Ma, L et al. 2025. Manipulation of the central autophagy component ZmATG8c affects thermotolerance in maize. Plant Physiol. :doi: 10.1093/plphys/kiaf299.
   Manipulation of the central autophagy component ZmATG8c affects thermotolerance in maize.

This study identifies the maize autophagy gene ZmATG8c as a critical regulator of thermotolerance. Heat stress induces the bZIP transcription factor ZmGBF1, which directly binds to the ZmATG8c promoter (via G-box motifs) and activates its expression. Functional analyses reveal that ZmATG8c knockout mutants exhibit severe sensitivity to heat, with reduced seedling survival, increased electrolyte leakage, reactive oxygen species accumulation, and impaired autophagosome formation. Conversely, ZmATG8c overexpression lines show enhanced thermotolerance, correlating with elevated ATG8 protein levels, increased autophagosome abundance, and reduced cytotoxic ubiquitinated protein aggregates under heat stress. Crucially, field trials demonstrate that overexpression lines maintain higher pollen viability and grain yield (~11.85% increase per ear) under reproductive-stage heat stress, while knockout lines suffer significant yield losses (up to 57.82% reduction) due to reduced kernel set. Similarly, ZmGBF1 mutants exhibit impaired ZmATG8c induction and heat sensitivity, confirming the ZmGBF1-ZmATG8c module’s role. Notably, a favorable ZmATG8c promoter SNP allele associated with thermotolerance is enriched in tropical/subtropical maize. The study establishes ZmATG8c as a key executor of autophagy-mediated heat resilience by clearing damaged proteins and provides two validated breeding targets (ZmATG8c and ZmGBF1) for climate-adaptive maize.

Ma, L et al. 2025. Manipulation of the central autophagy component ZmATG8c affects thermotolerance in maize. Plant Physiol. :doi: 10.1093/plphys/kiaf299.
   Manipulation of the central autophagy component ZmATG8c affects thermotolerance in maize.
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Kerry Bubb et al. 2024. The regulatory potential of transposable elements in maize. Nature Plants. doi: 10.1038/s41477-025-02002-z
   The regulatory potential of transposable elements in maize

Transposable elements (TEs), also known as "jumping genes," are DNA sequences capable of moving within the genome. Remarkably, they constitute more than 80% of the maize genome. In plants, TEs regulate gene expression through several mechanisms: (1) disruption of cis-regulatory elements (CREs); (2) enhancement of expression when a CRE is located within a TE; and (3) repression of expression via DNA methylation. Causal variants in key genes such as Teosinte branched1 (Tb1) and flowering time genes including Vgt1-ZmRap2.7, ZmCCT9, and ZmCCT10 have all been identified as TEs. In essence, TEs are central to shaping both genomic architecture and phenotypic variation in maize. A recent study by Bubb et al., published in Nature Plants, presents a comprehensive landscape of TE-mediated regulation in the maize genome. Conventional short-read sequencing technologies often fall short in resolving the repetitive nature of TEs and their associated regulatory elements. To address this, the authors employed long-read chromatin fiber sequencing (Fiber-seq), which enables high-resolution detection of accessible chromatin regions (ACRs) and CpG methylation patterns. Compared to ATAC-seq, Fiber-seq is capable of identifying a larger number of ACRs—particularly short fragments (<200 bp)—with greater sensitivity and single-nucleotide resolution. The study revealed that LTR retrotransposons can harbor either paired or single ACRs. These configurations are evolutionarily informative: LTR retrotransposons with paired ACRs tend to be younger than those with single ACRs. The paired promoter- and enhancer-like elements found within these LTRs are enriched with transcription factor (TF) motifs, underscoring their active roles in both gene regulation and mobilization. However, these regulatory features—such as chromatin accessibility and 5mCpG methylation—gradually degenerate with age. Notably, 12% of LTR retrotransposons contain annotated genes, some of which appear to utilize the LTR’s ACRs as promoters to drive expression. The colored aleurone 1 (C1) gene, which is known to be a target of hAT TE insertions, exhibits characteristics such as chromatin accessibility and hypo-5mCpG methylation. In conclusion, this study provides the maize research community with a valuable Fiber-seq resource and offers new insights into how TEs regulate gene expression. Furthermore, it highlights how the regulatory roles of TEs are closely linked to their evolutionary age, offering a fresh perspective on gene expression, regulation, and genome evolution.

Kerry Bubb et al. 2024. The regulatory potential of transposable elements in maize. Nature Plants. doi: 10.1038/s41477-025-02002-z
   The regulatory potential of transposable elements in maize
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Brar, MS et al. 2025. Temporal analysis of physiological phenotypes identifies metabolic and genetic underpinnings of senescence in maize. Plant Cell. :doi: 10.1093/plcell/koaf176.
   Temporal analysis of physiological phenotypes identifies metabolic and genetic underpinnings of senescence in maize.

This study investigates the physiological and metabolic basis of leaf senescence in a diverse panel of maize inbred lines, highlighting natural variation in the stay-green trait. It begins with comprehensive temporal phenotyping of several senescence-associated physiological traits, revealing substantial variation among genotypes. Time-course analyses combining targeted and untargeted metabolomics were then performed on stay-green and non-stay-green lines, identifying 48 primary and 141 specialized metabolites—including those involved in phenylpropanoid and flavonoid biosynthesis—associated with senescence progression. A subset of these metabolites was further linked to candidate genes implicated in leaf senescence. To evaluate the functional role of the flavonoids naringenin chalcone and eriodictyol in leaf senescence, the study examined maize c2 and a1 mutants, alongside Arabidopsis thaliana flavonoid-deficient mutants transparent testa (tt4-1, deficient in chalcone synthase) and dfr (dihydroflavonol 4-reductase). These mutants exhibited accelerated visual senescence and reduced Fv/Fm values, supporting a conserved role for these flavonoids in regulating leaf senescence across both monocots and dicots. Collectively, the candidate genes and metabolite markers identified here provide promising targets for genetic improvement strategies aimed at enhancing maize productivity through delayed senescence.

Brar, MS et al. 2025. Temporal analysis of physiological phenotypes identifies metabolic and genetic underpinnings of senescence in maize. Plant Cell. :doi: 10.1093/plcell/koaf176.
   Temporal analysis of physiological phenotypes identifies metabolic and genetic underpinnings of senescence in maize.
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Han, Xu et al. 2025. A copy number variation in the ZmMADS1 promoter enhances maize adaptation to high altitudes. J Integr Plant Biol. :doi: 10.1111/jipb.13924.
   A copy number variation in the ZmMADS1 promoter enhances maize adaptation to high altitudes.

This study reveals that a 178-bp copy number variation (CNV178) in the promoter of the maize flowering gene ZmMADS1 is a key genetic adaptation enabling maize to spread into high-altitude regions. Lines carrying two copies of CNV178 (2xCNV178) exhibit significantly later flowering than those with one copy (1xCNV178), as CNV178 acts as a dosage-dependent repressor of ZmMADS1 expression—higher copy numbers lead to greater suppression. Critically, geographical analysis of maize landraces shows the early-flowering 1xCNV178 allele is strongly associated with higher altitudes in both North and South America, with its frequency increasing dramatically with elevation and becoming nearly fixed above 3,000 meters. This indicates strong natural selection for the 1xCNV178 allele in high-altitude environments, where its promotion of earlier flowering shortens the growth period. Functionally, ZmMADS1 promotes flowering through the autonomous pathway by directly activating the flowering promoter ZmMADS69 and the florigen gene ZCN8, while repressing the flowering inhibitor ZmRap2.7. Beyond elucidating this adaptation mechanism, CNV178 serves as a valuable molecular marker for breeding; reducing its copies can accelerate flowering for high-altitude adaptation, while increasing copies can delay flowering to enhance biomass in tropical lowlands. Thus, selection on CNV178 facilitated maize's geographical expansion by fine-tuning flowering time to altitudinal constraints.

Han, Xu et al. 2025. A copy number variation in the ZmMADS1 promoter enhances maize adaptation to high altitudes. J Integr Plant Biol. :doi: 10.1111/jipb.13924.
   A copy number variation in the ZmMADS1 promoter enhances maize adaptation to high altitudes.
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Galli, M et al. 2025. Transcription factor binding divergence drives transcriptional and phenotypic variation in maize Nature Plants. :doi: 10.1038/s41477-025-02007-8.
   Transcription factor binding divergence drives transcriptional and phenotypic variation in maize

Motifs are short sequences within non-coding cis-regulatory regions that serve as binding sites for transcription factors (TFs). Variations in these motifs play a crucial role in altering gene expression, leading to phenotypic diversity. Therefore, understanding the diversity and patterns of TF binding can enhance our knowledge of gene expression modulation. Furthermore, such insights provide valuable evidence for fine-tuning gene expression and facilitating crop engineering for agricultural improvement. Recent research by Galli et al., published in Nature Plants, employed DNA affinity purification sequencing (DAP-seq) in two elite maize inbred lines representing distinct heterotic groups: B73 (Stiff Stalk) and Mol17 (Lancaster), to map transcription factor binding sites for 200 TFs belonging to 36 TF families. Their findings indicated that structural variations primarily drive TF binding differences across genomes. Additionally, significant enrichment was observed between important SNPs identified in the Nested Association Mapping (NAM) population and DAP-seq binding sites. TFs from different families were found to cooperate, forming DAP-cis-regulatory modules (DAP-CRMs) to modulate gene expression. The study revealed that over 63% of TF binding peaks are shared between the two genomes, while 37% are genome-specific, offering novel insights into genomic and phenotypic variation resulting from domestication. Furthermore, the authors conducted CRISPR–Cas9 genome editing at binding sites within DAP-CRMs to validate the functional roles of these cis-regulatory regions. Overall, this research provides valuable resources for identifying TF binding sites and potential cis-regulatory elements, opening new avenues for genome engineering and crop improvement.

Galli, M et al. 2025. Transcription factor binding divergence drives transcriptional and phenotypic variation in maize Nature Plants. :doi: 10.1038/s41477-025-02007-8.
   Transcription factor binding divergence drives transcriptional and phenotypic variation in maize
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Zhang, M et al. 2025. A SnRK2-HAK regulatory module confers natural variation of salt tolerance in maize Nat Commun. 16:4026.
   A SnRK2-HAK regulatory module confers natural variation of salt tolerance in maize

This study elucidates the role of the SnRK2-HAK pathway in mediating salt tolerance in maize (Zea mays). The authors identified two independent mutant lines deficient in the SNF1-related protein kinase genes ZmSnRK2.9 and ZmSnRK2.10. Under salt stress, these genes exhibit increased transcript levels and kinase activity. Further research shows that these SnRK2 kinases interact with and phosphorylate ZmHAK4 at Ser5, thereby activating the Na+ transporter ZmHAK4 and enhancing salt tolerance through shoot Na+ exclusion. A 20-bp deletion in the ZmSnRK2.10 promoter reduces its transcript level, while the favorable ZmSnRK2.10 allele promotes Na+ exclusion from shoot tissue under salt stress. Overall, the findings support a breeding program aimed at advancing the development of salt-tolerant maize.

Zhang, M et al. 2025. A SnRK2-HAK regulatory module confers natural variation of salt tolerance in maize Nat Commun. 16:4026.
   A SnRK2-HAK regulatory module confers natural variation of salt tolerance in maize
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Marand, AP et al. 2025. The genetic architecture of cell type–specific cis regulation in maize. Science 388 (6744) eads6601.
   The genetic architecture of cell type–specific cis regulation in maize

Structured Abstract: INTRODUCTION: Noncoding genetic variants are a major driver of phenotypic diversity. In Zea mays (maize), genetic variation within cis-regulatory regions accounts for ~40% of phenotypic variability in agronomically important traits. Missing from past studies, however, is the role of cell context in shaping regulatory variant effects and a clear definition of the molecular mechanisms underlying phenotypic variation. Thus, resolving the genetic and molecular principles that give rise to phenotypic diversity in a cell state–aware framework is paramount to advancing crop improvement efforts. RATIONALE: Single-cell genomic methods offer a powerful approach for understanding the genetic sources of gene expression and chromatin accessibility variation. We generated and analyzed single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) and single-nuclei RNA sequencing (snRNA-seq) data across 172 genetically and phenotypically diverse inbred maize lines for insight into the regulatory mechanisms underlying phenotypic variability. RESULTS: Our single-cell dataset comprises >700,000 nuclei from 33 distinct cell states. We first used this resource to investigate the extent of cis-regulatory variation among diverse genetic backgrounds, identifying binding sites for specific transcription factor (TF) families as being critical determinants of regulatory sequence conservation and functional activity. Through comparisons with 21 teosinte (a progenitor of modern maize) genomes, we identified 1587 accessible chromatin regions that were unique and fixed in the domesticated maize lineage. These accessible chromatin regions were enriched for hAT and PIF/Harbinger transposons, implicating co-option of transposon cis-regulatory elements as a major source of new regulatory sequences specific to domesticated maize. By applying the principles of population genetics, we identified 107,623 cis chromatin accessibility quantitative trait loci (cis-caQTL) within accessible chromatin regions and validated their effects on enhancer activity using self-transcribing active regulatory region sequencing (STARR-seq). We found that cell state–specific cis-caQTL are common and often overlap with phenotype-associated variants identified by genome-wide association studies (GWASs). Deep investigation of caQTL indicated that variants within TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP)–binding sites are strong determinants of chromatin accessibility. Moreover, all caQTL variants with decreased TCP-binding affinity were concomitant with loss of chromatin accessibility. Construction of cell state–specific gene-regulatory networks indicated that TCP TFs are highly cell state specific and controlled by master cell identity regulators. Analysis of caQTL affecting distal accessible chromatin regions further implicated TCP TFs as being major contributors toward chromatin accessibility variation and, as a result, chromatin interactions. Through transcriptome-wide association mapping, chromatin accessibility–wide association mapping, and integration of caQTL with expression QTL and GWAS variants, we found that caQTL were commonly associated with flowering-related phenotypes. We hypothesized that the transition of modern maize from tropical to temperate climates may have been a significant contributor of extant chromatin accessibility variation. Indeed, we found that caQTL are associated with signatures of population differentiation, and that these population-divergent variants occur within binding sites for TFs previously implicated in flowering time and floral morphology nonuniformly among cell states. CONCLUSIONS: These analyses advance our understanding of how cell context and molecular diversity contribute to innovations in phenotype, providing the blueprints for future crop improvement efforts.

Editor’s summary: A transcription factor’s ability to act requires access to the DNA to which it binds, which is called chromatin accessibility. However, identifying variants that causally affect chromatin accessibility is complicated by many factors, including linkage disequilibrium between variants. Taking advantage of maize’s low levels of linkage disequilibrium, Marand et al. examined single-cell chromatin accessibility from 172 inbred maize lines. They found about 22,000 variants associated with chromatin accessibility, many of which were specific to cell types and overlapped transposable elements. Many of these variants were linked to traits such as flowering time and affected binding sites for the transcription factor TCP. These results provide insight not only into important agricultural traits, but also regulatory element turnover during adaptation. —Corinne Simonti

Dongdong Li Editorial Board Comment May 2025: Cis-regulatory elements (CREs) are non-coding regions of the genome, such as promoters, enhancers, and silencers, that regulate gene expression. Although they constitute only a small fraction of the genome, CREs account for a significant portion of phenotypic variation. One of the key technologies for identifying potential CREs is transposase-accessible chromatin sequencing (ATAC-seq), which can be applied at both single-cell and bulk levels. Investigating CRE variation at the population level offers new insights into maize evolution and the genetic architecture of complex traits. A recent study published in Science by Marand et al. generated and analyzed single-cell ATAC-seq (scATAC-seq) and single-nucleus RNA-seq (snRNA-seq) data from 172 diverse inbred maize lines. The researchers identified 1,587 accessible chromatin regions (ACRs) enriched with hAT and PIF/Harbinger transposons that are fixed in domesticated maize, highlighting the crucial role of CREs in the domestication process. Innovatively, the authors treated chromatin accessibility as an intermediate phenotype to perform phenotype–genome associations. They identified 107,623 cis-chromatin accessibility quantitative trait loci (cis-caQTLs) within ACRs. The functional effects of these caQTLs on enhancer activity were validated using self-transcribing active regulatory region sequencing (STARR-seq). Notably, many caQTLs were associated with flowering-time traits, suggesting that human and environmental selection, such as the transition from tropical to temperate climates, have shaped the ACR landscape in domesticated maize. This finding aligns with previous evidence that causal variants of several flowering-time genes within the photoperiod pathway reside in CRE regions. Collectively, this study provides valuable resources of scATAC-seq, snRNA-seq, and STARR-seq data to the maize research community. The application of caQTL and caGWAS approaches advances our understanding of phenotype–genome associations and offers new avenues for crop improvement.

Marand, AP et al. 2025. The genetic architecture of cell type–specific cis regulation in maize. Science 388 (6744) eads6601.
   The genetic architecture of cell type–specific cis regulation in maize
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Zhenkai Feng et al. 2025. ZmGCT1/2 negatively regulate drought tolerance in maize by inhibiting ZmSLAC1 to maintain guard cell turgor. Proc Natl Acad Sci, USA. 122:e2423037122.
   ZmGCT1/2 negatively regulate drought tolerance in maize by inhibiting ZmSLAC1 to maintain guard cell turgor.

Stomata are important for the exchange of carbon dioxide and oxygen. The opening and closing of stomata is regulated by the turgor pressure of guard cells found within the stomatal complex. Two closely related RAF-like kinases were identified, Guard Cell Turgor Maintaining 1 (ZmGCT1) and ZmGCT2. Overexpression of ZmGCT1 and ZmGCT2 increased the sensitivity of maize to drought stress, while loss of function promoted drought stress resistance. Through stomatal closure analysis under abscisic acid (ABA) treatment in overexpression and mutant lines, it was shown that ZmGCT1 and ZmGCT2 are negative regulators of ABA-induced stomatal closure. ZmGCT1-GFP and ZmGCT2-GFP localized to the plasma membrane of protoplast cells and dissociated under ABA treatment. Through protein pull-downs and yeast two-hybrid assays, it was shown that ZmGCT1 interacts with ZmSnRK2.8/9/10, a known ABA-activated kinase. In vitro assays showed that ZmGCT1 can be phosphorylated by ZmSnRK2.8/9 at amino acid position T80, leading to the dissociation of ZmGCT1 partially from the plasma membrane. Additionally, ZmGCT1 and ZmGCT2 phosphorylate and directly inhibit ZmSLAC1, slow anion channel 1, promoting stomatal openness via increased turgor pressure. Overall, this paper provides insights into the role of ZmGCT1/2 kinases in regulating stomatal movement.

Zhenkai Feng et al. 2025. ZmGCT1/2 negatively regulate drought tolerance in maize by inhibiting ZmSLAC1 to maintain guard cell turgor. Proc Natl Acad Sci, USA. 122:e2423037122.
   ZmGCT1/2 negatively regulate drought tolerance in maize by inhibiting ZmSLAC1 to maintain guard cell turgor.
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Li, PC et al. 2025. Natural variation in a cortex/epidermis-specific transcription factor bZIP89 determines lateral root development and drought resilience in maize Sci Adv. 11:doi: 10.1126/sciadv.adt1113.
   Natural variation in a cortex/epidermis-specific transcription factor bZIP89 determines lateral root development and drought resilience in maize

This study investigates the genetic mechanisms underlying lateral root (LR) development and drought resilience in maize, focusing on the transcription factor ZmbZIP89. By integrating transcriptome-wide association studies (TWAS) and single-cell RNA sequencing (scRNA-seq) of 357 maize inbred lines, the authors identified ZmbZIP89 as a cortex/epidermis-specific regulator of LR elongation. Functional analyses revealed that ZmbZIP89 directly activates ZmPRX47, a peroxidase gene critical for reactive oxygen species (ROS) homeostasis. Overexpression of ZmbZIP89 increased LR length (LRL) by 30% and enhanced drought tolerance, while CRISPR-Cas9 knockout of ZmPRX47 reduced LRL and ROS scavenging capacity. Natural variations in the 3' untranslated region (UTR) of ZmbZIP89 were linked to increased mRNA stability and higher expression levels, correlating with improved drought resilience in maize germplasms. Population genetics highlighted selective breeding for drought-resistant ZmbZIP89 alleles in modern maize compared to teosinte. The study underscores the role of cell type-specific transcriptional networks in root architecture and stress adaptation, offering potential targets for breeding climate-resilient crops. This work bridges genetic variation, cellular resolution, and agronomic traits, advancing our understanding of root developmental plasticity under environmental stress.

Li, PC et al. 2025. Natural variation in a cortex/epidermis-specific transcription factor bZIP89 determines lateral root development and drought resilience in maize Sci Adv. 11:doi: 10.1126/sciadv.adt1113.
   Natural variation in a cortex/epidermis-specific transcription factor bZIP89 determines lateral root development and drought resilience in maize
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Hao Wu et al. 2025. Multiplexed transcriptomic analyzes of the plant embryonic hourglass. Nat Commun. 16:802.
   Multiplexed transcriptomic analyzes of the plant embryonic hourglass

The mature maize kernel develops from the fertilized ovule. This process usually takes around two months, depending on the maturity date of the genotype itself. The endosperm, embryo, and pericarp are three major parts of the maize kernel, which are developed from zygote, fertilized central cell, and maternal tissue, respectively. The core part of a kernel is an embryo, a miniature plant containing abundant, critical nutrition. After fertilization, three processes are involved in the embryogenesis of flowering plants. So far, understanding how genes regulate these three conserved processes is not well established. A recent study by Wu et al. presented a landscape of transcriptomic analysis during maize embryogenesis by leveraging cutting-edge sequencing technologies, such as single-cell sequencing, spatial RNA-seq, laser-microdissection RNA-seq, and multiplexed RNA-targeting in situ hybridizations. Two clear gene expression patterns were found in plants, similar to those in animals. A transcriptomic hourglass pattern of gene expression during maize embryogenesis was observed, which is characterized by the accumulation of evolutionarily older and conserved transcripts during mid-embryogenesis. In contrast, younger, less-conserved transcripts predominate at earlier and later embryonic stages. An inverse hourglass pattern was observed, which was characterized by high transcripts correlated during early and late stages but not during mid-embryo development in the comparisons of moss and maize or Arabidopsis. This study provides a new understanding of the relationship between genes regulating morphological changes and gene evolution during embryogenesis

Hao Wu et al. 2025. Multiplexed transcriptomic analyzes of the plant embryonic hourglass. Nat Commun. 16:802.
   Multiplexed transcriptomic analyzes of the plant embryonic hourglass
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Ma, LL et al. 2024. Single-cell RNA sequencing reveals a key regulator ZmEREB14 affecting shoot apex development and yield formation in maize. Plant Biotechnol J. :doi: 10.1111/pbi.14537.
   Single-cell RNA sequencing reveals a key regulator ZmEREB14 affecting shoot apex development and yield formation in maize.

The shoot apical meristem gives rise to all of the above-ground tissues in plants. However, mechanisms underlying shoot apical meristem (SAM) development in maize are still being unraveled. In this paper, Ma et al. performed single-cell RNA sequencing on three maize inbred A188 shoot apices and all captured cells were classified into 13 major cell-type clusters, including epidermis cell, vasculature cell, mesophyll cell, meristem cell, meristem determinacy cell, proliferating cell, etc. To determine the temporal and spatial patterns of marker genes during shoot apex development, continuous differentiation trajectories were made using Monocle 2, showing two branch points that diverged from meristematic cells into meristematic determinacy cells. From there, individual genes of interest could be traced to determine their expression pattern early or late in SAM development. AP2-EREBP-transcription factor 14 (ZmEREB14) was identified as a core transcription factor in meristem cells, while MYB histone 4 (ZmMYB4) was identified as a core transcription factor in meristem determinacy cells. Real-time quantitative PCR (qRT-PCR) performed on different tissues showed ZmEREB14 was most highly expressed in shoot tips and transient tobacco infiltration assays showed ZmEREB14 localized to the nucleus. Two mutants, zmereb14-1 and zmereb14-2, had smaller SAMs when compared to wild type. The zmereb14-1 and zmereb14-2 mutants also had decreased cell length when compared to wild type, which may lead to the decreased plant height, decreased primary tassel length, decreased ear height and decreased average length of internodes observed in the mutants. Additional phenotypic characterization also showed zmereb14-1 and zmereb14-2 mutants have decreased flowering time, less internodes, and less aboveground biomass when compared to wild type. Other yield related traits, such as hundred kernel weight, kernel number per ear, kernel length, and kernel width were all reduced in the zmereb14-1 and zmereb14-2 mutants. Transcriptomic analysis of zmereb14-1 mutants from RNA-seq showed downregulation of auxin biosynthesis, auxin transport, and auxin signal transduction-related genes, suggesting that ZmEREB14 may participate in the auxin biosynthesis and transport pathways, however further experiments are needed to validate this. Overall, this paper used single-cell RNA sequencing of the shoot apex and identified a core transcription factor, ZmEREB14, which may regulate SAM development and plant growth in maize.

Ma, LL et al. 2024. Single-cell RNA sequencing reveals a key regulator ZmEREB14 affecting shoot apex development and yield formation in maize. Plant Biotechnol J. :doi: 10.1111/pbi.14537.
   Single-cell RNA sequencing reveals a key regulator ZmEREB14 affecting shoot apex development and yield formation in maize.
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Guannan Jia et al. 2025. Ferredoxin-mediated mechanism for efficient nitrogen utilization in maize Nature Plants. :doi: 10.1038/s41477-025-01934-w.
   Ferredoxin-mediated mechanism for efficient nitrogen utilization in maize

This study elucidates the role of the ferredoxin gene ZmFd4 in enhancing nitrogen use efficiency (NUE) and grain yield in maize under nitrogen-limiting conditions. Using genome-wide association analysis, the authors identified ZmFd4 as a key regulator of shoot nitrate (NO₃⁻) accumulation. Functional characterization revealed that ZmFd4, a chloroplast-localized leaf-type ferredoxin, interacts with nitrite reductases (ZmNiRs) to promote their enzymatic activity, facilitating NO₃⁻ assimilation. Intriguingly, ZmFd4 forms a high-affinity heterodimer with its paralog ZmFd9, which competitively inhibits their interaction with ZmNiRs, thereby modulating electron transfer efficiency. Knockout of ZmFd4 disrupts this dimerization, freeing ZmFd9 to enhance ZmNiR activity, accelerating NO₃⁻ assimilation, and reducing shoot nitrate accumulation. Field trials demonstrated that Zmfd4 mutants exhibit improved grain yield and NUE under low-nitrogen conditions, without compromising other agronomic traits. A natural 604-bp deletion in the ZmFd4 promoter was linked to reduced gene expression and lower NO₃⁻ levels, suggesting this allele was selected during maize domestication. The study highlights a novel regulatory mechanism where ZmFd4 and ZmFd9 balance electron allocation between metabolic pathways, optimizing nitrogen utilization. These findings provide a genetic target for breeding maize varieties with enhanced productivity under nitrogen-deficient environments, offering insights applicable to other crops. The work underscores the importance of ferredoxin-mediated electron transport in nitrogen metabolism and its potential for sustainable agriculture.

Guannan Jia et al. 2025. Ferredoxin-mediated mechanism for efficient nitrogen utilization in maize Nature Plants. :doi: 10.1038/s41477-025-01934-w.
   Ferredoxin-mediated mechanism for efficient nitrogen utilization in maize
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Wang, XF et al. 2025. DBB2 regulates plant height and shade avoidance responses in maize. J Integr Plant Biol. :doi: 10.1111/jipb.13859.
   DBB2 regulates plant height and shade avoidance responses in maize.

One strategy often used to increase maize yields is dense planting. However, this can trigger shade avoidance responses, which can limit yield increases. To identify key regulators mediating the shade avoidance response, simulated shade treatment was done on B73 seedlings at the V3 stage followed by RNA-seq. Maize B-box (ZmBBX) family genes, such as ZmDBB2 (also known as BBX4), were upregulated in response to short-term far-red light treatment. To investigate the roles of ZmDBB2 and ZmDBB12, a close homolog of ZmDBB2, in maize, mutants in the KN5585 inbred were generated using CRISPR-Cas9. dbb2 single mutants and dbb2 dbb12 double mutants had a significant reduction in plant height and leaf length, while dbb12 single mutants were similar to wild-type. Further analysis revealed that the shorter height in dbb2 mutants is due to a reduction in cell length by approximately 30%, leading to decreased internode length and shorter plant height. dbb2 seedlings subjected to three hours of low red:far-red light treatment had increased sensitivity to shade treatment when compared to wild-type. Transcriptome analysis using RNA-seq showed alterations in expression profiles of genes associated with GA deactivation, cell elongation, and cell wall-related metabolism in dbb2 dbb12 double and dbb2 single mutants, suggesting that DBB2 regulates the shade avoidance response in maize through various pathways. To determine if DBB2 regulates cell elongation via the GA pathway by recruiting HY5 to repress the expression of GA2ox, interaction assays between DBB2 and HY5 were conducted and showed interaction in vivo and in vitro. This interaction repressed the binding of HY5 to ZmGA2ox4 promoter and negatively regulated the expression of ZmGA2ox4, affecting GA biosynthesis. Additionally, it was shown that PIF4 activated the expression of ZmDBB2 during shade avoidance response by binding to the G-box cis-element in the promoter, and interaction between PIF4.1 and DBB2 can increase the expression of ZmEXPA1 to promote cell elongation. Overall, DBB2 is important in regulating cell length during shade avoidance responses via various pathways.

Wang, XF et al. 2025. DBB2 regulates plant height and shade avoidance responses in maize. J Integr Plant Biol. :doi: 10.1111/jipb.13859.
   DBB2 regulates plant height and shade avoidance responses in maize.
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Yu, YH et al. 2025. A Zea genus-specific micropeptide controls kernel dehydration in maize Cell. 188:doi: 10.1016/j.cell.2024.10.030.
   A Zea genus-specific micropeptide controls kernel dehydration in maize

This study investigates the genetic mechanisms underlying kernel dehydration rate (KDR) in maize, a crucial trait affecting mechanical harvesting and kernel quality. The researchers identified a quantitative trait locus (QTL), qKDR1, which regulates KDR through a non-coding sequence controlling the expression of the RPG gene. RPG encodes a 31-amino-acid micropeptide, microRPG1, that modulates the expression of two ethylene signaling pathway genes, ZmETHYLENE-INSENSITIVE3-like 1 and 3, thereby influencing kernel dehydration after filling. MicroRPG1 is a Zea genus-specific micropeptide that originated de novo from a non-coding sequence. The study demonstrates that knocking out microRPG1 accelerates kernel dehydration, while its overexpression or exogenous application has the opposite effect. Additionally, the micropeptide's function was shown to be conserved in Arabidopsis, where it delayed silique ripening and increased moisture content. The findings provide insights into the molecular regulation of kernel dehydration and offer a valuable tool for future crop breeding aimed at improving maize varieties for mechanized harvesting.

Yu, YH et al. 2025. A Zea genus-specific micropeptide controls kernel dehydration in maize Cell. 188:doi: 10.1016/j.cell.2024.10.030.
   A Zea genus-specific micropeptide controls kernel dehydration in maize
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Rong Zeng et al. 2025. A natural variant of COOL1 gene enhances cold tolerance for high-latitude adaptation in maize Cell. :doi: 10.1016/j.cell.2024.12.018.
   A natural variant of COOL1 gene enhances cold tolerance for high-latitude adaptation in maize

Maize (Zea mays L.) originated in southwest Mexico about 9,000 years ago. Mexico is a typical tropical region with climate characteristics such as short days and high temperatures during the growing season. As maize spread from its origin to higher latitudes and altitudes, it had to gradually adapt to two completely different environmental conditions: colder temperatures and longer days. Regarding photoperiod sensitivity, many genes involved in flowering time have been cloned, such as ZCN8, ZmCCT9, and ZmCCT10. Significant progress has been made in studying how these genes regulate maize domestication and its adaptation to high latitudes. However, our knowledge of the molecular mechanisms behind maize’s adaptation to cold temperatures at high latitudes remains limited. A recent study published in Cell by Zeng et al. cloned a basic helix-loop-helix (bHLH) transcription factor, COLD-RESPONSIVE OPERATION LOCUS 1 (COOL1), which negatively regulates maize cold tolerance through genome-wide association study. The causal variants in the COOL1 promoter are positioned within an A-box motif, which affects binding by ELONGATED HYPOCOTYL5 (HY5), a transcription factor that represses COOL1 transcription. At the molecular level, CPK17, a negative regulator, interacts with COOL1 to modulate cold stress. The frequency of two COOL1 alleles was found to be unevenly distributed across South and North America. The frequency of the cold-tolerant allele was significantly higher at higher latitudes, whereas there was no significant difference in the frequencies of the two alleles at lower latitudes. This result suggests that the COOL1 gene enhances maize's cold resistance, facilitating its domestication and spreading to high-latitude regions.

Rong Zeng et al. 2025. A natural variant of COOL1 gene enhances cold tolerance for high-latitude adaptation in maize Cell. :doi: 10.1016/j.cell.2024.12.018.
   A natural variant of COOL1 gene enhances cold tolerance for high-latitude adaptation in maize
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Wang, T et al. 2025. Single-cell transcriptomes reveal spatiotemporal heat stress response in maize roots. Nat Commun. 16:177.
   Single-cell transcriptomes reveal spatiotemporal heat stress response in maize roots.

Heat stress significantly impacts crop productivity, particularly by disrupting root system architecture. To understand the cellular mechanisms underlying this response, authors performed single-cell RNA sequencing on maize root cells exposed to heat stress. They identified nine major cell types (columella, pericycle, endodermis, stele, xylem, cortex, phloem, epidermis, and initials) and characterized their distinct transcriptional responses, revealing cell-type-specific stress response pathways. Using pseudotime analysis, they reconstructed developmental trajectories for columella and cortex cell lineages and identified regulatory modules differentially activated in response to heat stress. They further identified cortex cell-type-specific genes crucial for apical cortex development and heat tolerance. Comparative analyses across maize, Arabidopsis, and rice highlighted conserved and divergent features of root cell-type transcriptomes in response to heat stress. This study provides a valuable resource for understanding the cellular and molecular mechanisms of heat stress tolerance in maize roots, paving the way for developing more heat-resilient crops.

Wang, T et al. 2025. Single-cell transcriptomes reveal spatiotemporal heat stress response in maize roots. Nat Commun. 16:177.
   Single-cell transcriptomes reveal spatiotemporal heat stress response in maize roots.
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Hao Wu et al. 2025. AutoGP: An Intelligent Breeding Platform for Enhancing Maize Genomic Selection Plant Commun. :doi: 10.1016/j.xplc.2025.101240.
   AutoGP: An Intelligent Breeding Platform for Enhancing Maize Genomic Selection

Genomic selection (GS) is a revolutionary breeding strategy that has significantly advanced plant breeding over the past decades by optimizing resource allocation, reducing phenotyping, and increasing genetic gain. Beyond traditional algorithms in GS, such as rrBLUP and GBLUP, leveraging machine learning and deep learning algorithms increases GS's power and flexibility in integrating prior biological, genetic, environmental, and high-throughput phenotyping data. Harnessing these data and knowledge in one platform is challenging but attractive for geneticists and breeders. A recent study by Wu et al. introduced a user-friendly intelligent breeding platform called AutoGP to simplify computational procedures in GS, making it accessible to breeders. Within AutoGP, three functions are included: (1) High-quality genotyping extraction based on existing gene regulatory networks; (2) High-throughput phenotype extraction with a mini-program on a phone; (3) Machine learning and deep learning pipelines for GS. For the GS function, five modules are provided: (1) Model training; (2) Phenotype prediction; (3) Integrated training and prediction; (4) Selection of optimal parents; (5) Integrated training and selection. A real-world case study using a Complete-diallel design plus Unbalanced Breeding-like Inter-Cross (CUBIC) population demonstrated reliable predictive ability when environmental information was embedded in the GS model. The advent of AutoGP is expected to accelerate the practical application of GS in maize breeding programs.

Hao Wu et al. 2025. AutoGP: An Intelligent Breeding Platform for Enhancing Maize Genomic Selection Plant Commun. :doi: 10.1016/j.xplc.2025.101240.
   AutoGP: An Intelligent Breeding Platform for Enhancing Maize Genomic Selection
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Mitchell E Baum et al. 2025. The optimum nitrogen fertilizer rate for maize in the US Midwest is increasing. Nat Commun. 16:404.
   The optimum nitrogen fertilizer rate for maize in the US Midwest is increasing.

The authors investigates the changes in the optimal nitrogen fertilizer rates for corn production in the US Midwest from 1991 to 2021. Through a combination of long-term (n = 379) and short-term (n = 176) experiments, the research reveals that the economic optimum nitrogen rate has increased by 2.7 kg N ha−1 yr−1 (1.2% per year), coinciding with increases in grain yields and nitrogen losses. The study also estimates the environmental optimum rate, which has risen over time but at a slower pace than the economic optimum rate. Reducing nitrogen rates from the economic to the environmental optimum could decrease US corn productivity by 6% while only slightly reducing nitrogen losses. The research underscores the need for enhanced assessments and predictability of both economic and environmental optimum nitrogen rates to meet growing corn production demands while minimizing unnecessary nitrogen losses. The findings are crucial for improving nitrogen management recommendations and policies in the region, balancing the need for increased food production with environmental sustainability. By establishing decadal trends in optimal N rates and quantitatively linking productivity with environmental sustainability, the research supports the development of more sustainable and efficient N management practices.

Mitchell E Baum et al. 2025. The optimum nitrogen fertilizer rate for maize in the US Midwest is increasing. Nat Commun. 16:404.
   The optimum nitrogen fertilizer rate for maize in the US Midwest is increasing.
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Tibbs Cortes, LE et al. 2024. Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize. Genome Res. :doi: 10.1101/gr.279027.124.
   Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize.

Phenotypic variation is shaped by genetic factors, environmental determinants, and their interplay. Identifying the causal genes and environmental variants underlying phenotypic plasticity, the property of a given genotype to produce different phenotypes in response to distinct environmental conditions, is challenging and will boost our understanding of genotype-by-environment. Utilizing the public 19 traits measured in the maize nested association mapping (NAM) population grown in 11 natural environments, comprehensive identification of genomic and environmental determinants was done by applying the critical environmental regressor through informed search - joint genomic regression analysis (CERIS-JGRA) framework. Environmental indices for each trait are the primary environmental factor that drives the phenotypic plasticity of the whole population and enable accurate prediction in new environments for each individual. Genome-wide association studies identify large numbers of candidate genes for phenotypic parameters (intercept and slope) and the results were deposited as a track on the MaizeGDB genome browser. Two alternative models, the regulatory gene model and the allelic sensitivity model were depicted to explain the different architecture of phenotypic plasticity.

Tibbs Cortes, LE et al. 2024. Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize. Genome Res. :doi: 10.1101/gr.279027.124.
   Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize.
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Wang, Q et al. 2024. ZmICE1a regulates the defence–storage trade-off in maize endosperm Nature Plants. :doi: 10.1038/s41477-024-01845-2.
   ZmICE1a regulates the defence–storage trade-off in maize endosperm

The article reveals the role of ZmICE1a, a monocot-specific transcription factor, in regulating the defense-response and storage trade-off in maize endosperm. The study found that ZmICE1a is predominantly expressed in the endosperm and affects starch content and kernel weight. Loss of function of ZmICE1a resulted in reduced starch synthesis and defense gene regulation. RNA sequencing and CUT&Tag-seq analyses showed that ZmICE1a activates genes related to starch synthesis while suppressing those involved in defense mechanisms and phytohormone synthesis, particularly indole-3-acetic acid (IAA) and jasmonic acid (JA). The research also identified a JA-ZmJAZ9-ZmICE1a-MPI signaling axis that plays a role in defense regulation. Overall, the study provides insights into the complex regulatory network in maize endosperm development, highlighting ZmICE1a as a key coordinator of defense and storage balance.

Wang, Q et al. 2024. ZmICE1a regulates the defence–storage trade-off in maize endosperm Nature Plants. :doi: 10.1038/s41477-024-01845-2.
   ZmICE1a regulates the defence–storage trade-off in maize endosperm
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Ze Li et al. 2024. The Heat shock factor 20-HSF4-Cellulose synthase A2 module regulates heat stress tolerance in maize. Plant Cell. :doi: 10.1093/plcell/koae106.
   The Heat shock factor 20-HSF4-Cellulose synthase A2 module regulates heat stress tolerance in maize.

Due to rising temperatures, it is important to understand the mechanisms underlying plant heat stress responses. Li et al. performed a RNA-seq of B73 seedlings exposed to 45°C for different times and identified a class B2a heat shock factor (HSF) Hsf20, as an essential transcription factor in heat stress responses. CRISPR generated hsf20 mutants displayed greater heat tolerance, less ion leakage and less reactive oxygen species (ROS) accumulation when compared to wild type, indicating that HSF20 negatively regulates heat stress response in maize. RNA-seq and DNA affinity purification sequencing (DAP-seq) identified Cellulose synthase A2 (CesA2) and Hsf4 as potential targets of HSF20. Through Cleavage Under Targets and Tagmentation followed by qPCR (CUT&Tag–qPCR) and electrophoretic mobility shift assays (EMSAs), it was found that HSF20 binds to the promoters of both CesA2 and Hsf4. This binding is sufficient to repress the transcription of both targets, as demonstrated by transient expression assays in N. benthamiana. CRISPR generated hsf4 mutants displayed decreased survival rate to heat stress, while Hsf4 and CesA2 overexpression (OE) lines had increased survival when compared to wild type, indicating that Hsf4 and CesA2 are positive regulators of heat stress responses. Cellulose content measurements from hsf20, hs4-OE, and CesA-OE lines accumulate more cellulose content than wild type, suggesting that more cellulose may improve heat tolerance. In all, this paper demonstrates that HSF20 decreases maize seedling tolerance to heat stress by repressing Hsf4 and CesA2 and causing a reduction in cellulose content, elucidating the importance between cell wall remodeling and heat tolerance in maize.

Ze Li et al. 2024. The Heat shock factor 20-HSF4-Cellulose synthase A2 module regulates heat stress tolerance in maize. Plant Cell. :doi: 10.1093/plcell/koae106.
   The Heat shock factor 20-HSF4-Cellulose synthase A2 module regulates heat stress tolerance in maize.
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