TraeALDH7B1-5A, encoding aldehyde dehydrogenase 7 in wheat, confers improved drought tolerance in Arabidopsis

Genome-Wide Identification and Expression Analysis of the Melon Aldehyde Dehydrogenase (ALDH) Gene Family in Response to Abiotic and Biotic Stresses

Through the integration of genomic information, transcriptome sequencing data, and bioinformatics methods, we conducted a comprehensive identification of the ALDH gene family in melon. We explored the impact of this gene family on melon growth, development, and their expression patterns in various tissues and under different stress conditions. Our study discovered a total of 17 ALDH genes spread across chromosomes 1, 2, 3, 4, 5, 7, 8, 11, and 12 in the melon genome. Through a phylogenetic analysis, these genes were classified into 10 distinct subfamilies. Notably, genes within the same subfamily exhibited consistent gene structures and conserved motifs. Our study discovered a pair of fragmental duplications within the melon ALDH gene. Furthermore, there was a noticeable collinearity relationship between the melon's ALDH gene and that of Arabidopsis (12 times), and rice (3 times). Transcriptome data reanalysis revealed that some ALDH genes consistently expressed highly across all tissues and developmental stages, while others were tissue- or stage-specific. We analyzed the ALDH gene's expression patterns under six stress types, namely salt, cold, waterlogged, powdery mildew, Fusarium wilt, and gummy stem blight. The results showed differential expression of CmALDH2C4 and CmALDH11A3 under all stress conditions, signifying their crucial roles in melon growth and stress response. RT-qPCR (quantitative reverse transcription PCR) analysis further corroborated these findings. This study paves the way for future genetic improvements in melon molecular breeding.

Discovery of Aldehyde Dehydrogenase as a Potential Fungicide Target and Screening of its Natural Inhibitors against Fusarium verticillioides

Fusarium verticillioides is the primary pathogen causing ear rot and stalk rot in corn (Zea mays). It not only affects yields but also produces mycotoxins endangering both human and animal health. Aldehyde dehydrogenase (ALDH) is essential for the oxidation of aldehydes in living organisms, making it a potential target for human drug design. However, there are limited reports on its function in plant pathogenic fungus. In this study, we analyzed the expression levels and gene knockout mutants, revealing that ALDH genes FvALDH-43 and FvALDH-96 in F. verticillioides played significant roles in pathogenicity and resistance to low-temperature stress by affecting antioxidant capacity. Virtual screening for natural product inhibitors and molecular docking were performed targeting FvALDH-43 and FvALDH-96. Following the biological activity analysis, three natural flavonoid compounds featuring a 2-hydroxyphenol chromene were identified. Among these, Taxifolin exhibited the highest biological activity and low toxicity. Both in vitro and in vivo biological evaluations confirmed that Taxifolin targeted ALDH and inhibited its activity. These findings indicate that aldehyde dehydrogenase may serve as a promising target for the design of novel fungicides.

Accurate Long-Read RNA Sequencing Analysis Reveals the Key Pathways and Candidate Genes under Drought Stress in the Seed Germination Stage in Faba Bean

Faba bean is an important pulse. It provides proteins for the human diet and is used in industrial foodstuffs, such as flours. Drought stress severely reduces the yield of faba bean, and this can be efficiently overcome through the identification and application of key genes in response to drought. In this study, PacBio and Illumina RNA sequencing techniques were used to identify the key pathways and candidate genes involved in drought stress response. During seed germination, a total of 17,927 full-length transcripts and 12,760 protein-coding genes were obtained. There were 1676 and 811 differentially expressed genes (DEGs) between the varieties E1 and C105 at 16 h and 64 h under drought stress, respectively. Six and nine KEGG pathways were significantly enriched at 16 h and 64 h under drought stress, which produced 40 and 184 nodes through protein-protein interaction (PPI) analysis, respectively. The DEGs of the PPI nodes were involved in the ABA (abscisic acid) and MAPK (mitogen-activated protein kinase) pathways, N-glycosylation, sulfur metabolism, and sugar metabolism. Furthermore, the ectopic overexpression of a key gene, AAT, encoding aspartate aminotransferase (AAT), in tobacco, enhanced drought tolerance. The activities of AAT and peroxidase (POD), the contents of cysteine and isoleucine, were increased, and the contents of malonaldehyde (MDA) and water loss decreased in the overexpressed plants. This study provides a novel insight into genetic response to drought stress and some candidate genes for drought tolerance genetic improvements in this plant.

Transcriptomic and metabolomic insights into the antimony stress response of tall fescue (Festuca arundinacea)

Antimony (Sb) is a toxic heavy metal that severely inhibits plant growth and development and threatens human health. Tall fescue, one of the most widely used grasses, has been reported to tolerate heavy metal stress. However, the adaptive mechanisms of Sb stress in tall fescue remain largely unknown. In this study, transcriptomic and metabolomic techniques were applied to elucidate the molecular mechanism of the Sb stress response in tall fescue. These results showed that the defense process in tall fescue was rapidly triggered during the early stages of Sb stress. Sb stress had toxic effects on tall fescue, and the cell wall and voltage-gated channels are crucial for regulating Sb permeation into the cells. In addition, the pathway of glycine, serine and threonine metabolism may play key roles in the Sb stress response of tall fescue. Genes such as ALDH7A1 and AGXT2 and metabolites such as aspartic acid, pyruvic acid, and biuret, which are related to biological processes and pathways, were key genes and compounds in the Sb stress response of tall fescue. Therefore, the regulatory mechanisms of specific genes and pathways should be investigated further to improve Sb stress tolerance.

Comprehensive analysis of the aldehyde dehydrogenase gene family in Phaseolus vulgaris L. and their response to saline-alkali stress

Background

Aldehyde dehydrogenase (ALDH) scavenges toxic aldehyde molecules by catalyzing the oxidation of aldehydes to carboxylic acids. Although ALDH gene family members in various plants have been extensively studied and were found to regulate plant response to abiotic stress, reports on ALDH genes in the common bean (Phaseolus vulgaris L.) are limited. In this study, we aimed to investigate the effects of neutral (NS) and basic alkaline (AS) stresses on growth, physiological and biochemical indices, and ALDH activity, ALDH gene expression of common bean. In addition, We used bioinformatics techniques to analyze the physical and chemical properties, phylogenetic relationships, gene replication, collinearity, cis-acting elements, gene structure, motifs, and protein structural characteristics of PvALDH family members.

Results

We found that both NS and AS stresses weakened the photosynthetic performance of the leaves, induced oxidative stress, inhibited common bean growth, and enhanced the antioxidative system to scavenge reactive oxygen species. Furthermore, we our findings revealed that ALDH in the common bean actively responds to NS or AS stress by inducing the expression of PvALDH genes. In addition, using the established classification criteria and phylogenetic analysis, 27 PvALDHs were identified in the common bean genome, belonging to 10 ALDH families. The primary expansion mode of PvALDH genes was segmental duplication. Cis-acting elemental analysis showed that PvALDHs were associated with abiotic stress and phytohormonal responses. Gene expression analysis revealed that the PvALDH gene expression was tissue-specific. For instance, PvALDH3F1 and PvALDH3H1 were highly expressed in flower buds and flowers, respectively, whereas PvALDH3H2 and PvALDH2B4 were highly expressed in green mature pods and young pods, respectively. PvALDH22A1 and PvALDH11A2 were highly expressed in leaves and young trifoliates, respectively; PvALDH18B2 and PvALDH18B3 were highly expressed in stems and nodules, respectively; and PvALDH2C2 and PvALDH2C3 were highly expressed in the roots. PvALDHs expression in the roots responded positively to NS-AS stress, and PvALDH2C3, PvALDH5F1, and PvALDH10A1 were significantly (P < 0.05) upregulated in the roots.

Conclusion

These results indicate that AS stress causes higher levels of oxidative damage than NS stress, resulting in weaker photosynthetic performance and more significant inhibition of common bean growth. The influence of PvALDHs potentially modulates abiotic stress response, particularly in the context of saline-alkali stress. These findings establish a basis for future research into the potential roles of ALDHs in the common bean.

Integration of mRNA and miRNA analysis reveals the molecular mechanisms of sugar beet (Beta vulgaris L.) response to salt stress

The continuous increase of saline-alkali areas worldwide has led to the emergence of saline-alkali conditions, which are the primary abiotic stress or hindering the growth of plants. Beet is among the main sources of sugar, and its yield and sugar content are notably affected by saline-alkali stress. Despite sugar beet being known as a salt-tolerant crop, there are few studies on the mechanisms underlying its salt tolerance, and previous studies have mainly delineated the crop's response to stress induced by NaCl. Recently, advancements in miRNA-mRNA network analysis have led to an increased understanding of how plants, including sugar beet, respond to stress. In this study, seedlings of beet variety "N98122" were grown in the laboratory using hydroponics culture and were exposed to salt stress at 40 days of growth. According to the phenotypic adaptation of the seedlings' leaves from a state of turgidity to wilting and then back to turgidity before and after exposure, 18 different time points were selected to collect samples for analysis. Subsequently, based on the data of real-time quantitative PCR (qRT-PCR) of salt-responsive genes, the samples collected at the 0, 2.5, 7.5, and 16 h time points were subjected to further analysis with experimental materials. Next, mRNA-seq data led to the identification of 8455 differentially expressed mRNAs (DEMs) under exposure to salt stress. In addition, miRNA-seq based investigation retrieved 3558 miRNAs under exposure to salt stress, encompassing 887 known miRNAs belonging to 783 families and 2,671 novel miRNAs. With the integrated analysis of miRNA-mRNA network, 57 miRNA-target gene pairs were obtained, consisting of 55 DEMIs and 57 DEMs. Afterwards, we determined the pivotal involvement of aldh2b7, thic, and δ-oat genes in the response of sugar beet to the effect of salt stress. Subsequently, we identified the miRNAs novel-m035-5p and novel-m0365-5p regulating the aldh gene and miRNA novel-m0979-3p regulating the thic gene. The findings of miRNA and mRNA expression were validated by qRT-PCR.

Transcriptomics reveals a core transcriptional network of K-type cytoplasmic male sterility microspore abortion in wheat (Triticum aestivum L.)

BACKGROUND

Cytoplasmic male sterility (CMS) plays a crucial role in hybrid production. K-type CMS, a cytoplasmic male sterile line of wheat with the cytoplasms of Aegilops kotschyi, is widely used due to its excellent characteristics of agronomic performance, easy maintenance and easy restoration. However, the mechanism of its pollen abortion is not yet clear.

RESULTS

In this study, wheat K-type CMS MS(KOTS)-90-110 (MS line) and it's fertile near-isogenic line MR (KOTS)-90-110 (MR line) were investigated. Cytological analysis indicated that the anthers of MS line microspore nucleus failed to divide normally into two sperm nucleus and lacked starch in mature pollen grains, and the key abortive period was the uninucleate stage to dinuclear stage. Then, we compared the transcriptome of MS line and MR line anthers at these two stages. 11,360 and 5182 differentially expressed genes (DEGs) were identified between the MS and MR lines in the early uninucleate and binucleate stages, respectively. Based on GO enrichment and KEGG pathways analysis, it was evident that significant transcriptomic differences were "plant hormone signal transduction", "MAPK signaling pathway" and "spliceosome". We identified 17 and 10 DEGs associated with the IAA and ABA signal transduction pathways, respectively. DEGs related to IAA signal transduction pathway were downregulated in the early uninucleate stage of MS line. The expression level of DEGs related to ABA pathway was significantly upregulated in MS line at the binucleate stage compared to MR line. The determination of plant hormone content and qRT-PCR further confirmed that hormone imbalance in MS lines. Meanwhile, 1 and 2 DEGs involved in ABA and Ethylene metabolism were also identified in the MAPK cascade pathway, respectively; the significant up regulation of spliceosome related genes in MS line may be another important factor leading to pollen abortion.

CONCLUSIONS

We proposed a transcriptome-mediated pollen abortion network for K-type CMS in wheat. The main idea is hormone imbalance may be the primary factor, MAPK cascade pathway and alternative splicing (AS) may also play important regulatory roles in this process. These findings provided intriguing insights for the molecular mechanism of microspore abortion in K-type CMS, and also give useful clues to identify the crucial genes of CMS in wheat.

Wheat adaptation to environmental stresses under climate change: Molecular basis and genetic improvement

Wheat (Triticum aestivum) is a staple food for about 40% of the world's population. As the global population has grown and living standards improved, high yield and improved nutritional quality have become the main targets for wheat breeding. However, wheat production has been compromised by global warming through the more frequent occurrence of extreme temperature events, which have increased water scarcity, aggravated soil salinization, caused plants to be more vulnerable to diseases, and directly reduced plant fertility and suppressed yield. One promising option to address these challenges is the genetic improvement of wheat for enhanced resistance to environmental stress. Several decades of progress in genomics and genetic engineering has tremendously advanced our understanding of the molecular and genetic mechanisms underlying abiotic and biotic stress responses in wheat. These advances have heralded what might be considered a "golden age" of functional genomics for the genetic improvement of wheat. Here, we summarize the current knowledge on the molecular and genetic basis of wheat resistance to abiotic and biotic stresses, including the QTLs/genes involved, their functional and regulatory mechanisms, and strategies for genetic modification of wheat for improved stress resistance. In addition, we also provide perspectives on some key challenges that need to be addressed.

Genome-wide characterization and gene expression analyses of ALDH gene family in response to drought stress in moso bamboo (Phyllostachys edulis)

Aldehyde dehydrogenase (ALDH) superfamily, comprising enzymes dependent on NAD+ or NADP+, plays an important role in controlling plant growth and development, as well as in responsing to phytohormone and environmental stress. These enzymes possess the ability to prevent toxic effects of aldehydes by converting them into their corresponding carboxylic acids. However, the potential function of ALDH genes in moso bamboo (Phyllostachys edulis) remains largely unknown. In this study, the ALDH gene superfamily in moso bamboo was analyzed through genome-wide screening, the evolutionary relationship of expansion genes was conducted. Tissue-specific expression patterns of ALDH genes were observed in 26 different tissues. Plant hormone and environmental stress responsive cis-elements were identified in the promoter of ALDH genes, which were supported by public databases data on the expression patterns under various abiotic stresses and hormone treatments. ALDH activity was increased in moso bamboo seedlings exposed to drought, compared to control condition. Furthermore, PeALDH2B2 was found to physically interact with PeGPB1 in response to drought. Overall, the study provides a comprehensive analysis of the ALDH family in moso bamboo and contributes to our understanding of the function of ALDH genes in growth, development, and adaptation to drought stresses.

Duplicate Genes Contribute to Variability in Abiotic Stress Resistance in Allopolyploid Wheat

Gene duplication is a universal biological phenomenon that drives genomic variation and diversity, plays a crucial role in plant evolution, and contributes to innovations in genetic engineering and crop development. Duplicated genes participate in the emergence of novel functionality, such as adaptability to new or more severe abiotic stress resistance. Future crop research will benefit from advanced, mechanistic understanding of the effects of gene duplication, especially in the development and deployment of high-performance, stress-resistant, elite wheat lines. In this review, we summarize the current knowledge of gene duplication in wheat, including the principle of gene duplication and its effects on gene function, the diversity of duplicated genes, and how they have functionally diverged. Then, we discuss how duplicated genes contribute to abiotic stress response and the mechanisms of duplication. Finally, we have a future prospects section that discusses the direction of future efforts in the short term regarding the elucidation of replication and retention mechanisms of repetitive genes related to abiotic stress response in wheat, excellent gene function research, and practical applications.

Unravelling the molecular mechanism underlying drought stress response in chickpea via integrated multi-omics analysis

Drought stress affects growth and productivity significantly in chickpea. An integrated multi-omics analysis can provide a better molecular-level understanding of drought stress tolerance. In the present study, comparative transcriptome, proteome and metabolome analyses of two chickpea genotypes with contrasting responses to drought stress, ICC 4958 (drought-tolerant, DT) and ICC 1882 (drought-sensitive, DS), was performed to gain insights into the molecular mechanisms underlying drought stress response/tolerance. Pathway enrichment analysis of differentially abundant transcripts and proteins suggested the involvement of glycolysis/gluconeogenesis, galactose metabolism, and starch and sucrose metabolism in the DT genotype. An integrated multi-omics analysis of transcriptome, proteome and metabolome data revealed co-expressed genes, proteins and metabolites involved in phosphatidylinositol signaling, glutathione metabolism and glycolysis/gluconeogenesis pathways, specifically in the DT genotype under drought. These stress-responsive pathways were coordinately regulated by the differentially abundant transcripts, proteins and metabolites to circumvent the drought stress response/tolerance in the DT genotype. The QTL-hotspot associated genes, proteins and transcription factors may further contribute to improved drought tolerance in the DT genotype. Altogether, the multi-omics approach provided an in-depth understanding of stress-responsive pathways and candidate genes involved in drought tolerance in chickpea.

Wide-Range Portrayal of AP2/ERF Transcription Factor Family in Maize (Zea mays L.) Development and Stress Responses

The APETALA2/Ethylene-Responsive Transcriptional Factors containing conservative AP2/ERF domains constituted a plant-specific transcription factor (TF) superfamily, called AP2/ERF. The configuration of the AP2/ERF superfamily in maize has remained unresolved. In this study, we identified the 229 AP2/ERF genes in the latest (B73 RefGen_v5) maize reference genome. Phylogenetic classification of the ZmAP2/ERF family members categorized it into five clades, including 27 AP2 (APETALA2), 5 RAV (Related to ABI3/VP), 89 DREB (dehydration responsive element binding), 105 ERF (ethylene responsive factors), and a soloist. The duplication events of the paralogous genes occurred from 1.724-25.855 MYA, a key route to maize evolution. Structural analysis reveals that they have more introns and few exons. The results showed that 32 ZmAP2/ERFs regulate biotic stresses, and 24 ZmAP2/ERFs are involved in responses towards abiotic stresses. Additionally, the expression analysis showed that DREB family members are involved in plant sex determination. The real-time quantitative expression profiling of ZmAP2/ERFs in the leaves of the maize inbred line B73 under ABA, JA, salt, drought, heat, and wounding stress revealed their specific expression patterns. Conclusively, this study unveiled the evolutionary pathway of ZmAP2/ERFs and its essential role in stress and developmental processes. The generated information will be useful for stress resilience maize breeding programs.

Aldehyde dehydrogenase superfamily in sorghum: genome-wide identification, evolution, and transcript profiling during development stages and stress conditions

BACKGROUND

Aldehyde dehydrogenases (ALDHs) are a family of NAD(P)⁺ dependent enzymes that detoxify aldehydes by promoting their oxidation to respective carboxylic acids. The role of ALDH enzymes in various plant species has been extensively studied, revealing their critical role in salinity, drought, heat, and heavy metal stress tolerance. Despite their physiological significance, ALDH genes in Sorghum bicolor have yet to be studied thoroughly.

RESULTS

In this study, a total of 19 ALDH genes have been identified that have been grouped into ten families based on the criteria of the ALDH gene nomenclature committee. Segmental duplication assisted more in the enhancement of SbALDH gene family members than tandem duplication. All the identified SbALDH members made a cluster with monocot rice and maize in the phylogenetic tree rather than dicot species, suggesting the pre-eudicot-monocot separation of the ALDH superfamily members. The gene structure and protein domain were found to be mostly conserved in separate phylogenetic classes, indicating that each family played an important role in evolution. Expression analysis revealed that several SbALDHs were expressed in various tissues, developmental stages, and in response to abiotic stresses, indicating that they can play roles in plant growth, development, or stress adaptation. Interestingly, the majority of the SbALDH genes were found to be highly responsive to drought stress, and the SbALDH18B1 transcript showed maximum enhancement in all the stress conditions. The presence of cis-acting elements (mainly ABRE and MBS) in the promoter region of these genes might have a significant role in drought tolerance.

CONCLUSIONS

Our findings add to the current understanding, evolutionary history, and contribution of SbALDHs in stress tolerance, and smooth the path of further functional validation of these genes.

Evolution, family expansion, and functional diversification of plant aldehyde dehydrogenases

Aldehyde dehydrogenases (ALDHs) act as "aldehyde scavengers" in plants, eliminating reactive aldehydes and hence performing a crucial part in response to stress. ALDH has been specified multiple activities since its identification in the mammalian system 72 years ago. But the most widely researched role in plants is their engagement in stress tolerance. Multiple ALDH families are found in both animals and plants, and many genes are substantially conserved within these two evolutionary diverse taxa, yet both have their unique members/families. A total of twenty-four ALDH protein family has been reported across organisms, where plants contain fourteen families. Surprisingly, the number of genes in the ALDH superfamily has risen in the higher plants because of genome duplication and expansion, indicating the functional versatilely. Observed expansion in the ALDH isoforms might provide high plasticity in their actions to achieve diversified roles in the plant. The physiological importance and functional diversity of ALDHs including plant development and environmental stress adaptability, and their evolution in plants has been studied extensively. Future investigations need to focus on evaluating the individual and interconnecting function of multiple ALDH isoforms across organisms in providing plants with proper development, maturation, and adaptability against harsh environmental conditions.

Multi-Omics-Based Identification and Functional Characterization of Gh_A06G1257 Proves Its Potential Role in Drought Stress Tolerance in Gossypium hirsutum

Cotton is one of the most important fiber crops globally. Despite this, various abiotic stresses, including drought, cause yield losses. We used transcriptome profiles to investigate the co-expression patterns of gene networks associated with drought stress tolerance. We identified three gene modules containing 3,567 genes highly associated with drought stress tolerance. Within these modules, we identified 13 hub genes based on intramodular significance, for further validation. The yellow module has five hub genes (Gh_A07G0563, Gh_D05G0221, Gh_A05G3716, Gh_D12G1438, and Gh_D05G0697), the brown module contains three hub genes belonging to the aldehyde dehydrogenase (ALDH) gene family (Gh_A06G1257, Gh_A06G1256, and Gh_D06G1578), and the pink module has five hub genes (Gh_A02G1616, Gh_D12G2599, Gh_D07G2232, Gh_A02G0527, and Gh_D07G0629). Based on RT-qPCR results, the Gh_A06G1257 gene has the highest expression under drought stress in different plant tissues and it might be the true candidate gene linked to drought stress tolerance in cotton. Silencing of Gh_A06G1257 in cotton leaves conferred significant sensitivity in response to drought stress treatments. Overexpression of Gh_A06G1257 in Arabidopsis also confirms its role in drought stress tolerance. L-valine, Glutaric acid, L-proline, L-Glutamic acid, and L-Tryptophan were found to be the most significant metabolites playing roles in drought stress tolerance. These findings add significantly to existing knowledge of drought stress tolerance mechanisms in cotton.

Recognizing the hidden half in wheat: root system attributes associated with drought tolerance

Improving drought tolerance in wheat is crucial for maintaining productivity and food security. Roots are responsible for the uptake of water from soil, and a number of root traits are associated with drought tolerance. Studies have revealed many quantitative trait loci and genes controlling root development in plants. However, the genetic dissection of root traits in response to drought in wheat is still unclear. Here, we review crop root traits associated with drought, key genes governing root development in plants, and quantitative trait loci and genes regulating root system architecture under water-limited conditions in wheat. Deep roots, optimal root length density and xylem diameter, and increased root surface area are traits contributing to drought tolerance. In view of the diverse environments in which wheat is grown, the balance among root and shoot traits, as well as individual and population performance, are discussed. The known functions of key genes provide information for the genetic dissection of root development of wheat in a wide range of conditions, and will be beneficial for molecular marker development, marker-assisted selection, and genetic improvement in breeding for drought tolerance.

Recent Development on Plant Aldehyde Dehydrogenase Enzymes and Their Functions in Plant Development and Stress Signaling

Abiotic and biotic stresses induce the formation of reactive oxygen species (ROS), which subsequently causes the excessive accumulation of aldehydes in cells. Stress-derived aldehydes are commonly designated as reactive electrophile species (RES) as a result of the presence of an electrophilic α, β-unsaturated carbonyl group. Aldehyde dehydrogenases (ALDHs) are NAD(P)⁺-dependent enzymes that metabolize a wide range of endogenous and exogenous aliphatic and aromatic aldehyde molecules by oxidizing them to their corresponding carboxylic acids. The ALDH enzymes are found in nearly all organisms, and plants contain fourteen ALDH protein families. In this review, we performed a critical analysis of the research reports over the last decade on plant ALDHs. Newly discovered roles for these enzymes in metabolism, signaling and development have been highlighted and discussed. We concluded with suggestions for future investigations to exploit the potential of these enzymes in biotechnology and to improve our current knowledge about these enzymes in gene signaling and plant development.

Morpho-physiological and molecular characterization of drought tolerance traits in Gossypium hirsutum genotypes under drought stress

Drought stress is one of the major abiotic stresses affecting lint yield and fibre quality in cotton. With increase in population, degrading natural resources and frequent drought occurrences, development of high yielding, drought tolerant cotton cultivars is critical for sustainable cotton production across countries. Six Gossypium hirsutum genotypes identified for drought tolerance, wider adaptability and better fibre quality traits were characterized for various morpho-physiological and biochemical characters and their molecular basis was investigated under drought stress. Under drought conditions, genotypes revealed statistically significant differences for all the morpho-physiological and biochemical traits. The interaction (genotype × treatment) effects were highly significant for root length, excised leaf water loss and cell membrane thermostability indicating differential interaction of genotypes under control and stress conditions. Correlation studies revealed that under drought stress, relative water content had significant positive correlation with root length and root-to-shoot ratio while it had significant negative correlation with excised leaf water loss, epicuticular wax, proline, potassium and total soluble sugar content. Analysis of expression of fourteen drought stress related genes under water stress indicated that both ABA dependent and ABA independent mechanisms of drought tolerance might be operating differentially in the studied genotypes. IC325280 and LRA5166 exhibited ABA mediated expression of stress responsive genes and traits. Molecular basis of drought tolerance in IC357406, Suraj, IC259637 and CNH 28I genotypes could be attributed to ABA independent pathway. Based on physiological phenotyping, the genotypes IC325280 and IC357406 were identified to possess better root traits and LRA5166 was found to have enhanced cellular level tolerance. Variety Suraj exhibited good osmotic adjustment and better root traits to withstand water stress. The identified drought component trait(s) in specific genotypes would pave way for their pyramiding through marker assisted cotton breeding.

Coordinated mechanisms of leaves and roots in response to drought stress underlying full-length transcriptome profiling in Vicia sativa L

BACKGROUND

Common vetch (Vicia sativa L.) is an important self-pollinating annual forage legume and is of interest for drought prone regions as a protein source to feed livestock and human consumption. However, the development and production of common vetch are negatively affected by drought stress. Plants have evolved common or distinct metabolic pathways between the aboveground and underground in response to drought stress. Little is known regarding the coordinated response of aboveground and underground tissues of common vetch to drought stress.

RESULTS

Our results showed that a total of 30,427 full-length transcripts were identified in 12 samples, with an average length of 2278.89 bp. Global transcriptional profiles of the above 12 samples were then analysed via Illumina-Seq. A total of 3464 and 3062 differentially expressed genes (DEGs) were identified in the leaves and roots, respectively. Gene Ontology (GO) enrichment analyses identified that the dehydrin genes and Δ¹-pyrroline-5-carboxylate synthase were induced for the biosynthesis of proline and water conservation. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis results indicated that the DEGs were significantly enriched in hormone signal transduction, starch and sucrose metabolism, and arginine and proline metabolism, and various drought response candidate genes were also identified. Abscisic acid (ABA; the AREB/ABF-SnRK2 pathway) regulates the activity of AMY3 and BAM1 to induce starch degradation in leaves and increase carbon export to roots, which may be associated with the drought stress responses in common vetch. Among the co-induced transcription factors (TFs), AREB/ABF, bHLH, MYB, WRKY, and AP2/ERF had divergent expression patterns and may be key in the crosstalk between leaves and roots during adaption to drought stress. In transgenic yeast, the overexpression of four TFs increased yeast tolerance to osmotic stresses.

CONCLUSION

The multipronged approach identified in the leaves and roots broadens our understanding of the coordinated mechanisms of drought response in common vetch, and further provides targets to improve drought resistance through genetic engineering.

Exogenous methylglyoxal enhances the reactive aldehyde detoxification capability and frost-hardiness of wheat

Cold-acclimation is essential for the development of adequate frost-hardiness in cereals and therefore sudden freezes can cause considerable damage to the canopy. However, timely adding of an appropriate signal in the absence of cold acclimation may also harden wheat for the upcoming freeze. The feasibility of the promising signal molecule methylglyoxal was tested here for such applications and the signal mechanism was studied in bread wheat (Triticum aestivum L.) and durum wheat (Triticum turgidum L. ssp. durum). Spraying with 10 mM methylglyoxal did not decrease the fresh weight and photosynthetic parameters in most wheat varieties at growth temperature (21 °C). Photosynthetic parameters even improved and chlorophyll content increased in some cases. Increased transcript level of glutathione-S-transferases and omega-3 fatty acid desaturases was detected by qPCR 6 h after the last methylglyoxal spray. Aldo-keto reductase and glyoxalase enzyme activities, as well as sorbitol content of wheat plants increased 24 h after the last 10 mM methylglyoxal spray in most of the cultivars. These mechanisms may explain the increased freezing survival of methylglyoxal pretreated wheat plants from less than 10% to over 30%. Our results demonstrate that exogenous methylglyoxal treatment can be safely added to wheat plants as preparatory treatment without detrimental effects but inducing some of the stress-protective mechanisms, which contribute to frost-hardiness.

Genome-wide Association Study of a Panel of Vietnamese Rice Landraces Reveals New QTLs for Tolerance to Water Deficit During the Vegetative Phase

BACKGROUND

Drought tolerance is a major challenge in breeding rice for unfavorable environments. In this study, we used a panel of 180 Vietnamese rice landraces genotyped with 21,623 single-nucleotide polymorphism markers to perform a genome-wide association study (GWAS) for different drought response and recovery traits during the vegetative stage. These landraces originate from different geographical locations and are adapted to different agrosystems characterized by contrasted water regimes. Vietnamese landraces are often underrepresented in international panels used for GWAS, but they can contain original genetic determinants related to drought resistance.

RESULTS

The panel of 180 rice varieties was phenotyped under greenhouse conditions for several drought-related traits in an experimental design with 3 replicates. Plants were grown in pots for 4 weeks and drought-stressed by stopping irrigation for an additional 4 weeks. Drought sensitivity scores and leaf relative water content were measured throughout the drought stress. The recovery capacity was measured 2 weeks after plant rewatering. Several QTLs associated with these drought tolerance traits were identified by GWAS using a mixed model with control of structure and kinship. The number of detected QTLs consisted of 14 for leaf relative water content, 9 for slope of relative water content, 12 for drought sensitivity score, 3 for recovery ability and 1 for relative crop growth rate. This set of 39 QTLs actually corresponded to a total of 17 different QTLs because 9 were simultaneously associated with two or more traits, which indicates that these common loci may have pleiotropic effects on drought-related traits. No QTL was found in association with the same traits in both the indica and japonica subpanels. The possible candidate genes underlying the quantitative trait loci are reviewed.

CONCLUSIONS

Some of the identified QTLs contain promising candidate genes with a function related to drought tolerance by osmotic stress adjustment.

Molecular and phenotypic characterization of transgenic wheat and sorghum events expressing the barley alanine aminotransferase

The expression of a barley alanine aminotransferase gene impacts agronomic outcomes in a C3 crop, wheat. The use of nitrogen-based fertilizers has become one of the major agronomic inputs in crop production systems. Strategies to enhance nitrogen assimilation and flux in planta are being pursued through the introduction of novel genetic alleles. Here an Agrobacterium-mediated approach was employed to introduce the alanine aminotransferase from barley (Hordeum vulgare), HvAlaAT, into wheat (Triticum aestivum) and sorghum (Sorghum bicolor), regulated by either constitutive or root preferred promoter elements. Plants harboring the transgenic HvAlaAT alleles displayed increased alanine aminotransferase (alt) activity. The enhanced alt activity impacted height, tillering and significantly boosted vegetative biomass relative to controls in wheat evaluated under hydroponic conditions, where the phenotypic outcome across these parameters varied relative to time of year study was conducted. Constitutive expression of HvAlaAT translated to elevation in wheat grain yield under field conditions. In sorghum, expression of HvAlaAT enhanced enzymatic activity, but no changes in phenotypic outcomes were observed. Taken together these results suggest that positive agronomic outcomes can be achieved through enhanced alt activity in a C3 crop, wheat. However, the variability observed across experiments under greenhouse conditions implies the phenotypic outcomes imparted by the HvAlaAT allele in wheat may be impacted by environment.

Induction of the PDH bypass and upregulation of the ALDH7B4 in plants treated with herbicides inhibiting amino acid biosynthesis

Imazamox and glyphosate represent two classes of herbicides that inhibit the activity of acetohydroxyacid synthase in the branched-chain amino acid biosynthesis pathway and the activity of 5-enolpyruvylshikimate-3-phosphate synthase in the aromatic amino acid biosynthesis pathway, respectively. However, it is still unclear how imazamox and glyphosate lead to plant death. Both herbicides inhibit amino-acid biosynthesis and were found to induce ethanol fermentation in plants, but an Arabidopsis mutant deficient in alcohol dehydrogenase 1 was neither more susceptible nor more resistant than the wild-type to the herbicides. In this study, we investigated the effects of the amino acid biosynthesis inhibitors, imazamox and glyphosate, on the pyruvate dehydrogenase bypass reaction and fatty acid metabolism in A. thaliana. We found that the pyruvate dehydrogenase bypass was upregulated following the treatment by the two herbicides. Our results suggest that the Arabidopsis aldehyde dehydrogenase 7B4 gene might be participating in the pyruvate dehydrogenase bypass reaction. We evaluated the potential role of the aldehyde dehydrogenase 7B4 upon herbicide treatment in the plant defence mechanism. Plants that overexpressed the ALDH7B4 gene accumulated less soluble sugars, starch, and fatty acids and grew better than the wild-type after herbicide treatment. We discuss how the upregulation of the ALDH7B4 alleviates the effects of the herbicides, potentially through the detoxification of the metabolites produced in the pyruvate dehydrogenase bypass.

Genome-wide characterization and expression analysis of the aldehyde dehydrogenase (ALDH) gene superfamily under abiotic stresses in cotton

In plants, aldehyde dehydrogenases (ALDHs) function as 'aldehyde scavengers' by removing reactive aldehydes and thus play important roles in stress responses. To date, 30 ALDHs have been identified in Gossypium raimondii, whereas ALDHs have not been studied in Gossypium arboreum or in tetraploid cotton. In this study, we identified 30, 59 and 59 aldehyde dehydrogenase (ALDH) genes from G. arboreum, G. hirsutum and G. barbadense, respectively. Gene structure analysis revealed that members of the same family exhibit similar exon-intron structures and structural domains, and all members of the ALDH18 family possess a distinct AA-kinase domain. Synteny analysis showed that segmental and tandem duplications have played an important role in the expansion and evolution of ALDHs in cotton. Phylogenetic and synteny analysis between G. arboreum and G. raimondii demonstrated that all GaALDHs and GrALDHs are orthologous and that most GaALDHs are located in syntenic blocks corresponding to those of G. raimondii, implying that these genes appeared before the divergence of G. arboreum and G. raimondii and that no expansion of the ALDH superfamily has occurred in these two cotton species. Quantitative real-time PCR analysis revealed that the majority of GaALDHs and GhALDHs are up-regulated under conditions of high salinity and drought, indicating that these genes may be stress responsive. The findings of this study, based on genome-wide identification of ALDHs in Gossypium and analysis of their evolution and expression, provide a foundation for further analysis of ALDHs and suggest potential target genes for improving stress resistance in cotton.

Genome-wide characterization of the aldehyde dehydrogenase gene superfamily in soybean and its potential role in drought stress response

BACKGROUND

Aldehyde dehydrogenases (ALDHs) represent a group of enzymes that detoxify aldehydes by facilitating their oxidation to carboxylic acids, and have been shown to play roles in plant response to abiotic stresses. However, the comprehensive analysis of ALDH superfamily in soybean (Glycine max) has been limited.

RESULTS

In present study, a total of 53 GmALDHs were identified in soybean, and grouped into 10 ALDH families according to the ALDH Gene Nomenclature Committee and phylogenetic analysis. These groupings were supported by their gene structures and conserved motifs. Soybean ALDH superfamily expanded mainly by whole genome duplication/segmental duplications. Gene network analysis identified 1146 putative co-functional genes of 51 GmALDHs. Gene Ontology (GO) enrichment analysis suggested the co-functional genes of these 51 GmALDHs were enriched (FDR < 1e-3) in the process of lipid metabolism, photosynthesis, proline catabolism, and small molecule catabolism. In addition, 22 co-functional genes of GmALDHs are related to plant response to water deprivation/water transport. GmALDHs exhibited various expression patterns in different soybean tissues. The expression levels of 13 GmALDHs were significantly up-regulated and 14 down-regulated in response to water deficit. The occurrence frequencies of three drought-responsive cis-elements (ABRE, CRT/DRE, and GTGCnTGC/G) were compared in GmALDH genes that were up-, down-, or non-regulated by water deficit. Higher frequency of these three cis-elements was observed for the group of up-regulated GmALDH genes as compared to the group of down- or non- regulated GmALDHs by drought stress, implying their potential roles in the regulation of soybean response to drought stress.

CONCLUSIONS

A total of 53 ALDH genes were identified in soybean genome and their phylogenetic relationships and duplication patterns were analyzed. The potential functions of GmALDHs were predicted by analyses of their co-functional gene networks, gene expression profiles, and cis-regulatory elements. Three GmALDH genes, including GmALDH3H2, GmALDH12A2 and GmALDH18B3, were highly induced by drought stress in soybean leaves. Our study provides a foundation for future investigations of GmALDH gene function in soybean.

Comparative genomic study of ALDH gene superfamily in Gossypium: A focus on Gossypium hirsutum under salt stress

Aldehyde dehydrogenases (ALDHs) are a superfamily of enzymes which play important role in the scavenging of active aldehydes molecules. In present work, a comprehensive whole-genomic study of ALDH gene superfamily was carried out for an allotetraploid cultivated cotton species, G. hirsutum, as well as in parallel relative to their diploid progenitors, G. arboreum and G. raimondii. Totally, 30 and 58 ALDH gene sequences belong to 10 families were identified from diploid and allotetraploid cotton species, respectively. The gene structures among the members from same families were highly conserved. Whole-genome duplication and segmental duplication might be the major driver for the expansion of ALDH gene superfamily in G. hirsutum. In addition, the expression patterns of GhALDH genes were diverse across tissues. Most GhALDH genes were induced or repressed by salt stress in upland cotton. Our observation shed lights on the molecular evolutionary properties of ALDH genes in diploid cottons and their alloallotetraploid derivatives. It may be useful to mine key genes for improvement of cotton response to salt stress.

Proteomic analysis of soybean root including hypocotyl during recovery from drought stress

Soybean is a nutritionally important crop that exhibits reductions in growth and yield under drought stress. To investigate soybean responses during post-drought recovery, a gel-free proteomic technique was used. Two-day-old soybeans were treated with drought stress for 4days and recovered for 4days. Root including hypocotyl was collected during the drought treatment and recovery stage. Seedling growth was suppressed by drought stress, but recovered following stress removal. The malondialdehyde content increased under drought stress, but decreased during the recovery stage. A total of 792 and 888 proteins were identified from the control and recovering seedlings, respectively. The identified proteins were related to functional categories of stress, hormone metabolism, cell wall, secondary metabolism, and fermentation. Cluster analysis indicated that abundances of peroxidase and aldehyde dehydrogenase were highly changed in the seedlings during the post-drought recovery. The activity of peroxidase decreased under drought conditions, but increased during recovery. In contrast, the activity of aldehyde dehydrogenase was increased in response to drought stress, but decreased during the recovery stage. These results suggest that peroxidase and aldehyde dehydrogenase play key roles in post-drought recovery in soybean by scavenging toxic reactive oxygen species and reducing the load of harmful aldehydes.

BIOLOGICAL SIGNIFICANCE

Post-drought recovery response mechanisms in soybean root including hypocotyl were analyzed using gel-free proteomic technique. A total of 643 common proteins between control and drought-stressed soybeans changed significantly in abundance over time. The proteins that changed during post-drought recovery were assigned to protein, stress, hormone metabolism, secondary metabolism, cell wall, redox, and glycolysis categories. The analysis revealed that peroxidase and aldehyde dehydrogenase were increased in protein abundance under drought stress. The enzyme activity of peroxidase decreased under drought but increased during recovery. The activity of aldehyde dehydrogenase was increased under drought stress but decreased during recovery stage. Peroxidase and aldehyde dehydrogenase reduce the toxic reactive oxygen species and aldehydes from the plant, respectively, and help to recover from drought stress. The study provides information about post-drought recovery mechanism in soybean.

Transcriptomic and Metabolomic Studies Disclose Key Metabolism Pathways Contributing to Well-maintained Photosynthesis under the Drought and the Consequent Drought-Tolerance in Rice

In contrast to wild species, drought-tolerance in crops requires a fully functional metabolism during drought (particularly photosynthetic processes). However, the link between drought-tolerance, photosynthetic regulation during drought, and the associated transcript and metabolic foundation, remains largely unknown. For this study, we used two rice cultivars with contrasting drought-tolerance (the drought-intolerant cultivar IRAT109 and the drought-tolerant cultivar IAC1246) to explore transcript and metabolic responses to long-term drought. The drought-tolerant cultivar represented higher osmotic adjustment and antioxidant capacity, as well as higher relative photosynthesis rate under a progressive drought stress occurred in a modified field with shallow soil-layers. A total of 4059 and 2677 differentially expressed genes (DEGs) were identified in IRAT109 and IAC1246 between the drought and well-watered conditions, respectively. A total of 69 and 47 differential metabolites (DMs) were identified between the two treatments in IRAT109 and IAC1246, respectively. Compared to IRAT109, the DEGs of IAC1246 displayed enhanced regulatory amplitude during drought. We found significant correlations between DEGs and the osmolality and total antioxidant capacity (AOC) of both cultivars. During the early stages of drought, we detected up-regulation of DEGs in IAC1246 related to photosynthesis, in accordance with its higher relative photosynthesis rate. The contents of six differential metabolites were correlated with the osmotic potential and AOC. Moreover, they were differently regulated between the two cultivars. Particularly, up-regulations of 4-hydroxycinnamic acid and ferulic acid were consistent with the performance of photosynthesis-related DEGs at the early stages of drought in IAC1246. Therefore, 4-hydroxycinnamic acid and ferulic acid were considered as key metabolites for rice drought-tolerance. DEGs involved in pathways of these metabolites are expected to be good candidate genes to improve drought-tolerance. In conclusion, well-maintained photosynthesis under drought should contribute to improved drought-tolerance in rice. Metabolites play vital roles in protecting photosynthesis under dehydration via osmotic adjustments and/or antioxidant mechanisms. A metabolite-based method was thus an effective way to explore drought candidate genes. Metabolic accompanied by transcript responses to drought stress should be further studied to find more useful metabolites, pathways, and genes.