls per fruiting branch (1.39), number of bolls per plant (23.73), boll weight (4.1 g), lint percent (41.9%), seed index (11.8 g), and lint index (8.2), while the plants treated with 100% N rates exhibited highest seed cotton yield (4.3 ton/ha) and lint cotton yield (5.6 ton/ha), as average in both seasons. Combining plant spacing at 40 cm between plants with a 100% N fertilizer rate recorded the highest lint cotton yield (5.67 ton/ha), while the highest seed cotton yield (4.43 and 4.50 ton/ha) was obtained from 125% N fertilizer rate under planting spacing 20 and 40 cm, respectively. Conclusively, a wide density (40 cm) with 125% N is a promising option for improved biomass, cotton growth, yield, physiological traits, and fiber quality.

Determination of morpho-physiological and yield traits of maize inbred lines (Zea mays L.) under optimal and drought stress conditions

Globally, climate change could hinder future food security that concurrently implies the importance of investigating drought stress and genotype screening under stressed environments. Hence, the current study was performed to screen 45 diverse maize inbred lines for 18 studied traits comprising phenological, physiological, morphological, and yield characters under optimum and water stress conditions for two successive growing seasons (2018 and 2019). The results showed that growing seasons and water regimes significantly influenced (p < 0.01) most of the studied traits, while inbred lines had a significant effect (p < 0.01) on all of the studied traits. The findings also showed a significant increase in all studied characters under normal conditions compared to drought conditions, except chlorophyll content, transpiration rate, and proline content which exhibited higher levels under water stress conditions. Furthermore, the results of the principal component analysis indicated a notable distinction between the performance of the 45 maize inbred lines under normal and drought conditions. In terms of grain yield, the drought tolerance index (DTI) showed that Nub60 (1.56), followed by Nub32 (1.46), Nub66 (1.45), and GZ603 (1.44) were the highest drought-tolerant inbred lines, whereas Nub46 (0.38) was the lowest drought-tolerant inbred line. These drought-tolerant inbred lines were able to maintain a relatively high grain yield under normal and stress conditions, whereas those drought-sensitive inbred lines showed a decline in grain yield when exposed to drought conditions. The hierarchical clustering analysis based on DTI classified the forty-five maize inbred lines and eighteen measured traits into three column- and row-clusters, as inbred lines in cluster-3 followed by those in cluster-2 exhibited greater drought tolerance in most of the studied traits. Utilizing the multi-trait stability index (MTSI) criterion in this study identified nine inbred lines, including GZ603, as stable genotypes in terms of the eighteen studied traits across four environments. The findings of the current investigation motivate plant breeders to explore the genetic potential of the current maize germplasm, especially in water-stressed environments.

Morpho-physiological growth performance and phytoremediation capabilities of selected xerophyte grass species toward Cr and Pb stress

Being sessile organisms, plants cannot escape unwanted changes in the environment. The rapid human population explosion caused significant environmental problems. Heavy metals produced through various sources can cause severe damage to living organisms. The study was planned to evaluate four grass species' morpho-physiological growth characteristics and phytoremediation capabilities under chromium (Cr) and lead stress (Pb) in the arid climate. Typha angustifolia, Tragus roxburghii, Aeluropus logopoides, and Cenchrus ciliaris grass species were used for the study. One-year-old stubbles from the Cholistan desert were used for the experiment. Cr treatments in the form of K₂Cr₂O₇ were applied at 0, 20, 40, and 80 mg L^-1, whereas Pb was applied as PbCl₂ at 0, 50, 200, and 500 mg L^-1 as control, low, moderate and high-stress, respectively. After 6 weeks of heavy metals treatments, plants were harvested and analyzed for growth performance and phytoremediation capabilities. Results depicted that, regarding morphological attributes, T. angustifolia performed better, followed by C. ciliaris; no clear pattern was observed for T. roxburghii and A. logopoides. The CO₂ assimilation rate (Co₂d) and water use efficiency (WUE) increased as the heavy metal stress increased in all species under both metals. In contrast, total chlorophyll content was higher under low stress. Other physiological parameters, such as relative humidity (RHd), net photosynthetic rate (A), transpiration rate (E), stomatal conductance (Gs), leaf internal CO2 concentration (Ci) and membrane stability index (MSI) gradually decreased as the Cr, and Pb stress levels increased among all the species. Moreover, Cr and Pb absorption contents of T. angustifolia were higher than the other three species at each stress level. Overall, T. angustifolia thrived against heavy metals stress and showed higher biomass, maximum photosynthetic measurements, WUE and higher metal absorption among all the selected species. Results concluded that although all the selected species behaved fine under stress conditions, T. angustifolia performance was better; thus, it can be used to remediate the soil near industrial estates.