Variation Among Spring Wheat (Triticum aestivum L.) Genotypes in Response to the Drought Stress. II-Root System Structure

Response of the root anatomical structure of Carex moorcroftii to habitat drought in the Western Sichuan Plateau of China

MAIN CONCLUSION

The anatomical structures of Carex moorcroftii roots showing stronger plasticity during drought had a lower coefficient of variation in cell size in the same habitats, while those showing weaker plasticity had a higher coefficient of variation. The complementary relationship between these factors comprises the adaptation mechanism of the C. moorcroftii root to drought. To explore the effects of habitat drought on root anatomy of hygrophytic plants, this study focused on roots of C. moorcroftii. Five sample plots were set up along a soil moisture gradient in the Western Sichuan Plateau to collect experimental materials. Paraffin sectioning was used to obtain root anatomy, and one-way ANOVA, correlation analysis, linear regression analysis, and RDA ranking were applied to analyze the relationship between root anatomy and soil water content. The results showed that the root transverse section area, thickness of epidermal cells, exodermis and Casparian strips, and area of aerenchyma were significantly and positively correlated with soil moisture content (P < 0.01). The diameter of the vascular cylinder and the number and total area of vessels were significantly and negatively correlated with the soil moisture content (P < 0.01). The plasticity of the anatomical structures was strong for the diameter and area of the vascular cylinder and thickness of the Casparian strip and epidermis, while it was weak for vessel diameter and area. In addition, there was an asymmetrical relationship between the functional adaptation of root anatomical structure in different soil moisture and the variation degree of root anatomical structure in the same soil moisture. Therefore, the roots of C. moorcroftii can shorten the water transport distance from the epidermis to the vascular cylinder, increase the area of the vascular cylinder and the number of vessels, and establish a complementary relationship between the functional adaptation of root anatomical structure in different habitats and the variation degree of root anatomical structure in the same habitat to adapt to habitat drought. This study provides a scientific basis for understanding the response of plateau wetland plants to habitat changes and their ecological adaptation strategies. More scientific experimental methods should be adopted to further study the mutual coordination mechanisms of different anatomical structures during root adaptation to habitat drought for hygrophytic plants.

A bird's-eye view: exploration of the flavin-containing monooxygenase superfamily in common wheat

The Flavin Monooxygenase (FMO) gene superfamily in plants is involved in various processes most widely documented for its involvement in auxin biosynthesis, specialized metabolite biosynthesis, and plant microbial defense signaling. The roles of FMOs in defense signaling and disease resistance have recently come into focus as they may present opportunities to increase immune responses in plants including leading to systemic acquired resistance, but are not well characterized. We present a comprehensive catalogue of FMOs found in genomes across vascular plants and explore, in depth, 170 wheat TaFMO genes for sequence architecture, cis-acting regulatory elements, and changes due to Transposable Element insertions. A molecular phylogeny separates TaFMOs into three clades (A, B, and C) for which we further report gene duplication patterns, and differential rates of homoeologue expansion and retention among TaFMO subclades. We discuss Clade B TaFMOs where gene expansion is similarly seen in other cereal genomes. Transcriptome data from various studies point towards involvement of subclade B2 TaFMOs in disease responses against both biotrophic and necrotrophic pathogens, substantiated by promoter element analysis. We hypothesize that certain TaFMOs are responsive to both abiotic and biotic stresses, providing potential targets for enhancing disease resistance, plant yield and other important agronomic traits. Altogether, FMOs in wheat and other crop plants present an untapped resource to be exploited for improving the quality of crops.

Identification of Salt-Sensitive and Salt-Tolerant Genes through Weighted Gene Co-Expression Networks across Multiple Datasets: A Centralization and Differential Correlation Analysis

Salt stress is a significant challenge that severely hampers rice growth, resulting in decreased yield and productivity. Over the years, researchers have identified biomarkers associated with salt stress to enhance rice tolerance. However, the understanding of the mechanism underlying salt tolerance in rice remains incomplete due to the involvement of multiple genes. Given the vast amount of genomics and transcriptomics data available today, it is crucial to integrate diverse datasets to identify key genes that play essential roles during salt stress in rice. In this study, we propose an integration of multiple datasets to identify potential key transcription factors. This involves utilizing network analysis based on weighted co-expression networks, focusing on gene-centric measurement and differential co-expression relationships among genes. Consequently, our analysis reveals 86 genes located in markers from previous meta-QTL analysis. Moreover, six transcription factors, namely LOC_Os03g45410 (OsTBP2), LOC_Os07g42400 (OsGATA23), LOC_Os01g13030 (OsIAA3), LOC_Os05g34050 (OsbZIP39), LOC_Os09g29930 (OsBIM1), and LOC_Os10g10990 (transcription initiation factor IIF), exhibited significantly altered co-expression relationships between salt-sensitive and salt-tolerant rice networks. These identified genes hold potential as crucial references for further investigation into the functions of salt stress response in rice plants and could be utilized in the development of salt-resistant rice cultivars. Overall, our findings shed light on the complex genetic regulation underlying salt tolerance in rice and contribute to the broader understanding of rice's response to salt stress.

Exploiting DNA methylation in cassava under water deficit for crop improvement

DNA methylation plays a key role in the development and plant responses to biotic and abiotic stresses. This work aimed to evaluate the DNA methylation in contrasting cassava genotypes for water deficit tolerance. The varieties BRS Formosa (bitter) and BRS Dourada (sweet) were grown under greenhouse conditions for 50 days, and afterwards, irrigation was suspended. The stressed (water deficit) and non-stressed plants (negative control) consisted the treatments with five plants per variety. The DNA samples of each variety and treatment provided 12 MethylRAD-Seq libraries (two cassava varieties, two treatments, and three replicates). The sequenced data revealed methylated sites covering 18 to 21% of the Manihot esculenta Crantz genome, depending on the variety and the treatment. The CCGG methylated sites mapped mostly in intergenic regions, exons, and introns, while the CCNGG sites mapped mostly intergenic, upstream, introns, and exons regions. In both cases, methylated sites in UTRs were less detected. The differentially methylated sites analysis indicated distinct methylation profiles since only 12% of the sites (CCGG and CCNGG) were methylated in both varieties. Enriched gene ontology terms highlighted the immediate response of the bitter variety to stress, while the sweet variety appears to suffer more potential stress-damages. The predicted protein-protein interaction networks reinforced such profiles. Additionally, the genomes of the BRS varieties uncovered SNPs/INDELs events covering genes stood out by the interactomes. Our data can be useful in deciphering the roles of DNA methylation in cassava drought-tolerance responses and adaptation to abiotic stresses.

Ectopic Expression of a Wheat R2R3-Type MYB Gene in Transgenic Tobacco Enhances Osmotic Stress Tolerance via Maintaining ROS Balance and Improving Root System Architecture

Water scarcity is a critical cause of plant yield loss and decreased quality. Manipulation of root system architecture to minimize the impact of water scarcity stresses may greatly contribute towards an improved distribution of roots in the soil and enhanced water and nutrient uptake abilities. In this study, we explored the potential of TaMYB20 gene, a wheat gene belonging to the R2R3-MYB transcription factor family, to improve root system architecture in transgenic tobacco plants. The full-length TaMYB20 gene was isolated from Triticum aestivum.cv. Sakha94 and used to produce genetically engineered tobacco plants. The transgenic plants exhibited enhanced tolerance to extended osmotic stress and were able to maintain their root system architecture traits, including total root length (TRL), lateral root number (LRN), root surface area (RSa), and root volume (RV), while the wild-type plants failed to maintain the same traits. The transgenic lines presented greater relative water content in their roots associated with decreased ion leakage. The oxidative stress resulted in the loss of mitochondrial membrane integrity in the wild-type (WT) plants due to the overproduction of reactive oxygen species (ROS) in the root cells, while the transgenic lines were able to scavenge the excess ROS under stressful conditions through the activation of the redox system. Finally, we found that the steady-state levels of three PIN gene transcripts were greater in the TaMYB20-transgenic lines compared to the wild-type tobacco. Taken together, these findings confirm that TaMYB20 is a potentially useful gene candidate for engineering drought tolerance in cultivated plants.

Genetic dissection of protein and starch during wheat grain development using QTL mapping and GWAS

Protein, starch, and their components are important for wheat grain yield and end-products, which are affected by wheat grain development. Therefore, QTL mapping and a genome-wide association study (GWAS) of grain protein content (GPC), glutenin macropolymer content (GMP), amylopectin content (GApC), and amylose content (GAsC) were performed on wheat grain development at 7, 14, 21, and 28 days after anthesis (DAA) in two environments using a recombinant inbred line (RIL) population of 256 stable lines and a panel of 205 wheat accessions. A total of 29 unconditional QTLs, 13 conditional QTLs, 99 unconditional marker-trait associations (MTAs), and 14 conditional MTAs significantly associated (p < 10^-4) with four quality traits were found to be distributed on 15 chromosomes, with the phenotypic variation explained (PVE) ranging from 5.35% to 39.86%. Among these genomic variations, three major QTLs [QGPC3B, QGPC2A, and QGPC(S3|S2)3B] and SNP clusters on the 3A and 6B chromosomes were detected for GPC, and the SNP TA005876-0602 was stably expressed during the three periods in the natural population. The QGMP3B locus was detected five times in three developmental stages in two environments with 5.89%-33.62% PVE, and SNP clusters for GMP content were found on the 3A and 3B chromosomes. For GApC, the QGApC3B.1 locus had the highest PVE of 25.69%, and SNP clusters were found on chromosomes 4A, 4B, 5B, 6B, and 7B. Four major QTLs of GAsC were detected at 21 and 28 DAA. Most interestingly, both QTL mapping and GWAS analysis indicated that four chromosomes (3B, 4A, 6B, and 7A) were mainly involved in the development of protein, GMP, amylopectin, and amylose synthesis. Of these, the wPt-5870-wPt-3620 marker interval on chromosome 3B seemed to be most important because it played an important role in the synthesis of GMP and amylopectin before 7 DAA, in the synthesis of protein and GMP from 14 to 21 DAA, and in the development of GApC and GAsC from 21 to 28 DAA. Using the annotation information of IWGSC Chinese Spring RefSeq v1.1 genome assembly, we predicted 28 and 69 candidate genes for major loci from QTL mapping and GWAS, respectively. Most of them have multiple effects on protein and starch synthesis during grain development. These results provide new insights and information for the potential regulatory network between grain protein and starch synthesis.

Genome-wide identification and analysis of the evolution and expression pattern of the HVA22 gene family in three wild species of tomatoes

Wild tomato germplasm is a valuable resource for improving biotic and abiotic stresses in tomato breeding. The HVA22 is widely present in eukaryotes and involved in growth and development as well as stress response, such as cold, salt, drought, and biotic stress. In the present study, we identified 45 HVA22 genes in three wild species of tomatoes. The phylogenetic relationships, gene localization to chromosomes, gene structure, gene collinearity, protein interactions, and cis-acting element prediction of all 45 HVA22 genes (14 in Solanum pennellii, 15 in S. pimpinellifolium, and 16 in S. lycopersicoides) were analyzed. The phylogenetic analysis showed that the all HVA22 proteins from the family Solanaceae were divided into three branches. The identified 45 HVA22 genes were grouped into four subfamilies, which displayed similar number of exons and expanded in a fragmentary replication manner. The distribution of HVA22 genes on the chromosomes of the three wild tomato species was also highly similar. RNA-seq and qRT-PCR revealed that HVA22 genes were expressed in different tissues and induced by drought, salt, and phytohormone treatments. These results might be useful for explaining the evolution, expression patterns, and functional divergence of HVA22 genes in Lycopersicon.

Instigating prevalent abiotic stress resilience in crop by exogenous application of phytohormones and nutrient

In recent times, the demand for food and feed for the ever-increasing population has achieved unparalleled importance, which cannot afford crop yield loss. Now-a-days, the unpleasant situation of abiotic stress triggers crop improvement by affecting the different metabolic pathways of yield and quality advances worldwide. Abiotic stress like drought, salinity, cold, heat, flood, etc. in plants diverts the energy required for growth to prevent the plant from shock and maintain regular homeostasis. Hence, the plant yield is drastically reduced as the energy is utilized for overcoming the stress in plants. The application of phytohormones like the classical auxins, cytokinins, ethylene, and gibberellins, as well as more recent members including brassinosteroids, jasmonic acids, etc., along with both macro and micronutrients, have enhanced significant attention in creating key benefits such as reduction of ionic toxicity, improving oxidative stress, maintaining water-related balance, and gaseous exchange modification during abiotic stress conditions. Majority of phytohormones maintain homeostasis inside the cell by detoxifying the ROS and enhancing the antioxidant enzyme activities which can enhance tolerance in plants. At the molecular level, phytohormones activate stress signaling pathways or genes regulated by abscisic acid (ABA), salicylic acid (SA), Jasmonic acid (JA), and ethylene. The various stresses primarily cause nutrient deficiency and reduce the nutrient uptake of plants. The application of plant nutrients like N, K, Ca, and Mg are also involved in ROS scavenging activities through elevating antioxidants properties and finally decreasing cell membrane leakage and increasing the photosynthetic ability by resynthesizing the chlorophyll pigment. This present review highlighted the alteration of metabolic activities caused by abiotic stress in various crops, the changes of vital functions through the application of exogenous phytohormones and nutrition, as well as their interaction.

Phenotypic and Genotypic Diversity of Roots Response to Salt in Durum Wheat Seedlings

Soil salinity is a serious threat to food production now and in the near future. In this study, the root system of six durum wheat genotypes, including one highly salt-tolerant (J. Khetifa) used as a check genotype, was evaluated, by a high-throughput phenotyping system, under control and salt conditions at the seedling stage. Genotyping was performed using 11 SSR markers closely linked with genome regions associated with root traits. Based on phenotypic cluster analysis, genotypes were grouped differently under control and salt conditions. Under control conditions, genotypes were clustered mainly due to a root angle, while under salt stress, genotypes were grouped according to their capacity to maintain higher roots length, volume, and surface area, as J. Khetifa, Sebatel, and Azeghar. SSR analysis identified a total of 42 alleles, with an average of about three alleles per marker. Moreover, quite a high number of Private alleles in total, 18 were obtained. The UPGMA phenogram of the Nei (1972) genetic distance clusters for 11 SSR markers and all phenotypic data under control conditions discriminate genotypes almost into the same groups. The study revealed as the combination of high-throughput systems for phenotyping with SSR markers for genotyping it's a useful tool to provide important data for the selection of suitable parental lines for salt-tolerance breeding. Nevertheless, the narrow root angle, which is an important trait in drought tolerance, is not a good indicator of salt tolerance. Instated for salt tolerance is more important the amount of roots.

Genome-wide association study in two-row spring barley landraces identifies QTL associated with plantlets root system architecture traits in well-watered and osmotic stress conditions

Water availability is undoubtedly one of the most important environmental factors affecting crop production. Drought causes a gradual deprivation of water in the soil from top to deep layers and can occur at diverse stages of plant development. Roots are the first organs that perceive water deficit in soil and their adaptive development contributes to drought adaptation. Domestication has contributed to a bottleneck in genetic diversity. Wild species or landraces represent a pool of genetic diversity that has not been exploited yet in breeding program. In this study, we used a collection of 230 two-row spring barley landraces to detect phenotypic variation in root system plasticity in response to drought and to identify new quantitative trait loci (QTL) involved in root system architecture under diverse growth conditions. For this purpose, young seedlings grown for 21 days in pouches under control and osmotic-stress conditions were phenotyped and genotyped using the barley 50k iSelect SNP array, and genome-wide association studies (GWAS) were conducted using three different GWAS methods (MLM GAPIT, FarmCPU, and BLINK) to detect genotype/phenotype associations. In total, 276 significant marker-trait associations (MTAs; p-value (FDR)< 0.05) were identified for root (14 and 12 traits under osmotic-stress and control conditions, respectively) and for three shoot traits under both conditions. In total, 52 QTL (multi-trait or identified by at least two different GWAS approaches) were investigated to identify genes representing promising candidates with a role in root development and adaptation to drought stress.

Genome-Wide Identification and Characterization of Receptor-Like Protein Kinase 1 (RPK1) Gene Family in Triticum aestivum Under Drought Stress

Receptor-like protein kinase1 (RPK1) genes play crucial roles in plant growth and development processes, root architecture, and abiotic stress regulation. A comprehensive study of the RPK1 gene family has not been reported in bread wheat (Triticum aestivum). Here, we reported the genome-wide identification, characterization, and expression patterns of the RPK1 gene family in wheat. Results confirmed 15 TaRPK1 genes, classified mainly into three sub-clades based on a phylogenetic tree. The TaRPK1 genes were mapped on chromosomes 1–3 in the respective A, B, and D genomes. Gene structure, motif conservation, collinearity prediction, and synteny analysis were carried out systematically. A Gene ontology study revealed that TaRPK1 genes play a vital role during molecular and biological processes. We also identified 18 putative miRNAs targeting TaRPK1 genes, suggesting their roles in growth, development, and stress responses. Cis-Regulatory elements interpreted the presence of light-related elements, hormone responsiveness, and abiotic stress-related motifs in the promoter regions. The SWISS_MODEL predicted the successful models of TaRPK1 proteins with at least 30% identity to the template, a widely accepted threshold for successful modeling. In silico expression analysis in different tissues and stages suggested that TaRPK1 genes exhibited the highest expression in root tissues. Moreover, qRT-PCR further validated the higher expression of TaRPK1 genes in roots of drought-tolerant varieties compared to the drought-susceptible variety. Collectively, the present study renders valuable information on the functioning of TaRPK1 genes in wheat that will be useful in further functional validation of these genes in future studies.

Plants' Physio-Biochemical and Phyto-Hormonal Responses to Alleviate the Adverse Effects of Drought Stress: A Comprehensive Review

Water, a necessary component of cell protoplasm, plays an essential role in supporting life on Earth; nevertheless, extreme changes in climatic conditions limit water availability, causing numerous issues, such as the current water-scarce regimes in many regions of the biome. This review aims to collect data from various published studies in the literature to understand and critically analyze plants' morphological, growth, yield, and physio-biochemical responses to drought stress and their potential to modulate and nullify the damaging effects of drought stress via activating natural physiological and biochemical mechanisms. In addition, the review described current breakthroughs in understanding how plant hormones influence drought stress responses and phytohormonal interaction through signaling under water stress regimes. The information for this review was systematically gathered from different global search engines and the scientific literature databases Science Direct, including Google Scholar, Web of Science, related studies, published books, and articles. Drought stress is a significant obstacle to meeting food demand for the world's constantly growing population. Plants cope with stress regimes through changes to cellular osmotic potential, water potential, and activation of natural defense systems in the form of antioxidant enzymes and accumulation of osmolytes including proteins, proline, glycine betaine, phenolic compounds, and soluble sugars. Phytohormones modulate developmental processes and signaling networks, which aid in acclimating plants to biotic and abiotic challenges and, consequently, their survival. Significant progress has been made for jasmonates, salicylic acid, and ethylene in identifying important components and understanding their roles in plant responses to abiotic stress. Other plant hormones, such as abscisic acid, auxin, gibberellic acid, brassinosteroids, and peptide hormones, have been linked to plant defense signaling pathways in various ways.

Root System Architecture Plasticity of Bread Wheat in Response to Oxidative Burst under Extended Osmotic Stress

There is a demand for an increase in crop production because of the growing population, but water shortage hinders the expansion of wheat cultivation, one of the most important crops worldwide. Polyethylene glycol (PEG) was used to mimic drought stress due to its high osmotic potentials generated in plants subjected to it. This study aimed to determine the root system architecture (RSA) plasticity of eight bread wheat genotypes under osmotic stress in relation to the oxidative status and mitochondrial membrane potential of their root tips. Osmotic stress application resulted in differences in the RSA between the eight genotypes, where genotypes were divided into adapted genotypes that have non-significant decreased values in lateral roots number (LRN) and total root length (TRL), while non-adapted genotypes have a significant decrease in LRN, TRL, root volume (RV), and root surface area (SA). Accumulation of intracellular ROS formation in root tips and elongation zone was observed in the non-adapted genotypes due to PEG-induced oxidative stress. Mitochondrial membrane potential (∆Ψm) was measured for both stress and non-stress treatments in the eight genotypes as a biomarker for programmed cell death as a result of induced osmotic stress, in correlation with RSA traits. PEG treatment increased scavenging capacity of the genotypes from 1.4-fold in the sensitive genotype Gemmiza 7 to 14.3-fold in the adapted genotype Sakha 94. The adapted genotypes showed greater root trait values, ∆Ψm plasticity correlated with high scavenging capacity, and less ROS accumulation in the root tissue, while the non-adapted genotypes showed little scavenging capacity in both treatments, accompanied by mitochondrial membrane permeability, suggesting mitochondrial dysfunction as a result of oxidative stress.

Physio-Morphological and Biochemical Trait-Based Evaluation of Ethiopian and Chinese Wheat Germplasm for Drought Tolerance at the Seedling Stage

For Ethiopia’s wheat production, drought is a major natural disaster. Exploration of drought-resistant varieties from a bulk of wheat germplasm conserved in the gene bank is of paramount importance for breeding climate change-resilient modern cultivars. The present study was aimed at identifying the best performing drought-resistant genotypes under non-stress and polyethylene glycol simulated (PEG) stress conditions in a growth chamber. Forty diverse Ethiopian bread and durum wheat cultivars along with three Chinese bread wheat cultivars possessing strong drought resistance and susceptibility were evaluated. After acclimation with the natural environment, the seedlings were imposed to severe drought stress (20% PEG6000), and 15 seedling traits including photosynthetic and free proline were investigated. Our findings indicated that drought stress caused a profound decline in plant water consumption (83.0%), shoot fresh weight (64.9%), stomatal conductance (61.6%), root dry weight (55.2%), and other investigated traits except root to shoot length ratio and proline content which showed a significant increase under drought stress. A significant and positive correlation was found between photosynthetic pigments in both growth conditions. Proline exhibited a negative correlation with most of the investigated traits except root to shoot length ratio and all photosynthetic pigments which showed a positive and non-significant association. Our result also showed a wide range of genetic variation (CV) ranging from 3.23% to 47.3%; the highest in shoot dry weight (SDW) (47.3%) followed by proline content (44.63%) and root dry weight (36.03%). Based on multivariate principal component biplot analysis and average sum of ranks (ASR), G12, G16 and G25 were identified as the best drought tolerant and G6, G42, G4, G11, and G9 as bottom five sensitive. The potential of these genotypes offers further investigation at a molecular and cellular level to identify the novel gene associated with the stress response.

Knockdown of a Novel Gene OsTBP2.2 Increases Sensitivity to Drought Stress in Rice

Drought stress is a major environmental stress, which adversely affects the biological and molecular processes of plants, thereby impairing their growth and development. In the present study, we found that the expression level of OsTBP2.2 which encodes for a nucleus-localized protein member belonging to transcription factor IID (TFIID) family, was significantly induced by polyethylene glycol (PEG) treatment. Therefore, knockdown mutants of OsTBP2.2 gene were generated to investigate the role of OsTBP2.2 in rice response to drought stress. Under the condition of drought stress, the photosynthetic rate, transpiration rate, water use efficiency, and stomatal conductance were significantly reduced in ostbp2.2 lines compared with wild type, Dongjin (WT-DJ). Furthermore, the RNA-seq results showed that several main pathways involved in "MAPK (mitogen-activated protein kinase) signaling pathway", "phenylpropanoid biosynthesis", "defense response" and "ADP (adenosine diphosphate) binding" were altered significantly in ostbp2.2. We also found that OsPIP2;6, OsPAO and OsRCCR1 genes were down-regulated in ostbp2.2 compared with WT-DJ, which may be one of the reasons that inhibit photosynthesis. Our findings suggest that OsTBP2.2 may play a key role in rice growth and the regulation of photosynthesis under drought stress and it may possess high potential usefulness in molecular breeding of drought-tolerant rice.