The inhibited growth of primary roots (PRs) is a typical adaptive response of Arabidopsis to low phosphate (LP) stress. The role of auxin and its relationship with iron (Fe) in this process, however, remains unclear. In this study, we demonstrated that auxin acts as a positive regulator. A high concentration of auxin at the tips of PRs stimulates vigorous PR growth in both LP-arf7 arf19 and LP-yucca mutants. The application of a low dose of exogenous auxin can partially mitigate LP-induced PR growth inhibition. Enhanced auxin signaling, achieved through overexpression of ARF7 or ARF19, also promotes PR growth in LP-transgenic plants. Conversely, LP stress negatively regulates the polar transport of auxin, leading to reduced PIN activity at PRs. Mutations of PINs and application of NPA, therefore, exacerbate the impact of LP stress on PR growth. Consistently, PIN activity remains stable in the PRs of LP-arf7 arf19 mutants, and mutation of PINs normalizes the inhibited growth of these mutants. Furthermore, a correlation is observed between decreased auxin activity and increased Fe at LP-PRs. Fe accumulation triggers a burst of reactive oxygen species (ROS), which inhibits polar auxin transport and distribution at the tips of PRs. Changes in Fe and ROS levels influence auxin activity at LP-PRs, while auxin conversely affects Fe accumulation at these sites. Consequently, Fe levels are low at the PRs of LP-arf7 arf19 mutants, LP-yucca mutants, and auxin-treated LP-WT plants. Conversely, they are high in PRs of LP-pin2 mutant and NPA-treated LP-WT plants. In conclusion, accumulated Fe triggers a burst of ROS, disrupting auxin transport by decreasing PIN activity at LP-PRs. This disruption subsequently inhibits cell division and overall PR growth.

Plants must coordinate chloroplast biogenesis with environmental conditions during seedling establishment, as failure to do so results in impaired phototrophic growth. Despite the biological importance of this early developmental stage, the influence of environmental factors on chloroplast biogenesis remains poorly understood. Here, we reveal a crucial role for GENOMES UNCOUPLED1 (GUN1)-mediated biogenic retrograde signaling in safeguarding chloroplast development and supporting seedling growth under heat stress. Loss of GUN1 causes severe bleaching and impaired photomorphogenesis at elevated temperatures. Genetic interaction analyses show that EXECUTER1 (EX1) and EXECUTER2 (EX2), key components of chloroplast ROS-associated operational retrograde signaling, modulate the heat-sensitive phenotype of gun1 mutants, indicating crosstalk between biogenic and operational retrograde pathways. We further demonstrate that the de-repressed expression of photosynthesis-associated nuclear genes, that is, genomes uncoupled expression, is a major contributor to the heat sensitivity and failed chloroplast biogenesis in gun1 seedlings under heat stress. These findings extend the current understanding of GUN1 function by showing its contribution to chloroplast development and thermotolerance through biogenic retrograde signaling during early seedling growth.

Soil salinization poses a global threat to agricultural productivity by degrading arable land. Preventing the rapid degradation of chlorophyll caused by saline–alkali stress is a crucial means to improve plant resistance and productivity. In this study, RNA sequencing identified CsPPH, a pheophytinase-encoding gene that functions as a negative regulator of both photosynthesis and saline–alkali tolerance in cucumber (Cucumis sativus L.). Saline–alkali stress rapidly induces the expression of related to APETALA2 2.12 (CsRAP2.12). Subsequently, CsRAP2.12 activates the transcription of both ethylene response factor 113-like (CsERF113L) and CsRAP2.7, while CsERF113L further transcriptionally regulates CsRAP2.7. CsERF113L promotes chlorophyll degradation and reactive oxygen species (ROS) accumulation both through direct transcriptional upregulation of CsPPH, chlorophyll b reductase (CsNYC1), and chlorophyllase 2 (CsCLH2) and by indirectly stimulating ethylene synthesis via upregulation of 1-aminocyclopropane-1-carboxylic acid synthase 6/9/10 (CsACS6/9/10), thereby impairing photosynthesis and accelerating senescence. CsRAP2.7 indirectly promotes saline–alkali stress-induced chlorophyll degradation and photosynthetic inhibition by facilitating CsERF113L-mediated transcriptional activation of CsPPH, CsCLH2, and CsACS6/9/10. Therefore, knockout of either CsRAP2.12, CsERF113L, or CsRAP2.7 significantly alleviated chlorophyll degradation and enhanced photosynthetic performance under saline–alkali stress, ultimately improving antioxidant capacity and stress tolerance. These findings reveal that the CsRAP2.12–CsERF113L/CsRAP2.7 module promotes saline–alkali stress-induced chlorophyll degradation and photosynthetic inhibition via a dual regulatory mechanism. Genetic disruption of this module significantly improves cucumber tolerance to saline–alkali stress.

The assembly of functional biological materials requires precise control over the synthesis and deposition of their constituent polymers. In plants, specialized cells gain exceptional strength from their secondary cell walls (SCWs), though the mechanisms ensuring the coordinated production of SCW components remain poorly understood. Using cotton fiber as a model for massive cellulose deposition, we uncover a multi-tiered transcriptional cascade involving the R2R3-MYB transcription factor GhMYB44. We show that GhMYB44 functions as a positive regulator that directly activates the pivotal NAC factor, GhFSN43, which in turn commands key cellulose synthesis genes, establishing a complete regulatory module from an upstream MYB to downstream structural genes. Crucially, we reveal that this entire pathway is potentiated at two distinct nodes through protein–protein interactions: an upstream GhMYB44–GhREV5 complex enhances the initial signal, while a downstream GhFSN43–GhFSN1 complex functions cooperatively to strengthen downstream transcriptional activation. Our findings suggest that GhMYB44 participates in a multi-tiered regulatory module where transcriptional output is enhanced by layered synergistic protein–protein interactions. This work clarifies a key regulatory pathway controlling SCW biosynthesis and offers novel targets for improving cotton fiber quality.

Somatic embryogenesis (SE) enables somatic cells to develop directly into embryos. SE is a major approach of regeneration, but recalcitrance to SE has become one of the main obstacles to biotechnology-aided breeding, especially for perennial woody plants. Citrus is one of the most important fruit crops in the world, and glycerol has long been used to induce SE from the embryogenic callus (EC) of citrus. Recently, we reported that CsIAA4-mediated repression of auxin signaling plays a critical role in glycerol-induced citrus SE, but the downstream signaling cascade remains to be elucidated. In this study, the HD-Zip transcription factor CsHAT14 was identified as a key downstream regulator of auxin signaling in citrus SE. CsARF5 directly promoted CsHAT14 expression, which repressed SE through suppression of critical regeneration-related genes (CsDOF3.4 and CsWOX13) and the auxin efflux gene CsPILS5. CsIAA4 interacted with CsARF5, and this interaction attenuated CsARF5-mediated transcriptional activation of CsHAT14, thereby de-repressed CsHAT14- directly suppressed genes including CsDOF3.4, and thus promoted SE. Knockdown of CsDOF3.4 resulted in downregulation of cell cycle-related genes and impaired SE. Our findings established the CsIAA4–CsARF5 and CsHAT14–CsDOF3.4 modules-mediated auxin signaling cascade that coordinates citrus SE, which advanced our understanding of the mechanisms underlying SE and supported improvement of regeneration efficiency in citrus biotechnology applications.

The burgeoning multi-omics data have provided deep insights into the regulatory mechanisms underlying plant growth and development. However, revealing the complete landscape of gene regulatory networks underpinning various developmental processes remains challenging. Here, a multi-omics integrative gene network of the pear fruit development process was constructed through integrating 3D genomic, transcriptomic, transcription factor (TF) binding, chromatin accessibility, protein structure, and proteomic data. This integrative network comprises over 45,678 elements interconnected by more than 3.15 million edges and exhibits great potential in predicting regulatory and interactive relationships involved in the formation of key fruit quality traits (e.g., sugar, stone cell). In particular, the integrative network was applied to predict interactors of PbrII5, an inhibitor of vacuolar sucrose hydrolysis, and the predicted interactors were further validated through molecular experiments. Moreover, the network showed good performance in automatically predicting fruit trait-related genes by leveraging machine learning models. Specifically, a set of sugar metabolism-related genes was newly predicted, and their functions were verified through overexpression in pear fruit. In addition, extensive regulatory network divergence was observed between duplicated genes, with neofunctionalization being the dominant evolutionary process reshaping network connections of duplicated genes. Lastly, a multi-omics network database, pearGRN (http://peargrn.njau.edu.cn), was developed to facilitate further research for resolving complex gene regulatory relationships. This study lays a strong foundation for revealing novel regulatory mechanisms underlying fruit development and quality formation.

Biomass allocation is crucial for predicting ecosystem responses to global change, and yet, whether patterns follow the plastic optimal partitioning theory (OPT) or the constrained allometric partitioning theory (APT) remains contentious across different biomes. A key uncertainty is whether vast, functionally distinct ecosystems, such as temperate and alpine drylands, show different allocation strategies. Here, we investigated root:shoot ratio (R/S) patterns across 120 sites spanning temperate and alpine drylands in northern China. Significant differences in allocation were observed, with temperate drylands showing lower R/S than alpine regions. In temperate drylands, R/S scaled allometrically with plant community size, consistent with APT, with key soil factors exerting only an indirect influence through their effects on plant community size. Conversely, in alpine drylands, R/S was insensitive to plant community size and instead responded directly to the mean annual temperature, a pattern indicative of OPT. We propose that this strategic divergence is linked to their underlying community functional structures. Communities with greater functional dissimilarity may achieve higher niche complementarity, providing the necessary capacity to optimize allocation in response to environmental constraints. Our findings demonstrate that climatic regimes drive alternative biomass allocation strategies, providing both a predictive framework for vegetation responses and a theoretical basis for dryland ecosystem restoration under climate change.

Sphingolipids, including ceramides, are structural membrane lipids that function in membrane trafficking and cell polarity. Very-long-chain (VLC) ceramide synthases are essential for plant growth and development, but how VLC ceramide synthases affect developmental programs and their exact roles in plant growth remain unclear. Here, we report that two VLC ceramide synthases, LONGEVITY ASSURANCE GENE ONE HOMOLOG 1 (LOH1) and LOH3, link sphingolipid metabolism and thermomorphogenesis, that is, plant morphogenesis in response to higher temperatures. We found that high ambient temperature (28°C) induced an increase in plant VLC ceramide contents, and defects in LOH1 or LOH3 function inhibited hypocotyl elongation at this temperature. PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) potentiates the thermal sensitivity of hypocotyl morphogenesis in a LOH1- and LOH3-dependent manner, directly binding to the LOH1 and LOH3 promoters to enhance their expression. Strikingly, LOH1 and LOH3 also enhance PIF4-dependent transcriptional activation of downstream genes, including PIF4 itself, LOH1, and LOH3. Our study reveals a regulatory mechanism in which PIF4 activates the transcription of LOH1 and LOH3; in turn, LOH1 and LOH3 enhance PIF4 signaling by supporting PIF4-mediated transcriptional responses, thereby controlling plant growth in response to temperature.

Transposable elements (TEs) are abundant and evolutionarily important components of plant genomes, yet the population-scale landscape of TE insertion polymorphisms (TIPs) and their regulatory roles in gene expression and trait variation remain insufficiently understood. In this study, genomic resequencing, RNA-seq, and agronomic trait data from a panel of 381 Brassica napus accessions were integrated to characterize population-level TIP dynamics and assess their impacts on gene regulation, ecotype differentiation, and phenotypic innovation. Using a developed computational pipeline, a robust pan-TE library was constructed based on 28 diverse reference genomes, and 77,603 TIP loci were profiled by mapping resequencing data from 381 accessions. Most TE insertions were found to be dispensable and weakly linked to neighboring SNPs, suggesting that they represent recent or ecotype-specific variants that serve as independent sources of regulatory and adaptive diversity in B. napus. The regulatory roles of TEs were examined through two complementary strategies (direct-effect analyses and TIP-based eQTL mapping), which together revealed that TEs modulate gene expression via both cis- and long-range trans-effects. Notably, TE-mediated trans-regulation, rarely investigated in previous studies, was found to be widespread, with trans-effects predominating and displaying strong tissue specificity, emphasizing the extensive regulatory influence of TEs on the plant transcriptome. Furthermore, selective sweep analyses identified ecotype-specific TIPs associated with adaptive divergence, particularly those contributing to semi-winter type diversification. TIP-based genome-wide association studies (GWAS) revealed 1,102 candidate insertions significantly associated with key agronomic traits, including flowering time, fatty acid composition, and glucosinolate content, some of which were not detected by SNP-based analyses. This study provides the population-scale atlas of TE insertions in B. napus, uncovers their extensive regulatory roles, and demonstrates their contribution to adaptation and trait variation, offering valuable resources for breeding and functional genomics.

Low light is one of the main environmental factors influencing the content of soluble sugar in oriental melon fruit under protected cultivation. As a supplementary light source, light-emitting diodes have been widely used to improve fruit quality. However, the regulatory mechanism of light quality on oriental melon fruit quality remains unclear. Here, the high sucrose melon fruit was treated with different light qualities during the development stage in a greenhouse, and the results showed that red light significantly increased the sucrose content and upregulated the expression of sucrose transport and metabolism-related genes (CmSUT2, CmSWEET10, and CmSUS2) in melon fruit. In addition, CmWRKY28 was found using a yeast single-hybrid cDNA library, which responded to red light treatment and could bind to the promoters of CmSUT2, CmSWEET10, and CmSUS2 to activate their expression. Moreover, CmHY5 acted as a positive regulator of sucrose accumulation by directly binding to CmSUT2 and CmWRKY28 promoters. CmHY5 also interacted with CmWRKY28 at the protein level to participate in the regulation of sucrose accumulation. Taken together, these findings revealed that red light induced CmHY5 and CmWRKY28 to positively regulate the expression of target genes, promoting the accumulation of more sucrose in melon fruit. This study provided new insights into alleviating the effects of low-light conditions on melon fruit quality.

Jasmonic acid (JA), a key phytohormone in plant defense, plays essential roles in regulating plant stress responses and growth. However, how JA signaling and nitrate signaling regulate nitrate uptake in maize (Zea mays L.) remains elusive. Here, we report that low-nitrate stress promotes JA accumulation in maize roots, and JA treatment leads to a low-nitrate phenotype. JA triggers ZmbHLH99 expression, encoding a transcription factor that binds to ZmNLP3.2 promoter and inhibits ZmNLP3.2 expression, thereby regulating nitrate uptake. In addition, the JA ZIM-domain (JAZ) transcriptional repressor ZmZIM13 interacts with ZmbHLH99 to release its inhibitory effect on the ZmNLP3.2–ZmNRT cascade and promotes ZmNLP3.2 expression. Furthermore, loss of ZmbHLH99 or overexpression of ZmZIM13 promotes plant growth and nitrate uptake, leading to higher grain yield. These findings reveal the transcriptional regulatory landscape of how JA signaling regulates nitrate uptake via the ZmZIM13–ZmbHLH99–ZmNLP3.2 module and integrates with nitrate signaling to coordinate plant growth and stress responses.

Argonaute proteins (AGOs) are central to RNA silencing pathways and play critical roles in plant antiviral defense. However, the functions of individual AGOs in rice remain incompletely understood. In this study, we demonstrate that rice AGO2 contributes to resistance against rice ragged stunt virus (RRSV) through a regulatory module involving miR167g-3p and its target gene, SNAP32. Immunoprecipitation coupled with small RNA sequencing revealed that AGO2 associates not only with virus-derived small interfering RNAs (vsiRNAs) but also preferentially associates with miR167g-3p during RRSV infection. Functional analyses further showed that miR167g-3p expression is induced upon infection. Transgenic rice lines overexpressing miR167g-3p exhibited enhanced resistance, whereas knockdown lines were more susceptible. SNAP32 was validated as a direct target of miR167g-3p through transient expression assays in Nicotiana benthamiana and dual-luciferase assays in rice protoplasts. Expression analyses confirmed that miR167g-3p represses SNAP32 at the transcript level. Consistently, SNAP32-overexpressing plants displayed increased susceptibility to RRSV, while snap32 knockout plants showed enhanced resistance, supporting a negative role of SNAP32 in antiviral defense. Together, these findings establish a regulatory pathway in which AGO2 promotes antiviral immunity by stabilizing miR167g-3p to repress SNAP32, thereby restricting RRSV infection. This work advances our understanding of AGO2-mediated defense in rice and highlights the use of a miRNA 3p strand within an AGO–miRNA-target module as an important layer of resistance against viral pathogens.

Parent-of-origin effects are usually caused by selective expression of maternal or paternal alleles. Although genome-wide studies suggest that imprinted gene expression occurs primarily in the endosperm in plants, detailed studies of allele-specific gene expression and its associations with parent-of-origin phenotypes are scarce. NAC20 and NAC26 (NAC20/26 hereafter), a pair of tightly linked NAC-family transcription factors, redundantly regulate grain filling and albumin accumulation in rice endosperm. Here, we show that NAC20/26 exhibited allele-specific maternal expression, and the floury endosperm phenotype of the nac20/26 double mutant was inherited with a maternal effect. Further studies showed that the imprinted NAC20/26 expression and floury endosperm phenotype with a maternal effect are associated with insertions of two TEs in NAC20/26 of two Japonica rice varieties, but not in two Indica ones examined. The maternal NAC20/26 expression was associated with elevated DNA methylation in their paternal DMRs, and deletions of those TEs by gene editing led to decreased methylation in these DMRs, and biallelic NAC20/26 expression. Geographical analyses showed that Japonica varieties with high-latitude origins examined carried these TEs. These results establish that TE-mediated DNA methylation lead to grain filling with a maternal effect in high-latitude Japonica rice varieties, which may associate with northward expansion of rice during domestication.