Comparative physiological, transcriptomic, and WGCNA analyses reveal the key genes and regulatory pathways associated with drought tolerance in Tartary buckwheat

Changes in the Content of Dietary Fiber, Flavonoids, and Phenolic Acids in the Morphological Parts of Fagopyrum tataricum (L.) Gaertn Under Drought Stress

BACKGROUND

Tartary buckwheat is a plant recognized for its resistance to various environmental stresses. Due to its valuable source of phenolic compounds, Fagopyrum tataricum is also characterized as a medicinal plant; therefore, the aim of this study was to investigate the drought stress for the levels of phenolic compounds in the morphological parts of the plant.

METHODS

This experiment was conducted in 7 L pots under laboratory conditions. Phenolic compounds were identified using a UHPLC-MS chromatography system. Antioxidant activity was assessed using well-known methods, including the DPPH scavenging activity and ferrous ion chelating activity.

RESULTS

In Tartary buckwheat leaves, stems, seeds, and husks, 57 phenolic compounds were identified, with a predominance of quercetin 3-rutinoside, quercetin, kaempferol-3-rutinoside, kaempferol, and derivatives of coumaric acid. It was observed that the Tartary buckwheat samples subjected to drought stress exhibited a slight decrease in the majority of individual phenolic compounds.

CONCLUSIONS

The measurement of biological parameters indicated that plant regeneration after drought stress demonstrated a rapid recovery, which can be a positive response to the progression of climate changes.

Genome-wide associated study identifies FtPMEI13 gene conferring drought resistance in Tartary buckwheat

Tartary buckwheat is known for its ability to adapt to intricate growth conditions and to possess robust stress-resistant properties. Nevertheless, it remains vulnerable to drought stress, which can lead to reduced crop yield. To identify potential genes involved in drought resistance, a genome-wide association study on drought tolerance in Tartary buckwheat germplasm was conducted. A gene encoding pectin methylesterase inhibitors protein (FtPMEI13) was identified, which is not only associated with drought tolerance but also showed induction during drought stress and abscisic acid (ABA) treatment. Further analysis revealed that overexpression of FtPMEI13 leads to improved drought tolerance by altering the activities of antioxidant enzymes and the levels of osmotically active metabolites. Additionally, FtPMEI13 interacts with pectin methylesterase (PME) and inhibits PME activity in response to drought stress. Our results suggest that FtPMEI13 may inhibit the activity of FtPME44/FtPME61, thereby affecting pectin methylesterification in the cell wall and modulating stomatal closure in response to drought stress. Yeast one-hybrid, dual-luciferase assays, and electrophoretic mobility shift assays demonstrated that an ABA-responsive transcription factor FtbZIP46, could bind to the FtPMEI13 promoter, enhancing FtPMEI13 expression. Further analysis indicated that Tartary buckwheat accessions with the genotype resulting in higher FtPMEI13 and FtbZIP46 expression exhibited higher drought tolerance compared to the others. This suggests that this genotype has potential for application in Tartary buckwheat breeding. Furthermore, the natural variation of FtPMEI13 was responsible for decreased drought tolerance during Tartary buckwheat domestication. Taken together, these results provide basic support for Tartary buckwheat breeding for drought tolerance.

Unveiling Salt Tolerance Mechanisms and Hub Genes in Alfalfa (Medicago sativa L.) Through Transcriptomic and WGCNA Analysis

Alfalfa (Medicago sativa L.), an important forage crop with high nutritional value and good palatability, plays a vital role in the development of animal husbandry in China. In Northeast China, there are vast areas of saline-alkali land that remain undeveloped. Given that alfalfa is a highly adaptable forage crop, exploring its salt tolerance at the molecular transcriptional level and identifying salt-tolerant genes has great significance for breeding salt-resistant alfalfa varieties. This also provides valuable genetic resources for better utilization of saline-alkali land. In this study, we conducted two rounds of screening on 41 alfalfa varieties and identified WL168 as a salt-sensitive variety and Longmu801 as a salt-tolerant variety. After 7 days of 300 mM salt stress, both varieties showed a decreasing trend in plant height, fresh weight, and dry weight over time, but Longmu801 demonstrated better water retention ability compared to WL168. Chlorophyll content also declined, but chlorophyll a and total chlorophyll levels in Longmu801 were higher than in WL168. Hydrogen peroxide and malondialdehyde levels increased overall, but Longmu801 had significantly lower levels than WL168 under prolonged stress. Both varieties showed increasing trends in soluble sugars, proline, and antioxidant enzymes (SOD, POD, CAT), with Longmu801 significantly outperforming WL168. This suggests that the two varieties share similar growth and physiological response mechanisms, with their differences primarily arising from variations in indicator levels. In the above, comparisons between varieties were conducted based on the relative values of the indicators in relation to their controls. Transcriptomic analysis revealed that under salt stress, Longmu801 had 16,485 differentially expressed genes (DEGs) relative to its control, while WL168 had 18,726 DEGs compared to its control. Among these, 2164 DEGs shared the same expression trend, with GO functions enriched in response to oxidative stress, nucleus, plasma membrane, and others. The KEGG pathways were enriched in phenylpropanoid biosynthesis, protein processing in the endoplasmic reticulum, starch and sucrose metabolism, and others. This suggests that alfalfa's transcriptional response mechanism to salt stress involves these pathways. Additionally, the variety-specific DEGs were also enriched in the same KEGG pathways and GO functions, indicating that the differences between the two varieties stem from their unique stress-responsive DEGs, while their overall mechanisms for coping with stress remain similar. To further identify salt stress-related genes, this study conducted WGCNA analysis using 32,683 genes and physiological indicators. Six modules closely related to physiological traits were identified, and the top five genes ranked by degree in each module were selected as hub genes. Further analysis of these hub genes identified five genes directly related to salt stress: Msa085011, Msa0605650, Msa0397400, Msa1258740, and Msa0958830. Mantel test analysis revealed that these genes showed strong correlations with physiological indicators. This study will provide important insights for breeding salt-tolerant alfalfa varieties.

Transcriptional Profiling Analysis Providing Insights into the Harsh Environments Tolerance Mechanisms of Krascheninnikovia arborescens

Krascheninnikovia arborescens, an endemic shrub in China, thrives in desertification-prone environments due to its robust biomass, hairy leaves, and extensive root system. It is vital for ecological restoration and serves as a valuable forage plant. This study explored the molecular mechanisms underlying K. arborescens' adaptation to desert conditions, focusing on its physiological, biochemical, and transcriptomic responses to drought, salt, and alkali stresses. The results revealed that the three stresses have significant impacts on the photosynthetic, antioxidant, and ion balance systems of the plants, with the alkali stress inducing the most pronounced changes and differential gene expression. The clustering and functional enrichment analyses of differentially expressed genes (DEGs) highlighted the enrichment of the induced genes in pathways related to plant hormone signaling, phenylpropanoid biosynthesis, and transcription factors following stress treatments. In these pathways, the synthesis and signal transduction of abscisic acid (ABA) and ethylene, as well as the flavonoid and lignin synthesis pathways, and transcription factors such as MYB, AP2/ERF, bHLH, NAC, and WRKY responded actively to the stress and played pivotal roles. Through the WGCNA analysis, 10 key modules were identified, with the yellow module demonstrating a high correlation with the ABA and anthocyanin contents, while the turquoise module was enriched in the majority of genes related to hormone and phenylpropanoid pathways. The analysis of hub genes in these modules highlighted the significant roles of the bHLH and MYB transcription factors. These findings could offer new insights into the molecular mechanisms that enable the adaptation of K. arborescens to desert environments, enhancing our understanding of how other desert plants adapt to harsh conditions. These insights are crucial for exploring and utilizing high-quality forage plant germplasm resources and ecological development, with the identified candidate genes serving as valuable targets for further research on stress-resistant genes.

Advancements in multi-omics for nutraceutical enhancement and traits improvement in buckwheat

Buckwheat (Fagopyrum spp.) is a typical pseudocereal, valued for its extensive nutraceutical potential as well as its centuries-old cultivation. Tartary buckwheat and common buckwheat have been used globally and become well-known nutritious foods due to their high quantities of: proteins, flavonoids, and minerals. Moreover, its increasing demand makes it critical to improve nutraceutical, traits and yield. In this review, bioactive compounds accumulated in buckwheat were comprehensively evaluated according to their chemical structure, properties, and physiological function. Biosynthetic pathways of flavonoids, phenolic acids, and fagopyrin were methodically summarized, with the regulation of flavonoid biosynthesis. Although there are classic synthesis pathways presented in the previous research, the metabolic flow of how these certain compounds are being synthesized in buckwheat still remains uncovered. The functional genes involved in the biosynthesis of flavonols, stress response, and plant development were identified based on multi-omics research. Furthermore, it delves into the applications of multi-omics in improving buckwheat's agronomic traits, including: yield, nutritional content, stress resilience, and bioactive compounds biosynthesis. While pangenomics combined with other omics to mine elite genes, the regulatory network and mechanism of specific agronomic traits and biosynthetic of bioactive components, and developing a more efficient genetic transformation system for genetic engineering require further investigation for the execution of breeding designs aimed at enhancing desirable traits in buckwheat. This critical review will provide a comprehensive understanding of multi-omics for nutraceutical enhancement and traits improvement in buckwheat.

Comprehensive Transcriptome and Proteome Analyses Reveal the Drought Responsive Gene Network in Potato Roots

The root system plays a decisive role in the growth and development of plants. The water requirement of a root system depends strongly on the plant species. Potatoes are an important food and vegetable crop grown worldwide, especially under irrigation in arid and semi-arid regions. However, the expected impact of global warming on potato yields calls for an investigation of genes related to root development and drought resistance signaling pathways in potatoes. In this study, we investigated the molecular mechanisms of different drought-tolerant potato root systems in response to drought stress under controlled water conditions, using potato as a model. We analyzed the transcriptome and proteome of the drought-sensitive potato cultivar Atlantic (Atl) and the drought-tolerant cultivar Qingshu 9 (Q9) under normal irrigation (CK) and weekly drought stress (D). The results showed that a total of 14,113 differentially expressed genes (DEGs) and 5596 differentially expressed proteins (DEPs) were identified in the cultivars. A heat map analysis of DEGs and DEPs showed that the same genes and proteins in Atl and Q9 exhibited different expression patterns under drought stress. Weighted gene correlation network analysis (WGCNA) showed that in Atl, Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG)-enriched pathways were related to pyruvate metabolism and glycolysis, as well as cellular signaling and ion transmembrane transporter protein activity. However, GO terms and KEGG-enriched pathways related to phytohormone signaling and the tricarboxylic acid cycle were predominantly enriched in Q9. The present study provides a unique genetic resource to effectively explore the functional genes and uncover the molecular regulatory mechanism of the potato root system in response to drought stress.

Physiological responses to drought stress of three pine species and comparative transcriptome analysis of Pinus yunnanensis var. pygmaea

Drought stress can significantly affect plant growth, development, and yield. Fewer comparative studies have been conducted between different species of pines, particularly involving Pinus yunnanensis var. pygmaea (P. pygmaea). In this study, the physiological indices, photosynthetic pigment and related antioxidant enzyme changes in needles from P. pygmaea, P. elliottii and P. massoniana under drought at 0, 7, 14, 21, 28 and 35 d, as well as 7 days after rehydration, were measured. The PacBio single-molecule real-time (SMRT) and Illumina RNA sequencing were used to uncover the gene expression differences in P. pygmaea under drought and rehydration conditions. The results showed that the total antioxidant capacity (TAOC) of P. pygmaea was significantly higher than P. massoniana and P. elliottii. TAOC showed a continuous increase trend across all species. Soluble sugar (SS), starch content and non-structural carbohydrate (NSC) of all three pines displayed a "W" pattern, declining initially, increasing, and then decreasing again. P. pygmaea exhibits stronger drought tolerance and greater recovery ability under prolonged drought conditions. Through the PacBio SMRT-seq, a total of 50,979 high-quality transcripts were generated, and 6,521 SSR and 5,561 long non-coding RNAs (LncRNAs) were identified. A total of 2310, 1849, 5271, 5947, 7710, and 6854 differentially expressed genes (DEGs) were identified compared to the control (Pp0D) in six pair-wise comparisons of treatment versus control. bHLH, NAC, ERF, MYB_related, C3H transcription factors (TFs) play an important role in drought tolerance of P. pygmaea. KEGG enrichment analysis and Gene set enrichment analysis (GSEA) analysis showed that P. pygmaea may respond to drought by enhancing metabolic processes such as ABA signaling pathway, alpha-linolenic acid. Weighted gene co-expression network analysis (WGCNA) revealed GST, CAT, LEC14B, SEC23 were associated with antioxidant enzyme activity and TAOC. This study provides a basis for further research on drought tolerance differences among coniferous species.

New strategies to address world food security and elimination of malnutrition: future role of coarse cereals in human health

As we face increasing challenges of world food security and malnutrition, coarse cereals are coming into favor as an important supplement to human staple foods due to their high nutritional value. In addition, their functional components, such as flavonoids and polyphenols, make them an important food source for healthy diets. However, we lack a systematic understanding of the importance of coarse cereals for world food security and nutritional goals. This review summarizes the worldwide cultivation and distribution of coarse cereals, indicating that the global area for coarse cereal cultivation is steadily increasing. This paper also focuses on the special adaptive mechanisms of coarse cereals to drought and discusses the strategies to improve coarse cereal crop yields from the perspective of agricultural production systems. The future possibilities, challenges, and opportunities for coarse cereal production are summarized in the face of food security challenges, and new ideas for world coarse cereal production are suggested.

Transcriptome and coexpression network analysis reveals properties and candidate genes associated with grape (Vitis vinifera L.) heat tolerance

Temperature is one of the most important environmental factors affecting grape season growth and geographical distribution. With global warming and the increasing occurrence of extreme high-temperature weather, the impact of high temperatures on grape production has intensified. Therefore, identifying the molecular regulatory networks and key genes involved in grape heat tolerance is crucial for improving the resistance of grapes and promoting sustainable development in grape production. In this study, we observed the phenotypes and cellular structures of four grape varieties, namely, Thompson Seedless (TS), Brilliant Seedless (BS), Jumeigui (JMG), and Shine Muscat (SM), in the naturally high-temperature environment of Turpan. Heat tolerance evaluations were conducted. RNA-seq was performed on 36 samples of the four varieties under three temperature conditions (28°C, 35°C, and 42°C). Through differential expression analysis revealed the fewest differentially expressed genes (DEGs) between the heat-tolerant materials BS and JMG, and the DEGs common to 1890 were identified among the four varieties. The number of differentially expressed genes within the materials was similar, with a total of 3767 common DEGs identified among the four varieties. KEGG enrichment analysis revealed that fatty acid metabolism, starch and sucrose metabolism, plant hormone signal transduction, the MAPK signaling pathway, and plant-pathogen interactions were enriched in both between different temperatures of the same material, and between different materials of the same temperature. We also conducted statistical and expression pattern analyses of differentially expressed transcription factors. Based on Weighted correlation network analysis (WGCNA), four specific modules highly correlated with grape heat tolerance were identified by constructing coexpression networks. By calculating the connectivity of genes within the modules and expression analysis, six candidate genes (VIT_04s0044g01430, VIT_17s0000g09190, VIT_01s0011g01350, VIT_01s0011g03330, VIT_04s0008g05610, and VIT_16s0022g00540) related to heat tolerance were discovered. These findings provide a theoretical foundation for further understanding the molecular mechanisms of grape heat tolerance and offer new gene resources for studying heat tolerance in grapes.

Comparative transcriptomic analyses of two sugarcane Saccharum L. cultivars differing in drought tolerance

Sugarcane (Saccharum spp.) is an important cash crop, and drought is an important factors limiting its yield. To study the drought resistance mechanism of sugarcane, the transcriptomes of two sugarcane varieties with different levels of drought resistance were compared under different water shortage levels. The results showed that the transcriptomes of the two varieties were significantly different. The differentially expressed genes were enriched in starch and sucrose metabolism, linoleic acid metabolism, glycolysis/gluconeogenesis, and glyoxylate and dicarboxylate metabolic pathways. Unique trend genes of the variety with strong drought resistance (F172) were significantly enriched in photosynthesis, mitogen-activated protein kinases signaling pathway, biosynthesis of various plant secondary metabolites, and cyanoamino acid metabolism pathways. Weighted correlation network analysis indicated that the blue4 and plum1 modules correlated with drought conditions, whereas the tan and salmon4 modules correlated with variety. The unique trend genes expressed in F172 and mapped to the blue4 module were enriched in photosynthesis, purine metabolism, starch and sucrose metabolism, beta-alanine metabolism, photosynthesis-antenna proteins, and plant hormone signal transduction pathways. The expression of genes involved in the photosynthesis-antenna protein and photosynthesis pathways decreased in response to water deficit, indicating that reducing photosynthesis might be a means for sugarcane to respond to drought stress. The results of this study provide insights into drought resistance mechanisms in plants, and the related genes and metabolic pathways identified may be helpful for sugarcane breeding in the future.

Integrating Full-Length Transcriptome and RNA Sequencing of Siberian Wildrye (Elymus sibiricus) to Reveal Molecular Mechanisms in Response to Drought Stress

Drought is one of the most significant limiting factors affecting plant growth and development on the Qinghai-Tibet Plateau (QTP). Mining the drought-tolerant genes of the endemic perennial grass of the QTP, Siberian wildrye (Elymus sibiricus), is of great significance to creating new drought-resistant varieties which can be used in the development of grassland livestock and restoring natural grassland projects in the QTP. To investigate the transcriptomic responsiveness of E. sibiricus to drought stress, PEG-induced short- and long-term drought stress was applied to two Siberian wildrye genotypes (drought-tolerant and drought-sensitive accessions), followed by third- and second-generation transcriptome sequencing analysis. A total of 40,708 isoforms were detected, of which 10,659 differentially expressed genes (DEGs) were common to both genotypes. There were 2107 and 2498 unique DEGs in the drought-tolerant and drought-sensitive genotypes, respectively. Additionally, 2798 and 1850 DEGs were identified in the drought-tolerant genotype only under short- and long-term conditions, respectively. DEGs numbering 1641 and 1330 were identified in the drought-sensitive genotype only under short- and long-term conditions, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that all the DEGs responding to drought stress in E. sibiricus were mainly associated with the mitogen-activated protein kinase (MAKP) signaling pathway, plant hormone signal transduction, the linoleic acid metabolism pathway, the ribosome pathway, and plant circadian rhythms. In addition, Nitrate transporter 1/Peptide transporter family protein 3.1 (NPF3.1) and Auxin/Indole-3-Acetic Acid (Aux/IAA) family protein 31(IAA31) also played an important role in helping E. sibiricus resist drought. This study used transcriptomics to investigate how E. sibiricus responds to drought stress, and may provide genetic resources and references for research into the molecular mechanisms of drought resistance in native perennial grasses and for breeding drought-tolerant varieties.