Transcriptome Profiling of Maize (Zea mays L.) Leaves Reveals Key Cold-Responsive Genes, Transcription Factors, and Metabolic Pathways Regulating Cold Stress Tolerance at the Seedling Stage

Improving chilling tolerance of peanut seedlings by enhancing antioxidant-modulated ROS scavenging ability, alleviating photosynthetic inhibition, and mobilizing nutrient absorption

Peanut production is threatened by climate change. Damage to seedlings from low temperatures in early spring can limit yield. Plant adaptations to chilling stress remain unclear in peanut seedlings. It is essential to understand how peanut acquires chilling tolerance. We evaluated effects of chilling stress on growth and recovery of peanut seedlings. We compared and analysed biological characteristics, antioxidants, photosynthesis, biochemical and physiological responses, and nutrient absorption at varying levels of chilling. Compared with chilling-sensitive FH18, the reduced impact of chilling stress on chilling-tolerant NH5 was associated with reduced ROS accumulation, higher ascorbate peroxidase activity and soluble sugar content, lower soluble protein content, and smaller reductions in nutrient content during stress. After removal of chilling stress, FH18 had significant accumulation of O2 •- and H2O2, which decreased photosynthesis, nutrient absorption, and transport. ROS-scavenging reduced damage from chilling stress, allowed remobilization of nutrients, improved chilling tolerance, and restored plant functioning after chilling stress removal. These findings provide a reference for targeted research on peanut seedling tolerance to chilling and lay the foundation for bioinformatics-based research on peanut chilling tolerance mechanisms.

Transcriptome Analysis Reveals POD as an Important Indicator for Assessing Low-Temperature Tolerance in Maize Radicles during Germination

Low-temperature stress (TS) limits maize (Zea mays L.) seed germination and agricultural production. Exposure to TS during germination inhibits radicle growth, triggering seedling emergence disorders. Here, we aimed to analyse the changes in gene expression in the radicles of maize seeds under TS by comparing Demeiya1 (DMY1) and Zhengdan958 (ZD958) (the main Northeast China cultivars) and exposing them to two temperatures: 15 °C (control) and 5 °C (TS). TS markedly decreased radicle growth as well as fresh and dry weights while increasing proline and malondialdehyde contents in both test varieties. Under TS treatment, the expression levels of 5301 and 4894 genes were significantly different in the radicles of DMY1 and ZD958, respectively, and 3005 differentially expressed genes coexisted in the radicles of both varieties. The phenylpropanoid biosynthesis pathway was implicated within the response to TS in maize radicles, and peroxidase may be an important indicator for assessing low-temperature tolerance during maize germination. Peroxidase-encoding genes could be important candidate genes for promoting low-temperature resistance in maize germinating radicles. We believe that this study enhances the knowledge of mechanisms of response and adaptation of the maize seed germination process to TS and provides a theoretical basis for efficiently assessing maize seed low-temperature tolerance and improving maize adversity germination performance.

Transcriptome profiling of Bergenia purpurascens under cold stress

Bergenia purpurascens is an important medicinal, edible and ornamental plant. It generally grows in high-altitude areas with complex climates. There have been no reports about how B. purpurascens survives under cold stress. Here, the B. purpurascens under low temperature were subjected to transcriptomics analysis to explore the candidate genes and pathways that involved in the cold tolerance of B. purpurascens. Compared with the control treatment, we found 9,600 up-regulated differentially expressed genes (DEGs) and 7,055 down-regulated DEGs. A significant number of DEGs were involved in the Ca2+ signaling pathway, mitogen-activated protein kinase (MAPK) cascade, plant hormone signaling pathway, and lipid metabolism. A total of 400 transcription factors were found to respond to cold stress, most of which belonged to the MYB and AP2/ERF families. Five novel genes were found to be potential candidate genes involved in the cold tolerance of B. purpurascens. The study provide insights into further investigation of the molecular mechanism of how B. purpurascens survives under cold stress.

Photosynthesis regulation, cell membrane stabilization and methylglyoxal detoxification seems major altered pathways under cold stress as revealed by integrated multi-omics meta-analysis

Climate change has altered cold weather patterns, resulting in irregular cold weather conditions, and changing the global plant distribution pattern affecting plant development processes resulting in severe yield losses. Although molecular mechanisms and interconnections are quite well studied, a cumulative understanding of plant responses to cold stress (CS) is still lacking. Through meta-analysis, integration of data at the multi-omics level and its correlation with known physiological changes to map and understand the global changes in response to CS was made. Meta-analysis was conducted using the metafor R package program based on physiological parameters like relative electrolytic leakage, malondialdehyde, soluble sugar, proline and antioxidant enzymes activity. Proline and soluble sugars showed the highest (> 1.5 mean fold) change over control thus qualifying as global markers for studying CS. Surprisingly most up-regulated (> 15-fold) DEGs corresponded with the dehydrin family and glyoxalase superfamily proteins. Functional annotations of DEGs corresponded with photosynthesis and glycolysis pathway. Proteins responsible for cell signalling and increased soluble sugars were common in all the datasets studied thus correlating with the transcriptome and proteomic data. Proline and soluble sugars were positively regulated in all the metabolomics datasets. This study supported the earlier known players like proline and soluble sugars. Surprisingly, a new player glyoxalase seems to be contributing in CS.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01367-9.

Unravelling the genetic framework associated with grain quality and yield-related traits in maize (Zea mays L.)

Maize serves as a crucial nutrient reservoir for a significant portion of the global population. However, to effectively address the growing world population's hidden hunger, it is essential to focus on two key aspects: biofortification of maize and improving its yield potential through advanced breeding techniques. Moreover, the coordination of multiple targets within a single breeding program poses a complex challenge. This study compiled mapping studies conducted over the past decade, identifying quantitative trait loci associated with grain quality and yield related traits in maize. Meta-QTL analysis of 2,974 QTLs for 169 component traits (associated with quality and yield related traits) revealed 68 MQTLs across different genetic backgrounds and environments. Most of these MQTLs were further validated using the data from genome-wide association studies (GWAS). Further, ten MQTLs, referred to as breeding-friendly MQTLs (BF-MQTLs), with a significant phenotypic variation explained over 10% and confidence interval less than 2 Mb, were shortlisted. BF-MQTLs were further used to identify potential candidate genes, including 59 genes encoding important proteins/products involved in essential metabolic pathways. Five BF-MQTLs associated with both quality and yield traits were also recommended to be utilized in future breeding programs. Synteny analysis with wheat and rice genomes revealed conserved regions across the genomes, indicating these hotspot regions as validated targets for developing biofortified, high-yielding maize varieties in future breeding programs. After validation, the identified candidate genes can also be utilized to effectively model the plant architecture and enhance desirable quality traits through various approaches such as marker-assisted breeding, genetic engineering, and genome editing.

Comparative analysis of tissue-specific genes in maize based on machine learning models: CNN performs technically best, LightGBM performs biologically soundest

Introduction: With the advancement of RNA-seq technology and machine learning, training large-scale RNA-seq data from databases with machine learning models can generally identify genes with important regulatory roles that were previously missed by standard linear analytic methodologies. Finding tissue-specific genes could improve our comprehension of the relationship between tissues and genes. However, few machine learning models for transcriptome data have been deployed and compared to identify tissue-specific genes, particularly for plants. Methods: In this study, an expression matrix was processed with linear models (Limma), machine learning models (LightGBM), and deep learning models (CNN) with information gain and the SHAP strategy based on 1,548 maize multi-tissue RNA-seq data obtained from a public database to identify tissue-specific genes. In terms of validation, V-measure values were computed based on k-means clustering of the gene sets to evaluate their technical complementarity. Furthermore, GO analysis and literature retrieval were used to validate the functions and research status of these genes. Results: Based on clustering validation, the convolutional neural network outperformed others with higher V-measure values as 0.647, indicating that its gene set could cover as many specific properties of various tissues as possible, whereas LightGBM discovered key transcription factors. The combination of three gene sets produced 78 core tissue-specific genes that had previously been shown in the literature to be biologically significant. Discussion: Different tissue-specific gene sets were identified due to the distinct interpretation strategy for machine learning models and researchers may use multiple methodologies and strategies for tissue-specific gene sets based on their goals, types of data, and computational resources. This study provided comparative insight for large-scale data mining of transcriptome datasets, shedding light on resolving high dimensions and bias difficulties in bioinformatics data processing.

Advances of Apetala2/Ethylene Response Factors in Regulating Development and Stress Response in Maize

Apetala2/ethylene response factor (AP2/ERF) is one of the largest families of transcription factors, regulating growth, development, and stress response in plants. Several studies have been conducted to clarify their roles in Arabidopsis and rice. However, less research has been carried out on maize. In this review, we systematically identified the AP2/ERFs in the maize genome and summarized the research progress related to AP2/ERF genes. The potential roles were predicted from rice homologs based on phylogenetic and collinear analysis. The putative regulatory interactions mediated by maize AP2/ERFs were discovered according to integrated data sources, implying that they involved complex networks in biological activities. This will facilitate the functional assignment of AP2/ERFs and their applications in breeding strategy.

A single-nucleotide polymorphism in WRKY33 promoter is associated with the cold sensitivity in cultivated tomato

Natural variations in cis-regulatory regions often affect crop phenotypes by altering gene expression. However, the mechanism of how promoter mutations affect gene expression and crop stress tolerance is still poorly understood. In this study, by analyzing RNA-sequencing (RNA-Seq) data and reverse transcription quantitative real-time PCR validation in the cultivated tomato and its wild relatives, we reveal that the transcripts of WRKY33 are almost unchanged in cold-sensitive cultivated tomato Solanum lycopersicum L. 'Ailsa Craig' but are significantly induced in cold-tolerant wild tomato relatives Solanum habrochaites LA1777 and Solanum pennellii LA0716 under cold stress. Overexpression of SlWRKY33 or ShWRKY33 positively regulates cold tolerance in tomato. Variant of the critical W-box in SlWRKY33 promoter results in the loss of self-transcription function of SlWRKY33 under cold stress. Analysis integrating RNA-Seq and chromatin immunoprecipitation sequencing data reveals that SlWRKY33 directly targets and induces multiple kinases, transcription factors, and molecular chaperone genes, such as CDPK11, MYBS3, and BAG6, thus enhancing cold tolerance. In addition, heat- and Botrytis-induced WRKY33s expression in both wild and cultivated tomatoes are independent of the critical W-box variation. Our findings suggest nucleotide polymorphism in cis-regulatory regions is crucial for different cold sensitivity between cultivated and wild tomato plants.

Exogenous 5-aminolevulinic acid alleviates low-temperature injury by regulating glutathione metabolism and β-alanine metabolism in tomato seedling roots

Food availability represents a major worldwide concern due to climate change and population growth. Low-temperature stress (LTS) severely restricts the growth of tomato seedlings. Exogenous 5-aminolevulinic acid (ALA) can alleviate the harm of abiotic stress including LTS; however, data on its protective mechanism on tomato seedling roots, the effects of organelle structure, and the regulation of metabolic pathways under LTS are lacking. In this study, we hope to fill the above gaps by exploring the effects of exogenous ALA on morphology, mitochondrial ultrastructure, reactive oxygen species (ROS) enrichment, physiological indicators, related gene expression, and metabolic pathway in tomato seedlings root under LTS. Results showed that ALA pretreatment could increase the activity of antioxidant enzymes and the content of antioxidant substances in tomato seedlings roots under LTS to scavenge the massively accumulated ROS, thereby protecting the mitochondrial structure of roots and promoting root development under LTS. Combined transcriptomic and metabolomic analysis showed that exogenous ALA pretreatment activated the glutathione metabolism and β-alanine metabolism of tomato seedling roots under LTS, further enhanced the scavenging ability of tomato seedling roots to ROS, and improved the low-temperature tolerance of tomato seedlings. The findings provide a new insight into the regulation of the low-temperature tolerance of tomato by exogenous ALA.

Dynamic changes in the transcriptome landscape of Arabidopsis thaliana in response to cold stress

Plants must reprogram gene expression to adapt constantly changing environmental temperatures. With the increased occurrence of extremely low temperatures, the negative effects on plants, especially on growth and development, from cold stress are becoming more and more serious. In this research, strand-specific RNA sequencing (ssRNA-seq) was used to explore the dynamic changes in the transcriptome landscape of Arabidopsis thaliana exposed to cold temperatures (4°C) at different times. In total, 7,623 differentially expressed genes (DEGs) exhibited dynamic temporal changes during the cold treatments. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the DEGs were enriched in cold response, secondary metabolic processes, photosynthesis, glucosinolate biosynthesis, and plant hormone signal transduction pathways. Meanwhile, long non-coding RNAs (lncRNAs) were identified after the assembly of the transcripts, from which 247 differentially expressed lncRNAs (DElncRNAs) and their potential target genes were predicted. 3,621 differentially alternatively spliced (DAS) genes related to RNA splicing and spliceosome were identified, indicating enhanced transcriptome complexity due to the alternative splicing (AS) in the cold. In addition, 739 cold-regulated transcription factors (TFs) belonging to 52 gene families were identified as well. This research analyzed the dynamic changes of the transcriptome landscape in response to cold stress, which reveals more complete transcriptional patterns during short- and long-term cold treatment and provides new insights into functional studies of that how plants are affected by cold stress.

Integrated methylome and transcriptome analysis unravel the cold tolerance mechanism in winter rapeseed(Brassica napus L.)

BACKGROUND

Cytosine methylation, the main type of DNA methylation, regulates gene expression in plant response to environmental stress. The winter rapeseed has high economic and ecological value in China's Northwest, but the DNA methylation pattern of winter rapeseed during freezing stress remains unclear.

RESULT

This study integrated the methylome and transcriptome to explore the genome-scale DNA methylation pattern and its regulated pathway of winter rapeseed, using freezing-sensitive (NF) and freezing-resistant (NS) cultivars.The average methylation level decreased under freezing stress, and the decline in NF was stronger than NS after freezing stress. The CG methylation level was the highest among the three contexts of CG, CHG, and CHH. At the same time, the CHH proportion was high, and the methylation levels were highest 2 kb up/downstream, followed by the intron region. The C sub-genomes methylation level was higher than the A sub-genomes. The methylation levels of chloroplast and mitochondrial DNA were much lower than the B. napus nuclear DNA, the SINE methylation level was highest among four types of transposable elements (TEs), and the preferred sequence of DNA methylation did not change after freezing stress. A total of 1732 differentially expressed genes associated with differentially methylated genes (DMEGs) were identified in two cultivars under 12 h and 24 h in three contexts by combining whole-genome bisulfite sequencing( and RNA-Seq data. Function enrichment analysis showed that most DMEGs participated in linoleic acid metabolism, alpha-linolenic acid metabolism, carbon fixation in photosynthetic organisms, flavonoid biosynthesis, and plant hormone signal transduction pathways. Meanwhile, some DMEGs encode core transcription factors in plant response to stress.

CONCLUSION

Based on the findings of DNA methylation, the freezing tolerance of winter rapeseed is achieved by enhanced signal transduction, lower lipid peroxidation, stronger cell stability, increased osmolytes, and greater reactive oxygen species (ROS) scavenging. These results provide novel insights into better knowledge of the methylation regulation of tolerance mechanism in winter rapeseed under freezing stress.

Full-length transcriptome analysis of maize root tips reveals the molecular mechanism of cold stress during the seedling stage

BACKGROUND

As maize originated in tropical or subtropical zones, most maize germplasm is extremely sensitive to low temperatures during the seedling stage. Clarifying the molecular mechanism of cold acclimation would facilitate the breeding of cold tolerant maize varieties, which is one of the major sustainability factors for crop production. To meet this goal, we investigated two maize inbred lines with contrasting levels of cold tolerance at the seedling stage (IL85, a cold tolerant line; B73, a cold sensitive line), and performed full-length transcriptome sequencing on the root tips of seedlings before and after 24 h of cold treatment.

RESULTS

We identified 152,263 transcripts, including 20,993 novel transcripts, and determined per-transcript expression levels. A total of 1,475 transcripts were specifically up-regulated in the cold tolerant line IL85 under cold stress. GO enrichment analysis revealed that 25 transcripts were involved in reactive oxygen species (ROS) metabolic processes and 15 transcripts were related to the response to heat. Eight genes showed specific differential alternative splicing (DAS) in IL85 under cold stress, and were mainly involved in amine metabolism. A total of 1,111 lncRNAs were further identified, 62 of which were up-regulated in IL85 or B73 under cold stress, and their corresponding target genes were enriched in protein phosphorylation.

CONCLUSIONS

These results provide new insights into the molecular mechanism of cold acclimation during the seedling stage in maize, and will facilitate the development of cultivars with improved cold stress tolerance.

Integrative Proteome and Phosphoproteome Profiling of Early Cold Response in Maize Seedlings

Cold limits the growth and yield of maize in temperate regions, but the molecular mechanism of cold adaptation remains largely unexplored in maize. To identify early molecular events during cold shock, maize seedlings were treated under 4 °C for 30 min and 2 h, and analyzed at both the proteome and phosphoproteome levels. Over 8500 proteins and 19,300 phosphopeptides were quantified. About 660 and 620 proteins were cold responsive at protein abundance or site-specific phosphorylation levels, but only 65 proteins were shared between them. Functional enrichment analysis of cold-responsive proteins and phosphoproteins revealed that early cold response in maize is associated with photosynthesis light reaction, spliceosome, endocytosis, and defense response, consistent with similar studies in Arabidopsis. Thirty-two photosynthesis proteins were down-regulated at protein levels, and 48 spliceosome proteins were altered at site-specific phosphorylation levels. Thirty-one kinases and 33 transcriptional factors were cold responsive at protein, phosphopeptide, or site-specific phosphorylation levels. Our results showed that maize seedlings respond to cold shock rapidly, at both the proteome and phosphoproteome levels. This study provides a comprehensive landscape at the cold-responsive proteome and phosphoproteome in maize seedlings that can be a significant resource to understand how C₄ plants respond to a sudden temperature drop.

Transcriptome analysis of the winter wheat Dn1 in response to cold stress

BACKGROUND

Heilongjiang Province has a long and cold winter season (the minimum temperature can reach -30 ℃), and few winter wheat varieties can safely overwinter. Dongnongdongmai1 (Dn1) is the first winter wheat variety that can safely overwinter in Heilongjiang Province. This variety fills the gap for winter wheat cultivation in the frigid region of China and greatly increases the land utilization rate. To understand the molecular mechanism of the cold response, we conducted RNA-sequencing analysis of Dn1 under cold stress.

RESULTS

Approximately 120,000 genes were detected in Dn1 under cold stress. The numbers of differentially expressed genes (DEGs) in the six comparison groups (0 ℃ vs. 5 ℃, -5 ℃ vs. 5 ℃, -10 ℃ vs. 5 ℃, -15 ℃ vs. 5 ℃, -20 ℃ vs. 5 ℃ and -25 ℃ vs. 5 ℃) were 11,313, 8313, 15,636, 13,671, 14,294 and 13,979, respectively. Gene Ontology functional annotation suggested that the DEGs under cold stress mainly had "binding", "protein kinase" and "catalytic" activities and were involved in "oxidation-reduction", "protein phosphorylation" and "carbohydrate metabolic" processes. Kyoto Encyclopedia of Genes and Genomes enrichment analysis indicated that the DEGs performed important functions in cold signal transduction and carbohydrate metabolism. In addition, major transcription factors (AP2/ERF, bZIP, NAC, WRKY, bHLH and MYB) participating in the Dn1 cold stress response were activated by low temperature.

CONCLUSION

This is the first study to explore the Dn1 transcriptome under cold stress. Our study comprehensively analysed the key genes involved in cold signal transduction and carbohydrate metabolism in Dn1 under cold stress. The results obtained by transcriptome analysis could help to further explore the cold resistance mechanism of Dn1 and provide basis for breeding of cold-resistant crops.

Higher Phytohormone Contents and Weaker Phytohormone Signal Transduction Were Observed in Cold-Tolerant Cucumber

Cucumbers (Cucumis sativus L.) originated from the South Asian subcontinent, and most of them are fragile to cold stress. In this study, we evaluated the cold tolerance of 115 cucumber accessions and screened out 10 accessions showing high resistance to cold stress. We measured and compared plant hormone contents between cold-tolerant cucumber CT90R and cold-sensitive cucumber CT57S in cold treatment. Most of the detected plant hormones showed significantly higher content in CT90R. To elucidate the role of plant hormones, we compared the leaf- and root-transcriptomes of CT90R with those of CT57S in cold stress treatment. In leaves, there were 1209 differentially expressed genes (DEGs) between CT90R and CT57S, while there were 703 in roots. These DEGs were not evenly distributed across the chromosomes and there were significant enrichments at particular positions, including qLTT6.2, a known QTL controlling cucumber cold tolerance. The GO and KEGG enrichment analysis showed that there was a significant difference in the pathway of plant hormone transductions between CT90R and CT57S in leaves. In short, genes involved in plant hormone transductions showed lower transcription levels in CT90R. In roots, the most significantly different pathway was phenylpropanoid biosynthesis. CT90R seemed to actively accumulate more monolignols by upregulating cinnamyl-alcohol dehydrogenase (CAD) genes. These results above suggest a new perspective on the regulation mechanism of cold tolerance in cucumbers.

Metabolic Insight into Cold Stress Response in Two Contrasting Maize Lines

Maize (Zea mays L.) is sensitive to a minor decrease in temperature at early growth stages, resulting in deteriorated growth at later stages. Although there are significant variations in maize germplasm in response to cold stress, the metabolic responses as stress tolerance mechanisms are largely unknown. Therefore, this study aimed at providing insight into the metabolic responses under cold stress at the early growth stages of maize. Two inbred lines, tolerant (B144) and susceptible (Q319), were subjected to cold stress at the seedling stage, and their corresponding metabolic profiles were explored. The study identified differentially accumulated metabolites in both cultivars in response to induced cold stress with nine core conserved cold-responsive metabolites. Guanosine 3′,5′-cyclic monophosphate was detected as a potential biomarker metabolite to differentiate cold tolerant and sensitive maize genotypes. Furthermore, Quercetin-3-O-(2″′-p-coumaroyl)sophoroside-7-O-glucoside, Phloretin, Phloretin-2′-O-glucoside, Naringenin-7-O-Rutinoside, L-Lysine, L-phenylalanine, L-Glutamine, Sinapyl alcohol, and Feruloyltartaric acid were regulated explicitly in B144 and could be important cold-tolerance metabolites. These results increase our understanding of cold-mediated metabolic responses in maize that can be further utilized to enhance cold tolerance in this significant crop.

Recent Advances in the Analysis of Cold Tolerance in Maize

Maize (Zea mays L.) is an annual grass that originated in tropical and subtropical regions of the New World. Maize is highly sensitive to cold stress during seed gemination and the seedling phase, which can lead to reductions in plant vigor and grain production. There are large differences in the morphological and physiological changes caused by cold stress among maize varieties. In general, cold tolerant varieties have a stronger ability to maintain such changes in traits related to seed germination, root phenotypes, and shoot photosynthesis. These morphological and physiological characteristics have been widely used to evaluate the cold tolerance of maize varieties in genetic analyses. In recent years, considerable progress has been made in elucidating the mechanisms of maize in response to cold tolerance. Several QTL, GWAS, and transcriptomic analyses have been conducted on various maize genotypes and populations that show large variations in cold tolerance, resulting in the discovery of hundreds of candidate cold regulation genes. Nevertheless, only a few candidate genes have been functionally characterized. In the present review, we summarize recent progress in molecular, physiological, genetic, and genomic analyses of cold tolerance in maize. We address the advantages of joint analyses that combine multiple genetic and genomic approaches to improve the accuracy of identifying cold regulated genes that can be further used in molecular breeding. We also discuss the involvement of long-distance signaling in plant cold tolerance. These novel insights will provide a better mechanistic understanding of cold tolerance in maize.