Transcriptome Analysis Reveals a Gene Expression Pattern That Contributes to Sugarcane Bud Propagation Induced by Indole-3-Butyric Acid

Sugarcane is a cash crop that plays an integral part in the sugar industry. The Sustainable Sugarcane Initiative (SSI) has been adopted globally, ensuring enough and aiming for more yield, helping increase disease-free sugarcane cultivation. Single-bud seeds could be the best approach for sugarcane cultivation. Indole-3-butyric acid (IBA) is a rooting agent utilized significantly in seedling propagation. Greenhouse experiment results discovered the significant growth promotion in sugarcane seedlings and accumulation of plant hormones at 100 ppm IBA. Next, we performed transcriptomic analysis of sugarcane buds using RNA sequencing and compared their gene expression during root development due to affect of IBA (100 ppm). A total of 113,475 unigenes were annotated with an average length of 836 bp (N50 = 1,536). The comparative RNA-seq study between the control (CK) and IBA-treated (T) buds showed significant differentially expressed unigenes (494 upregulated and 2086 downregulated). The IBA influenced major biological processes including metabolic process, the cellular process, and single-organism process. For cellular component category, cell, cell part, organelle, membrane, and organelle part were mainly affected. In addition, catalytic activity and binding were primarily affected in the molecular function categories. Furthermore, the expression of genes related to plant hormones and signaling pathways was analyzed by qRT-PCR, which was consistent with the RNA-seq expression profile. This study provides new insights into the IBA response to the bud sprouting in sugarcane based on RNA sequencing, and generated information could help further research on breeding improvement of sugarcane

High-Throughput Sequencing-Based Analysis of Rhizosphere and Diazotrophic Bacterial Diversity Among Wild Progenitor and Closely Related Species of Sugarcane (Saccharum spp. Inter-Specific Hybrids)

Considering the significant role of genetic background in plant-microbe interactions and that most crop rhizospheric microbial research was focused on cultivars, understanding the diversity of root-associated microbiomes in wild progenitors and closely related crossable species may help to breed better cultivars. This study is aimed to fill a critical knowledge gap on rhizosphere and diazotroph bacterial diversity in the wild progenitors of sugarcane, the essential sugar and the second largest bioenergy crop globally. Using a high-throughput sequencing (HTS) platform, we studied the rhizosphere and diazotroph bacterial community of SaccharumofficinarumL. cv. Badila (BRS), Saccharumbarberi (S. barberi) Jesw. cv Pansahi (PRS), Saccharum robustum [S. robustum; (RRS), Saccharum spontaneum (S. spontaneum); SRS], and Saccharum sinense (S. sinense) Roxb. cv Uba (URS) by sequencing their 16S rRNA and nifH genes. HTS results revealed that a total of 6,202 bacteria-specific operational taxonomic units (OTUs) were identified, that were distributed as 107 bacterial groups. Out of that, 31 rhizobacterial families are commonly spread in all five species. With respect to nifH gene, S. barberi and S. spontaneum recorded the highest and lowest number of OTUs, respectively. These results were validated by quantitative PCR analysis of both genes. A total of 1,099 OTUs were identified for diazotrophs with a core microbiome of 9 families distributed among all the sugarcane species. The core microbiomes were spread across 20 genera. The increased microbial diversity in the rhizosphere was mainly due to soil physiochemical properties. Most of the genera of rhizobacteria and diazotrophs showed a positive correlation, and few genera negatively correlated with the soil properties. The results showed that sizeable rhizospheric diversity exists across progenitors and close relatives. Still, incidentally, the rhizosphere microbial abundance of progenitors of modern sugarcane was at the lower end of the spectrum, indicating the prospect of Saccharum species introgression breeding may further improve nutrient use and disease and stress tolerance of commercial sugarcane. The considerable variation for rhizosphere microbiome seen in Saccharum species also provides a knowledge base and an experimental system for studying the evolution of rhizobacteria-host plant association during crop domestication

Nanobiotechnological Approaches to Enhance Drought Tolerance in <i>Catharanthus roseus</i> Plants Using Salicylic Acid in Bulk and Nanoform

Drought has a detrimental effect on crop production, affecting economically important plants’ growth rates and development. Catharanthus roseus is an important medicinal plant that produces many pharmacologically active compounds, some of which have significant antitumor activity. The effect of bulk salicylic acid (SA) and salicylic acid nanoparticles (SA-NPs) were evaluated on water-stressed Catharanthus roseus plants. The results showed that SA and SA-NPs alleviated the negative effects of drought in the treated plants by increasing their shoot and root weights, relative water content, leaf area index, chlorophyll content, and total alkaloids percentage. From the results, a low concentration (0.05 mM) of SA-NPs exerted positive effects on the treated plants, while the best results of the bulk SA were recorded after using the highest concentration (0.1 mM). Both treatments increased the expression level of WRKY1, WRKY2, WRKY40, LEA, and MYC2 genes, while the mRNA level of MPKK1 and MPK6 did not show a significant change. This study discussed the importance of SA-NPs in the induction of drought stress tolerance even when used in low concentrations, in contrast to bulk SA, which exerts significant results only at higher concentrations

Fractionation of Heavy Metals in Multi-Contaminated Soil Treated with Biochar Using the Sequential Extraction Procedure

Heavy metals (HMs) toxicity represents a global problem depending on the soil environment’s geochemical forms. Biochar addition safely reduces HMs mobile forms, thus, reducing their toxicity to plants. While several studies have shown that biochar could significantly stabilize HMs in contaminated soils, the study of the relationship of soil properties to potential mechanisms still needs further clarification; hence the importance of assessing a naturally contaminated soil amended, in this case with Paulownia biochar (PB) and Bamboo biochar (BB) to fractionate Pb, Cd, Zn, and Cu using short sequential fractionation plans. The relationship of soil pH and organic matter and its effect on the redistribution of these metals were estimated. The results indicated that the acid-soluble metals decreased while the fraction bound to organic matter increased compared to untreated pots. The increase in the organic matter metal-bound was mostly at the expense of the decrease in the acid extractable and Fe/Mn bound ones. The highest application of PB increased the organically bound fraction of Pb, Cd, Zn, and Cu (62, 61, 34, and 61%, respectively), while the BB increased them (61, 49, 42, and 22%, respectively) over the control. Meanwhile, Fe/Mn oxides bound represents the large portion associated with zinc and copper. Concerning soil organic matter (SOM) and soil pH, as potential tools to reduce the risk of the target metals, a significant positive correlation was observed with acid-soluble extractable metal, while a negative correlation was obtained with organic matter-bound metal. The principal component analysis (PCA) shows that the total variance represents 89.7% for the TCPL-extractable and HMs forms and their relation to pH and SOM, which confirms the positive effect of the pH and SOM under PB and BB treatments on reducing the risk of the studied metals. The mobility and bioavailability of these metals and their geochemical forms widely varied according to pH, soil organic matter, biochar types, and application rates. As an environmentally friendly and economical material, biochar emphasizes its importance as a tool that makes the soil more suitable for safe cultivation in the short term and its long-term sustainability. This study proves that it reduces the mobility of HMs, their environmental risks and contributes to food safety. It also confirms that performing more controlled experiments, such as a pot, is a disciplined and effective way to assess the suitability of different types of biochar as soil modifications to restore HMs contaminated soil via controlling the mobilization of these minerals

Assessment of Genetic Diversity of Bread Wheat Genotypes for Drought Tolerance Using Canopy Reflectance-Based Phenotyping and SSR Marker-Based Genotyping

This study investigated the genetic diversity of bread-wheat genotypes using canopy reflectance-based vegetation indices (VIs) and simple sequence repeat (SSR) marker-based genotyping for drought tolerance. A total of 56 wheat genotypes were assessed using phenotypic traits (combination of VIs and yield traits) and 30 SSR markers. The data of the phenotypic traits were averaged over two growing seasons under irrigated and drought-stressed conditions. The hierarchical clustering of the wheat genotypes unveiled three drought-tolerant groups. Cluster 1 genotypes showed minimal phenotypic alterations, conferring superior drought tolerance and yield stability than clusters 2 and 3. The polymorphism information content values for the SSR markers ranged from 0.434 to 0.932, averaging 0.83. A total of 458 alleles (18.32 alleles per locus) were detected, with the most polymorphic markers, wmc177 and wms292, having the most alleles (24). A comparative study of SSR diversity among phenotypic clusters indicated that genotypes under cluster 1 had higher genetic diversity (0.879) and unique alleles (47%), suggesting their potential in future breeding programs. The unweighted neighbor-joining tree grouped the wheat genotypes into five major clusters. Wheat genotypes from all phenotypic clusters were distributed throughout all SSR-based clusters, indicating that genetically heterogeneous genotypes were allocated to different drought-tolerant groups. However, SSR-based clusters and model-based populations showed significant co-linearity (86.7%). The findings of the present study suggest that combining reflectance-based indirect phenotyping with SSR-based genotyping might be an effective technique for assessing genetic diversity to improve the drought tolerance of bread-wheat genotypes

Improved Method of Boron Fertilization in Rice (Oryza sativa L.)–Mustard (Brassica juncea L.) Cropping System in Upland Calcareous Soils

Calcareous soils are highly deficient in boron (B) due to having high levels of free CaCO3 and low organic matter. This has become one of the most important deficient micronutrients in Indian soil after zinc (Zn). For various rice (Oryza sativa L.)-based cropping systems, B fertilization is essential for increasing crop productivity and the biofortification of the crop, thus a suitable soil application protocol for B fertilization is required for B-deficient soils. In a six-year experiment, different rates of B application, namely, 0.5, 1.0, 1.5, and 2.0 kg ha−1 y−1, were evaluated to determine the effects of three different modes of B fertilization, i.e., applied only in the first year, applied in alternating years, and applied every year, in a rice (Oryza sativa L.)–Indian mustard (Brassica juncea L.) cropping system. It was observed that the application of B at 1.5 kg ha−1 every year or 2 kg ha−1 in alternate years resulted in the highest yield of rice and mustard, as well as the maximum system productivity of the rice–mustard cropping system. Application of 2 kg ha−1 of B in the initial year showed the maximum B uptake by rice, while application of 1.5–2.0 kg ha−1 of B every year resulted in the maximum B uptake by the mustard crop. Application of B at 2 kg ha−1 in alternate years or 1.5 kg ha−1 every year was the best B-application protocol in B-deficient calcareous soils for ensuring the highest productivity of the rice–mustard cropping system and B availability in the soil

Assessment of Genetic Diversity of Bread Wheat Genotypes for Drought Tolerance Using Canopy Reflectance-Based Phenotyping and SSR Marker-Based Genotyping

This study investigated the genetic diversity of bread-wheat genotypes using canopy reflectance-based vegetation indices (VIs) and simple sequence repeat (SSR) marker-based genotyping for drought tolerance. A total of 56 wheat genotypes were assessed using phenotypic traits (combination of VIs and yield traits) and 30 SSR markers. The data of the phenotypic traits were averaged over two growing seasons under irrigated and drought-stressed conditions. The hierarchical clustering of the wheat genotypes unveiled three drought-tolerant groups. Cluster 1 genotypes showed minimal phenotypic alterations, conferring superior drought tolerance and yield stability than clusters 2 and 3. The polymorphism information content values for the SSR markers ranged from 0.434 to 0.932, averaging 0.83. A total of 458 alleles (18.32 alleles per locus) were detected, with the most polymorphic markers, wmc177 and wms292, having the most alleles (24). A comparative study of SSR diversity among phenotypic clusters indicated that genotypes under cluster 1 had higher genetic diversity (0.879) and unique alleles (47%), suggesting their potential in future breeding programs. The unweighted neighbor-joining tree grouped the wheat genotypes into five major clusters. Wheat genotypes from all phenotypic clusters were distributed throughout all SSR-based clusters, indicating that genetically heterogeneous genotypes were allocated to different drought-tolerant groups. However, SSR-based clusters and model-based populations showed significant co-linearity (86.7%). The findings of the present study suggest that combining reflectance-based indirect phenotyping with SSR-based genotyping might be an effective technique for assessing genetic diversity to improve the drought tolerance of bread-wheat genotypes

Thermal Response of Spring–Summer-Grown Black Gram (Vigna mungo L. Hepper) in Indian Subtropics

The thermal environment of a crop is one of the prime factors enhancing growth and production by regulating its physiological processes at different phenophases. To study the impact of thermal regime on spring–summer-grown black gram (variety Pant Urd 31), an experiment was conducted with different sowing dates (from the first to the third week of March), soil application of cobalt (Co) and foliar sprays of potassium (K) and boron (B) in various combinations in the split–split plot design during 2020 and 2021. The first-week-of-March-sown crop recorded more accumulated growing degree-days (GDD), photothermal units (PTU) and heliothermal units (HTU) with a longer duration than the later sown crop. Higher daily mean temperature during the reproductive stage of the later sown crop compelled it to complete the phenophases earlier than the normally sown crop, leading to yield reduction. Soil application of Co at 4 kg ha−1 and foliar sprays of K at 1.25% and B at 0.2% mitigated the adversities of excess heat irrespective of sowing dates. Variations in GDD and HTU, respectively, explained variations of about 75.8% and 87.3% in the final dry matter accumulation and of 72.9% and 84.8% in seed yield through polynomial regressions in the respective years. The maximum mean thermal use efficiency (TUE) for biomass production (0.24 g m−2/°C/day−1) and seed yield (0.11 g m−2/°C/day−1) were observed with Co soil application and combined foliar sprays of K and B due to higher dry matter production or seed yield with lower heat units accumulation in the first sown crop

Development of New Iso-Cytoplasmic Rice-Restorer Lines and New Rice Hybrids with Superior Grain Yield and Grain Quality Characteristics by Utilizing Restorers&rsquo; Fertility Genes

This research was carried out at the Experimental Farm of Sakha Agricultural Research Station, Sakha, Kafr El-Sheikh, Egypt, during the 2018&ndash;2020 rice-growing seasons to develop and evaluate four iso-cytoplasmic rice-restorer lines: NRL79, NRL80, NRL81, and NRL82, as well as Giza 178, with ten new hybrids in order to estimate genotypic coefficient, phenotypic coefficient, heritability in a broad sense, and advantage over Giza 178 as a check variety (control) of new restorer lines. This study also estimated combining ability, gene action, better-parent heterosis (BP), mid-parents heterosis (MP), and standard heterosis (SH) over Egyptian Hybrid one (IR69A &times; Giza 178) as a check hybrid (control) for grain yield, agronomic traits, and some grain quality characters in restorer lines and hybrids. The percentage of advantage over commercial-variety Giza 178 (check) was significant, and highly significant among the newly developed restorer fertility lines for all the studied traits. This indicates that the selection is a highly effective factor in improving these traits. New restorer fertility lines showed highly significant positive values over commercial restorer for grain yield; the values ranged from 51% for NRL80 to 100.4% for NRL82, respectively. Meanwhile, in regard to the grain shape of paddy rice, three lines of the promising lines showed highly significant negative desirable values compared with Giza 178; the values ranged from &minus;7.7% for the NRL80 to &minus;15.2% for NRL79, respectively. Based on the superiority of the new lines, the new lines can be used as new restorer fertility lines to breed promising new hybrids and new inbred rice lines or varieties. From the results of the testcross experiment, the four promising lines were identified as effective restorer fertility lines for two cytoplasmic male sterile (CMS) lines. Moreover, the six rice hybrids showed values for SH heterosis of grain yield/plant of more than 15% over the check hybrid variety, with high values of 1000-grain weight and desirable grain shape; these hybrids were G46A &times; NRL81 (125.1%), G46A &times; NRL80 (66.9%), IR69A &times; NRL79 (47.2%), G46A &times; NRL79 (24.6%), IR69A &times; NRL81 (23.4%), and IR69A &times; NRL82 (16.2%)

Antimycotoxigenic Activity of Beetroot Extracts against Alternaria alternata Mycotoxins on Potato Crop

Alternaria species, mainly air-borne fungi, affect potato plants, causing black spots symptoms. Morphological identification, pathogenicity assessment, and internal transcribed spacer (ITS) molecular identification confirmed that all isolates were Alternaria alternata. The annotated sequences were deposited in GenBank under accession numbers MN592771–MN592777. HPLC analysis revealed that the fungal isolates KH3 (133,200 ng/g) and NO3 (212,000 ng/g) produced higher levels of tenuazonic acid (TeA) and alternariol monomethyl ether (AME), respectively. Beet ethanol extract (BEE) and beet methanol extract (BME) at different concentrations were used as antimycotoxins. BME decreased the production of mycotoxins by 66.99–99.79%. The highest TeA reduction rate (99.39%) was reported in the KH3 isolate with 150 µg/mL BME treatment. In comparison, the most effective AME reduction rate (99.79%) was shown in the NO3 isolate with 150 µg/mL BME treatment. In the same way, BEE application resulted in 95.60–99.91% mycotoxin reduction. The highest TeA reduction rate (99.91%) was reported in the KH3 isolate with 150 µg/mL BEE treatment, while the greatest AME reduction rate (99.68%) was shown in the Alam1 isolate with 75 µg/mL BEE treatment. GC-MS analysis showed that the main constituent in BME was the antioxidant compound 1-dodecanamine, n,n-dimethyl with a peak area of 43.75%. In contrast, oxirane, methyl- (23.22%); hexadecanoic acid, methyl ester (10.72%); and n-hexadecanoic acid (7.32%) were the main components in BEE found by GC-MS. They are probably antimicrobial molecules and have an effect on the mycotoxin in general. To our knowledge, this is the first study describing the antimycotoxigenic activity of beet extracts against A. alternata mycotoxins-contaminated potato crops in Egypt, aimed to manage and save the environment