Shiliang Cao

Maize (Zea mays L.) is a globally important crop, but its sensitivity to cold stress leads to substantial yield losses in temperate zones, where low temperatures, particularly below 10 °C, critically constrain cultivation in high-altitude and high-latitude regions. Recent progress has identified key cold-tolerance genes, dissected natural variations, elucidated signaling pathways, and enabled multi-omics network construction. Some studies have provided evidence for the proposed coupling of ZmICE1 with amino acid metabolism and COR gene expression, the association of COOL1 promoter variation with HY5 binding and high-latitude adaptation, and the involvement of HSF21 in lipid homeostasis without an apparent yield penalty. Several novel genes (ZmWAK3, ZmMAPK4, TIP4;3, ZmDUF966-10) have been identified as promising candidates, expanding the genetic reservoir for further validation. Mechanistically, an unconventional ZmBSK4-ZmMAPK4 cascade, calcium-MAPK crosstalk, histone modifications, and small RNA-mediated regulation have been implicated in cold responses, although the extent to which each mechanism has been experimentally validated varies. Integrative approaches (chromatin accessibility, WGCNA, multi-omics) have revealed hierarchical synergies among transcription factors, epigenetics, hormones, and metabolism. Favorable alleles (COOL1HapA, HSF21Hap1, and the TIP4;3 beneficial haplotype) represent potential targets for molecular design, while CRISPR/Cas9 offers opportunities to accelerate gene editing and pyramiding. This review synthesizes these advances, and offers a comprehensive framework for cold-tolerance breeding in maize.

Maize (Zea mays L.), a typical thermophilic crop originating from tropical regions, exhibits an inherent sensitivity to low-temperature stress. Cold stress severely restricts maize seed germination, seedling growth, the physiological metabolism, and the final grain yield, which greatly limits its geographical cultivation range and sustainable industrial development. Elucidating the molecular regulatory mechanisms underlying maize cold tolerance and excavating cold-resistant functional genes are essential for the molecular breeding of cold-tolerant maize varieties and expanding maize planting areas in high-latitude and low-temperature-prone regions. In this study, using the strongly cold-tolerant maize inbred line B144 as the experimental material, we cloned the ZmMAPKKKA gene (NCBI accession: LOC103651289) and systematically screened and verified its cold-stress-specific interacting proteins via multiple molecular biological assays. The full-length coding sequence (CDS) of ZmMAPKKKA is 1134 bp, encoding a 377-amino-acid protein with a predicted molecular weight of 40.37 kDa. The quantitative real-time PCR (qRT-PCR) results demonstrated that the ZmMAPKKKA expression was significantly upregulated by 16.56-fold in maize roots after 12 h of low-temperature treatment, indicating a tissue-specific and robust cold response in root tissues. A total of 25 interacting proteins were identified through yeast two-hybrid screening, among which three stress-responsive proteins, including a protein kinase (LOC100286253), a protein phosphatase 2C (PP2C) (LOC542176), and a NAC transcription factor (LOC118474710), were selected for subsequent verification. The Pull-Down, Co-immunoprecipitation (Co-IP), and bimolecular fluorescence complementation (BiFC) assays consistently confirmed that ZmMAPKKKA specifically interacts with these three proteins both in vitro and in vivo under cold stress conditions. This study is the first to construct a ZmMAPKKKA-centered protein interaction module in the maize mitogen-activated protein kinase (MAPK) cascade under cold stress, establishing a novel kinase–phosphatase–transcription factor regulatory cascade that improves the current understanding of cold signal transduction mechanisms in maize. Homologous genes of ZmMAPKKKA in gramineous crops including rice (Oryza sativa) and sorghum (Sorghum bicolor) have been proven to participate in diverse abiotic stress responses, suggesting the conserved functional roles of MAPKKK family genes across gramineous species. Collectively, our findings provide comprehensive insights into the molecular mechanism of the maize MAPK signaling pathway mediating cold stress adaptation and supply valuable functional gene resources for cold-tolerant maize germplasm innovation and molecular breeding.

To elucidate the mechanisms by which the rhizosphere microbial community influences cold tolerance in maize, this study employed the metagenomic technology to systematically analyze the community composition, functional characteristics, and their association with host cold tolerance in the rhizosphere of maize genotypes with different cold tolerance (cold-tolerant material B144 and cold-sensitive material Q319, among others) (n = 3 biological replicates per genotype). The results revealed that the rhizosphere microbial community of the cold-tolerant genotype B144 exhibited higher species diversity and more complex genomic features. LEfSe analysis indicated that the rhizosphere soil microbiota of B144 was significantly enriched in two major phyla, Firmicutes and Actinobacteria, as well as microbial taxa with stress tolerance potential, such as the Bacillus and Streptomyces. Further functional analysis revealed that the microbial community was specifically enriched in metabolic pathways related to glycan biosynthesis and metabolism, as well as coenzyme and vitamin metabolism. We hypothesize that the physiological stability of maize under low temperatures can be enhanced through mechanisms such as the synthesis of extracellular polysaccharides to reduce the freezing point and the provision of vitamins and antioxidant substances. In contrast, the rhizosphere microorganisms of the cold-sensitive material Q319 were more enriched in basic metabolic functions. The present study elucidates the pivotal mechanisms by which rhizosphere microorganisms facilitate maize resistance to low-temperature stress from a functional perspective. This provides theoretical support and new strategies for enhancing crop stress resistance by regulating the rhizosphere microbiome.

Low temperature severely restricts maize seedling establishment and yield in northern China, but the proteomic basis of low-temperature tolerance in maize remains unclear. This study used TMT-labeled quantitative proteomics combined with data-independent acquisition (DIA) and liquid chromatography–tandem mass spectrometry (LC-MS/MS) to analyze dynamic proteome changes in two maize inbred lines (low-temperature-tolerant B144 and low-temperature-sensitive Q319) at the three-leaf stage under 5 °C treatment. A total of 4367 non-redundant proteins were identified. For differentially expressed proteins (DEPs, fold change >2.0 or p < 0.05, false discovery rate [FDR] < 0.05), B144 showed exclusive upregulation under stress (6 DEPs at 24 h; 16 DEPs at 48 h), while Q319 exhibited mixed regulation (9 DEPs at 24 h: 6 upregulated, 3 downregulated; 21 DEPs at 48 h: 19 upregulated, 2 downregulated). Functional annotation indicated that ribosomal proteins, oxidoreductases, glycerol-3-phosphate permease, and actin were significantly upregulated in both lines. Pathway enrichment analysis revealed associations with carbohydrate metabolism, amino acid biosynthesis, and secondary metabolite synthesis. Weighted gene co-expression network analysis (WGCNA) identified genotype-specific expression patterns: B144 showed differential expression of proteins related to acetyl-CoA synthetase and fatty acid β-oxidation at 24 h and of proteins related to D-3-phosphoglycerate dehydrogenase at 48 h; Q319 showed differential expression of proteasome-related proteins at 24 h and of proteins related to elongation factor 1α (EF-1α) at 48 h. Venn analysis found no shared DEPs between the two lines at 24 h but four overlapping DEPs at 48 h. These results clarify proteomic differences underlying low-temperature tolerance divergence between maize genotypes and provide candidate targets for molecular breeding of low-temperature-tolerant maize.

Abiotic stress constrains plant growth and productivity worldwide. To survive adverse environmental conditions, plants deploy sophisticated adaptive strategies involving transcriptional reprogramming and metabolic remodeling. Over the past decade, advancements in high-throughput sequencing and mass spectrometry have propelled transcriptomics and metabolomics as pivotal post-genomic disciplines, offering unprecedented opportunities to dissect molecular mechanisms underlying stress responses. This review synthesizes current progress in applying these omics technologies to investigate plant adaptations to key abiotic stresses (thermal, saline, water deficit/excess, and heavy metal stresses). We systematically evaluate the technical strengths and limitations of transcriptomic and metabolomic platforms, highlight recent breakthroughs in stress-responsive gene identification and metabolic pathway elucidation, and discuss emerging challenges in integrative data analysis. By bridging genotype–phenotype relationships through multi-omics approaches, this study aims to deepen our mechanistic understanding of plant stress resilience and inform the design of stress-resilient crops for sustainable agriculture.

Maize (Zea mays L.) is highly sensitive to temperature during its growth and development stage. A 1 °C drop in temperature can delay maturity by 10 days, resulting in a yield reduction of over 10%. Low-temperature tolerance in maize is a complex quantitative trait, and different germplasms exhibit significant differences in their responses to low-temperature stress. To explore the differences in gene expression and metabolites between B144 (tolerant) and Q319 (susceptible) during germination under low-temperature stress and to identify key genes and metabolites that respond to this stress, high-throughput transcriptome sequencing was performed on the leaves of B144 and Q319 subjected to low-temperature stress for 24 h and their respective controls using Illumina HiSeq^TM 4000 high-throughput sequencing technology. Additionally, high-throughput metabolite sequencing was conducted on the samples using widely targeted metabolome sequencing technology. The results indicated that low-temperature stress triggered the accumulation of stress-related metabolites such as amino acids and their derivatives, lipids, phenolic acids, organic acids, flavonoids, lignin, coumarins, and alkaloids, suggesting their significant roles in the response to low temperature. This stress also promoted gene expression and metabolite accumulation involved in the flavonoid biosynthesis pathway. Notably, there were marked differences in gene expression and metabolites related to the glyoxylate and dicarboxylate metabolism pathways between B144 and Q319. This study, through multi-omics integrated analysis, provides valuable insights into the identification of metabolites, elucidation of metabolic pathways, and the biochemical and genetic basis of plant responses to stress, particularly under low-temperature conditions.

Abiotic stress is a significant factor restricting the normal growth and development of plants. Under abiotic stress, plants maintain their life and continuous growth by reconfiguring transcriptional regulation and metabolic networks. In recent years, with the development of sequencing technology and mass spectrometry technology, transcriptomics and metabolomics have emerged as new disciplines following genomics and proteomics, which are conducive to identifying metabolites and regulatory genes in plants under abiotic stress. In this review, we mainly analyzes the technical characteristics, advantages, and disadvantages of transcriptomics and metabolomics, focusing on reviewing the research progress in the field of plant responses to abiotic stress (temperature stress, salt stress, water stress, and heavy metal stress) using transcriptomics and metabolomics both domestically and internationally in recent years. It also provides a prospective view on current issues, which helps accelerate the understanding of the mechanisms of plant responses to abiotic stress and provides new ideas for breeding stress-resistant varieties in the future.

Key message A stable genomic region conferring FSR resistance at ~250 Mb on chromosome 1 was identified by GWAS. Genomic prediction has the potential to improve FSR resistance. Abstract Fusarium stalk rot (FSR) is a global destructive disease in maize; the efficiency of phenotypic selection for improving FSR resistance was low. Novel genomic tools of genome-wide association study (GWAS) and genomic prediction (GP) provide an opportunity for genetic dissection and improving FSR resistance. In this study, GWAS and GP analyses were performed on 562 tropical maize inbred lines consisting of two populations. In total, 15 SNPs significantly associated with FSR resistance were identified across two populations and the combinedPOP consisting of all 562 inbred lines, with the P-values ranging from 1.99 × 10^–7 to 8.27 × 10^–13, and the phenotypic variance explained (PVE) values ranging from 0.94 to 8.30%. The genetic effects of the 15 favorable alleles ranged from −4.29 to −14.21% of the FSR severity. One stable genomic region at ~ 250 Mb on chromosome 1 was detected across all populations, and the PVE values of the SNPs detected in this region ranged from 2.16 to 5.18%. Prediction accuracies of FSR severity estimated with the genome-wide SNPs were moderate and ranged from 0.29 to 0.51. By incorporating genotype-by-environment interaction, prediction accuracies were improved between 0.36 and 0.55 in different breeding scenarios. Considering both the genome coverage and the threshold of the P-value of SNPs to select a subset of molecular markers further improved the prediction accuracies. These findings extend the knowledge of exploiting genomic tools for genetic dissection and improving FSR resistance in tropical maize.