Leaf transcriptomic response mediated by cold stress in two maize inbred lines with contrasting tolerance levels

Advances and opportunities in unraveling cold-tolerance mechanisms in the world's primary staple food crops

Temperatures below or above optimal growth conditions are among the major stressors affecting productivity, end-use quality, and distribution of key staple crops including rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays L.). Among temperature stresses, cold stress induces cellular changes that cause oxidative stress and slowdown metabolism, limit growth, and ultimately reduce crop productivity. Perception of cold stress by plant cells leads to the activation of cold-responsive transcription factors and downstream genes, which ultimately impart cold tolerance. The response triggered in crops to cold stress includes gene expression/suppression, the accumulation of sugars upon chilling, and signaling molecules, among others. Much of the information on the effects of cold stress on perception, signal transduction, gene expression, and plant metabolism are available in the model plant Arabidopsis but somewhat lacking in major crops. Hence, a complete understanding of the molecular mechanisms by which staple crops respond to cold stress remain largely unknown. Here, we make an effort to elaborate on the molecular mechanisms employed in response to low-temperature stress. We summarize the effects of cold stress on the growth and development of these crops, the mechanism of cold perception, and the role of various sensors and transducers in cold signaling. We discuss the progress in cold tolerance research at the genome, transcriptome, proteome, and metabolome levels and highlight how these findings provide opportunities for designing cold-tolerant crops for the future.

Induction of stomatal opening following a night-chilling event alleviates physiological damage in mango trees

Chilling events have become more frequent with climate change and are a significant abiotic factor causing physiological damage to plants and, consequently, reducing crop yield. Like other tropical and subtropical plants, mango (Mangifera indica L.) is particularly sensitive to chilling events, especially if they are followed by bright sunny days. It was previously shown that in mango leaves stomatal opening is restricted in the morning following a night-chilling event. This impairment results in restraint of carbon assimilation and subsequently, photoinhibition and reactive oxygen species production, which leads to chlorosis and in severe cases, cell death. Our detailed physiological analysis showed that foliar application of the guard cell H+-ATPase activator, fusicoccin, in the morning after a cold night, mitigates the physiological damage from 'cold night-bright day' abiotic stress. This application restored stomatal opening, thereby enabling gas exchange, releasing the photosynthetic machinery from harmful excess photon energy, and improving the plant's overall physiological state. The mechanisms by which plants react to this abiotic stress are examined in this work. The foliar application of compounds that cause stomatal opening as a potential method of minimizing physiological damage due to night chilling is discussed.

A multi-organ maize metabolic model connects temperature stress with energy production and reducing power generation

Climate change has adversely affected maize productivity. Thereby, a holistic understanding of metabolic crosstalk among its organs is important to address this issue. Thus, we reconstructed the first multi-organ maize metabolic model, iZMA6517, and contextualized it with heat and cold stress transcriptomics data using expression distributed reaction flux measurement (EXTREAM) algorithm. Furthermore, implementing metabolic bottleneck analysis on contextualized models revealed differences between these stresses. While both stresses had reducing power bottlenecks, heat stress had additional energy generation bottlenecks. We also performed thermodynamic driving force analysis, revealing thermodynamics-reducing power-energy generation axis dictating the nature of temperature stress responses. Thus, a temperature-tolerant maize ideotype can be engineered by leveraging the proposed thermodynamics-reducing power-energy generation axis. We experimentally inoculated maize root with a beneficial mycorrhizal fungus, Rhizophagus irregularis, and as a proof-of-concept demonstrated its efficacy in alleviating temperature stress. Overall, this study will guide the engineering effort of temperature stress-tolerant maize ideotypes.

Hub Gene Mining and Co-Expression Network Construction of Low-Temperature Response in Maize of Seedling by WGCNA

Weighted gene co-expression network analysis (WGCNA) is a research method in systematic biology. It is widely used to identify gene modules related to target traits in multi-sample transcriptome data. In order to further explore the molecular mechanism of maize response to low-temperature stress at the seedling stage, B144 (cold stress tolerant) and Q319 (cold stress sensitive) provided by the Maize Research Institute of Heilongjiang Academy of Agricultural Sciences were used as experimental materials, and both inbred lines were treated with 5 °C for 0 h, 12 h, and 24 h, with the untreated material as a control. Eighteen leaf samples were used for transcriptome sequencing, with three biological replicates. Based on the above transcriptome data, co-expression networks of weighted genes associated with low-temperature-tolerance traits were constructed by WGCNA. Twelve gene modules significantly related to low-temperature tolerance at the seedling stage were obtained, and a number of hub genes involved in low-temperature stress regulation pathways were discovered from the four modules with the highest correlation with target traits. These results provide clues for further study on the molecular genetic mechanisms of low-temperature tolerance in maize at the seedling stage.

Transcriptomic analysis revealed the candidate metabolic pathways and genes associated with cold tolerance in a mutant without anthocyanin accumulation in common vetch (Vicia sativa L.)

Common vetch (Vicia sativa L.) is a leguminous crop used to feed livestock with vegetative organs or fertilize soils by returning to the field. Survival of fall-seeded plants is often affected by freezing damage during overwintering. This study aims to investigate the transcriptomic profiling in response to cold in a mutant with reduced accumulation of anthocyanins under normal growth and low-temperature conditions for understanding the underlying mechanisms. The mutant had increased cold a tolerance with higher survival rate and biomass during overwintering compared to the wild type, which led to increased forage production. Transcriptomic analysis in combination with qRT-PCR and physiological measurements revealed that reduced anthocyanins accumulation in the mutant resulted from reduced expression of serial genes involving in anthocyanin biosynthesis, which led to the altered metabolism, with an increased accumulation of free amino acids and polyamines. The higher levels of free amino acids and proline in the mutant under low temperature were associated with improved cold tolerance. The altered expression of some genes involved in ABA and GA signaling was also associated with increased cold tolerance in the mutant.

Comparative protein analysis of two maize genotypes with contrasting tolerance to low temperature

BACKGROUND

Low temperature (LT) stress is one of the major environmental stress factors affecting the growth and yield of maize (Zea mays L.). Hence, it is important to unravel the molecular mechanisms behind LT stress tolerance to improve molecular breeding in LT tolerant genotypes. In the present study, two maize genotypes viz. Gurez local from Kashmir Himalaya and tropical grown GM6, were dissected for their LT stress response in terms of accumulation of differentially regulated proteins (DRPs). Leaf proteome analysis at three-leaf stage of maize seedlings subjected to LT stress of 6 °C for a total of 12 h duration was performed using two dimensional gel electrophoresis (2D-PAGE) followed by subsequent identification of the proteins involved.

RESULTS

After MALDI-TOF (Matrix-assisted laser desorption/ionization-time of flight) and bioinformatics analysis, 19 proteins were successfully identified in Gurez local, while as 10 proteins were found to get successful identification in GM6. The interesting observations from the present investigation is the identification of three novel proteins viz. threonine dehydratase biosynthetic chloroplastic, thylakoidal processing peptidase 1 chloroplastic, and nodulin-like protein, whose role in abiotic stress tolerance, in general, and LT stress, in particular, has not been reported so far. It is important to highlight here that most of LT responsive proteins including the three novel proteins were identified from Gurez local only, owing to its exceptional LT tolerance. From the protein profiles, obtained in both genotypes immediately after LT stress perception, it was inferred that stress responsive protein accumulation and their expression fashion help the Gurez local in seedling establishment and withstand unfavorable conditions as compared to GM6. This was inferred from the findings of pathway enrichment analysis like regulation of seed growth, timing of floral transition, lipid glycosylation, and aspartate family amino acid catabolic processes, besides other key stress defense mechanisms. However, in GM6, metabolic pathways enriched were found to be involved in more general processes including cell cycle DNA replication and regulation of phenylpropanoid metabolism. Furthermore, majority of the qRT-PCR results of the selected proteins demonstrated positive correlation between protein levels and transcript abundance, thereby strengthening our findings.

CONCLUSIONS

In conclusion, our findings reported majority of the identified proteins in Gurez local exhibiting up-regulated pattern under LT stress as compared to GM6. Furthermore, three novel proteins induced by LT stress were found in Gurez local, requiring further functional validation. Therefore, our results offer more insights for elucidating the molecular networks mediating LT stress tolerance in maize.

Response of waxy maize (Zea mays L. var. ceratina Kulesh) leaf photosynthesis to low temperature during the grain-filling stage

Low temperature (LT) during the grain-filling stage is an important factor that affects the source-sink relationship and leads to yield loss in maize (Zea mays L). In this study, field and pot trials were conducted to investigate the effects of LT during the grain-filling stage on leaf photosynthesis, antioxidant system, hormones, and grain yield of waxy maize cultivars Suyunuo 5 (S5) and Yunuo 7 (Y7). The results showed that LT treatment inhibited the chlorophyll biosynthesis and reduced the photosynthetic pigment levels during grain-filling stage. Ribulose-1,5-bisphosphate carboxylase and phosphoenolpyruvate carboxylase activities, photosynthetic rate, transpiration rate, and stomatal conductance decreased under LT treatment during the grain-filling stage. Furthermore, LT treatment increased the contents of malondialdehyde and reactive oxygen species, and decreased the activities of catalase, superoxide dismutase, peroxidase, and ascorbate peroxidase in the ear leaves, which accelerated the oxidative damage of leaf. The LT treatment also raised abscisic acid content and reduced indole acetic acid content in the ear leaves during grain-filling stage. The results of field and pot trials were verified by each other, but the field effect was greater than that of pot. Overall, LT treatment reduced the waxy maize dry matter accumulation after silking by affecting the physiological and biochemical processes of leaves, and ultimately decreased grain yield.

Genome-wide identification of the B3 gene family in soybean and the response to melatonin under cold stress

INTRODUCTION

Melatonin is a multipotent molecule that exists widely in animals and plants and plays an active regulatory role in abiotic stresses. The B3 superfamily is a ubiquitous transcription factor with a B3 functional domain in plants, which can respond temporally to abiotic stresses by activating defense compounds and plant hormones. Despite the fact that the B3 genes have been studied in a variety of plants, their role in soybean is still unknown.

METHODS

The regulation of melatonin on cold resistance of soybean and the response of B3 genes to cold stress were investigated by measuring biochemical indexes of soybean. Meanwhile, the genome-wide identification of B3 gene family was conducted in soybean, and B3 genes were analyzed based on phylogeny, motifs, gene structure, collinearity, and cis-regulatory elements analysis.

RESULTS

We found that cold stress-induced oxidative stress in soybean by producing excessive reactive oxygen species. However, exogenous melatonin treatment could increase the content of endogenous melatonin and other hormones, including IAA and ABA, and enhance the antioxidative system, such as POD activity, CAT activity, and GSH/GSSG, to scavenge ROS. Furthermore, the present study first revealed that melatonin could alleviate the response of soybean to cold stress by inducing the expression of B3 genes. In addition, we first identified 145 B3 genes in soybean that were unevenly distributed on 20 chromosomes. The B3 gene family was divided into 4 subgroups based on the phylogeny tree constructed with protein sequence and a variety of plant hormones and stress response cis-elements were discovered in the promoter region of the B3 genes, indicating that the B3 genes were involved in several aspects of the soybean stress response. Transcriptome analysis and results of qRT-PCR revealed that most GmB3 genes could be induced by cold, the expression of which was also regulated by melatonin. We also found that B3 genes responded to cold stress in plants by interacting with other transcription factors.

DISCUSSION

We found that melatonin regulates the response of soybean to cold stress by regulating the expression of the transcription factor B3 gene, and we identified 145 B3 genes in soybean. These findings further elucidate the potential role of the B3 gene family in soybean to resist low-temperature stress and provide valuable information for soybean functional genomics study.

Exogenous Proline Optimizes Osmotic Adjustment Substances and Active Oxygen Metabolism of Maize Embryo under Low-Temperature Stress and Metabolomic Analysis

Maize (Zea mays L.) is more sensitive to low-temperature stress in the early growth period. The study was to explore the response mechanism of proline to low-temperature stress during maize seed germination. Maize varieties Xinxin 2 (low-temperature insensitive) and Damin 3307 (low-temperature sensitive) were chosen as the test materials, setting the normal temperature for germination (22 °C/10 °C, 9d), low-temperature germination (4 °C/4 °C, 5d) and normal temperature recovery (22 °C/10 °C, 4d), combined with proline (15 mmol·L−1) soaking treatment, to study its effects on the osmotic regulation system and antioxidant protection system of maize embryos. Metabolomics analysis was carried out to initially reveal the basis of the metabolic regulation mechanism. The results showed that the activities of superoxide dismutase (SOD), peroxidase (POD), ascorbic acid peroxidase (APX) and glutathione reductase (GR) were induced to some extent under low-temperature stress. The activities of SOD, POD, APX and GR were further enhanced in the soaking seeds with proline. Proline treatment improved the activities of catalase (CAT), monodehydrated ascorbic acid reductase (MDHAR) and dehydroascorbic acid (DHAR), increased the contents of ascorbic acid (AsA) and glutathione (GSH) and decreased the contents of oxidized ascorbic acid (DHA) and reduced glutathione (GSSG) under low-temperature stress. The ratio of AsA/DHA and GSH/GSSG increased. The increase in antioxidant enzyme activity and the content of antioxidants can help to maintain the stability of the AsA-GSH cycle, and effectively reduce the production rate of superoxide anion (O2•−), hydrogen peroxide (H2O2) and malondialdehyde (MDA). Based on the UPLC-MS/MS detection platform and self-built database, 589 metabolites were detected in each treated maize embryo; 262 differential metabolites were obtained, including 32 organic acids, 28 amino acids, 20 nucleotides and their derivatives, 26 sugars and alcohols, 46 lipids, 51 alkaloids, 44 phenols and 15 other metabolites. Sixty-eight metabolic pathways involving different metabolites were obtained by KEGG enrichment analysis. The results showed that proline increased the accumulation of sorbitol, planteose, erythritose 4-phosphate, arabinose and other saccharides and alcohols in response to low-temperature stress, increased the content of osmoregulation substances under low-temperature stress. Proline also restored the TCA cycle by increasing the content of α-ketoglutarate and fumaric acid. Proline increased the contents of some amino acids (ornithine, proline, glycine, etc.), alkaloids (cocamidopropyl betaine, vanillylamine, 6-hydroxynicotinic acid, etc.), phenols (phenolic ayapin, chlorogenic acid, etc.) and vitamins (ascorbic acid, etc.) in the embryo under low-temperature stress. Combined with pathway enrichment analysis, proline could enhance the low-temperature stress resistance of germinated maize embryos by enhancing starch and sucrose metabolism, arginine and proline metabolism, biosynthesis of secondary metabolites, flavonoid biosynthesis and pentose phosphate pathway.

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.

Can we improve the chilling tolerance of maize photosynthesis through breeding?

Chilling tolerance is necessary for crops to thrive in temperate regions where cold snaps and lower baseline temperatures place limits on life processes; this is particularly true for crops of tropical origin such as maize. Photosynthesis is often adversely affected by chilling stress, yet the maintenance of photosynthesis is essential for healthy growth and development, and most crucially for yield. In this review, we describe the physiological basis for enhancing chilling tolerance of photosynthesis in maize by examining nine key responses to chilling stress. We synthesize current knowledge of genetic variation for photosynthetic chilling tolerance in maize with respect to each of these traits and summarize the extent to which genetic mapping and candidate genes have been used to understand the genomic regions underpinning chilling tolerance. Finally, we provide perspectives on the future of breeding for photosynthetic chilling tolerance in maize. We advocate for holistic and high-throughput approaches to screen for chilling tolerance of photosynthesis in research and breeding programmes in order to develop resilient crops for the future.

Dynamic Changes in Seed Germination under Low-Temperature Stress in Maize

Low-temperature stress delays seed germination in maize. Different maize inbred lines display various low-temperature resistance, but the dynamic changes in seed germination under low-temperature stress in maize remain unknown, especially at the transcriptome level. In this study, low-temperature-resistant maize (RM) inbred line 04Qun0522-1-1 had a significantly faster germination speed than low-temperature-sensitive maize (SM) line B283-1 under low-temperature stress. Moreover, the total antioxidant capacity, superoxide dismutase, and peroxidase activities were notably higher in the RM line than in the SM line from 3 to 6 d. In contrast, the SM line showed significantly higher malondialdehyde (MDA) content than the RM line at 6 d. Gene ontology (GO) enrichment analysis showed that in 2dvs0d, both SM and RM lines displayed the downregulation of ribosome-related genes. Moreover, photosystem II and heat shock protein binding-related genes were also downregulated in the SM line. In 4dvs2d, the RM line showed a higher degree of upregulation of the ribosome and peroxidase (POD)-related genes than the SM line. In 6dvs4d, POD-related genes were continuously upregulated in both SM and RM lines, but the degree of upregulation of the genes was higher in the SM line than in the RM line. Moreover, vitamin B6-related genes were specifically upregulated in the RM line. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that in 6dvs4d, phenylpropanoid biosynthesis was the most significantly enriched pathway in both SM and RM lines. Moreover, phenylpropanoid biosynthesis was also enriched in the RM line in 4dvs2d. More than half of the differentially expressed genes (DEGs) in phenylpropanoid biosynthesis were peroxidase, and the DEGs were similar to the GO enrichment analysis. The results provide new insights into maize seed germination in response to low-temperature stress.

Maize Seed Germination Under Low-Temperature Stress Impacts Seedling Growth Under Normal Temperature by Modulating Photosynthesis and Antioxidant Metabolism

Spring maize is usually subjected to low-temperature stress during seed germination, which retards seedling growth later even under a suitable temperature. However, the mechanism underlying maize seed germination under low-temperature stress impacting seedling growth is still ambiguous. In this study, we used one low-temperature sensitive maize (SM) and one low-temperature resistance maize (RM) to investigate the mechanism. The results showed that the SM line had higher malondialdehyde content and lower total antioxidant capacity (TAC) and germination percentage than the RM line under low-temperature stress, indicating the vulnerability of SM line to low-temperature stress. Further transcriptome analysis revealed that seed germination under low-temperature stress caused the down-regulation of photosynthesis-related gene ontology terms in two lines. Moreover, the SM line displayed down-regulation of ribosome and superoxide dismutase (SOD) related genes, whereas genes involved in SOD and vitamin B6 were up-regulated in the RM line. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that photosynthesis and antioxidant metabolism-related pathways played essential roles in response to low-temperature stress during seed germination. The photosynthetic system displayed a higher degree of damage in the SM line. Both qRT-PCR and physiological characteristics experiments showed similar results with transcriptome data. Taken together, we propose a model for maize seed germination in response to low-temperature stress.

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.

Transcriptomic Insight into Underground Floral Differentiation in Erythronium japonicum

Erythronium japonicum Decne (Liliaceae) flowers in early spring after overwintering. Its sexual reproduction process includes an underground development process of floral organs, but the underlying molecular mechanisms are obscure. The present study is aimed at exploring the transcriptional changes and key genes involved at underground floral developmental stages, including flower primordium differentiation, perianth differentiation, stamen differentiation, and pistil differentiation in E. japonicum. Multistage high-quality transcriptomic data resulted in identifying putative candidate genes for underground floral differentiation in E. japonicum. A total of 174,408 unigenes were identified, 28,508 of which were differentially expressed genes (DEGs) at different floral developmental stages, while only 44 genes were identified with conserved regulation between different stages. Further annotation of DEGs resulted in the identification of 270 DEGs specific to floral differentiation. In addition, ELF3, PHD, cullin 1, SE14, ZSWIM3, GIGNATEA, and SERPIN B were identified as potential candidate genes involved in the regulation of floral differentiation. Besides, we explored transcription factors with differential regulation at different developmental stages and identified bHLH, FAR1, mTERF, MYB-related, NAC, Tify, and WRKY TFs for their potential involvement in the underground floral differentiation process. Together, these results laid the foundation for future molecular works to improve our understanding of the underground floral differentiation process and its genetic regulation in E. japonicum.

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.

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

Cold tolerance is a complex trait that requires a critical perspective to understand its underpinning mechanism. To unravel the molecular framework underlying maize (Zea mays L.) cold stress tolerance, we conducted a comparative transcriptome profiling of 24 cold-tolerant and 22 cold-sensitive inbred lines affected by cold stress at the seedling stage. Using the RNA-seq method, we identified 2237 differentially expressed genes (DEGs), namely 1656 and 581 annotated and unannotated DEGs, respectively. Further analysis of the 1656 annotated DEGs mined out two critical sets of cold-responsive DEGs, namely 779 and 877 DEGs, which were significantly enhanced in the tolerant and sensitive lines, respectively. Functional analysis of the 1656 DEGs highlighted the enrichment of signaling, carotenoid, lipid metabolism, transcription factors (TFs), peroxisome, and amino acid metabolism. A total of 147 TFs belonging to 32 families, including MYB, ERF, NAC, WRKY, bHLH, MIKC MADS, and C₂H₂, were strongly altered by cold stress. Moreover, the tolerant lines’ 779 enhanced DEGs were predominantly associated with carotenoid, ABC transporter, glutathione, lipid metabolism, and amino acid metabolism. In comparison, the cold-sensitive lines’ 877 enhanced DEGs were significantly enriched for MAPK signaling, peroxisome, ribosome, and carbon metabolism pathways. The biggest proportion of the unannotated DEGs was implicated in the roles of long non-coding RNAs (lncRNAs). Taken together, this study provides valuable insights that offer a deeper understanding of the molecular mechanisms underlying maize response to cold stress at the seedling stage, thus opening up possibilities for a breeding program of maize tolerance to cold stress.

Identification and Functional Verification of Cold Tolerance Genes in Spring Maize Seedlings Based on a Genome-Wide Association Study and Quantitative Trait Locus Mapping

Maize (Zea mays L.) is a tropical crop, and low temperature has become one of the main abiotic stresses for maize growth and development, affecting many maize growth processes. The main area of maize production in China, Jilin province, often suffers from varying degrees of cold damage in spring, which seriously affects the quality and yield of maize. In the face of global climate change and food security concerns, discovering cold tolerance genes, developing cold tolerance molecular markers, and creating cold-tolerant germplasm have become urgent for improving maize resilience against these conditions and obtaining an increase in overall yield. In this study, whole-genome sequencing and genotyping by sequencing were used to perform genome-wide association analysis (GWAS) and quantitative trait locus (QTL) mapping of the two populations, respectively. Overall, four single-nucleotide polymorphisms (SNPs) and 12 QTLs were found to be significantly associated with cold tolerance. Through joint analysis, an intersection of GWAS and QTL mapping was found on chromosome 3, on which the Zm00001d002729 gene was identified as a potential factor in cold tolerance. We verified the function of this target gene through overexpression, suppression of expression, and genetic transformation into maize. We found that Zm00001d002729 overexpression resulted in better cold tolerance in this crop. The identification of genes associated with cold tolerance contributes to the clarification of the underlying mechanism of this trait in maize and provides a foundation for the adaptation of maize to colder environments in the future, to ensure food security.