Scossa F, Bulut M, Naake T
… +2 more, D'Auria JC, Fernie AR
J Integr Plant Biol
· 2026 Apr · PMID 41858065
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Convergence and parallelism are contentious terms in evolutionary biology, but both denote essentially a ubiquitous phenomenon: The occurrence of similar phenotypes, in different evolutionary lineages, in a way that cann...Convergence and parallelism are contentious terms in evolutionary biology, but both denote essentially a ubiquitous phenomenon: The occurrence of similar phenotypes, in different evolutionary lineages, in a way that cannot be easily reconducted to descent from a shared ancestor. In this article, we trace the historical definitions of the two terms and the current conceptual frameworks to classify instances of repeated evolution, presenting the limits of these approaches in considering convergence and parallelism as a strict dichotomy rather than as part of a continuum along the spectrum of phenotypic similarity. We then present cases of convergence-broadly defined-from plant domestication and specialized metabolism, with the objective of understanding the intricacies between natural selection, constraints and drift underlying the recurrent appearance of complex traits.
The accelerating global population growth and increasing environmental pressures driven by climate change have made food security an urgent scientific objective. In addition to genetic modifications aimed at yield improv...The accelerating global population growth and increasing environmental pressures driven by climate change have made food security an urgent scientific objective. In addition to genetic modifications aimed at yield improvement, minimizing yield reduction and postharvest decay caused by pathogenic infections is essential for reinforcing global food supply systems. Metabolites, as fundamental biochemical constituents of life, form the basis of many plant defense strategies that have evolved over millions of years to counter pathogen invasion-functioning both as direct antimicrobial and anti-herbivory agents as well as inducers of internal immune signaling networks. Despite the extensive diversity and intricate biosynthetic pathways of plant metabolites, advances in high-performance mass spectrometry and nucleotide sequencing have clarified the immune-related roles of several metabolites through conventional genetic and transcriptomic analyses. The emergence of artificial intelligence (AI) has provided a transformative means by which to integrate and interpret complex, large-scale data sets, offering insights unattainable through traditional approaches and expediting the mapping of metabolite-immunity interactions. This review summarizes recent progress in elucidating the functions of various plant metabolites, including primary metabolites and secondary metabolites, in plant immune responses. This study also details their reprogramming by pathogens. Finally, it examines the prospective applications of nanoscience, de novo domestication, and artificial intelligence in the rational design of next-generation artificial elicitors.
A transformation system exploits lily bulb scale propagation and de novo formation of bulblets, integrating tissue culture with non-tissue culture approaches. Through optimized scale propagation and disinfection treatmen...A transformation system exploits lily bulb scale propagation and de novo formation of bulblets, integrating tissue culture with non-tissue culture approaches. Through optimized scale propagation and disinfection treatments, it achieves efficient stable gene overexpression and editing in lily.
This commentary summarizes hybrid sterility models in plants, with an emphasis on a recent study that addresses the genetic basis of the RIS/RIA-RID-RIR system underlying S44-mediated hybrid sterility between Oryza longi...This commentary summarizes hybrid sterility models in plants, with an emphasis on a recent study that addresses the genetic basis of the RIS/RIA-RID-RIR system underlying S44-mediated hybrid sterility between Oryza longistaminata and indica rice, revealing a novel killer-protector-target model integrated with modifiers that regulate reproductive isolation.
Zhang X, Zhang R, Zhang Y
… +13 more, Yang T, Wu L, Cao Y, Xiao J, Li J, Gao X, Cao X, Liu J, Xin M, Zong Y, Ni Z, Sun Q, Yao Y
J Integr Plant Biol
· 2026 Jul · PMID 41840849
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Wheat (Triticum aestivum L.) yield and quality are critically influenced by starch and seed storage protein (SSP) content. In this study, we demonstrate that the transcriptional adapter ADA2 physically interacts with his...Wheat (Triticum aestivum L.) yield and quality are critically influenced by starch and seed storage protein (SSP) content. In this study, we demonstrate that the transcriptional adapter ADA2 physically interacts with histone acetyltransferase GENERAL CONTROL NONDEREPRESSIBLE 5 (GCN5) and regulates starch synthesis and SSP content in wheat grains. In ada2 mutants, reduced H3K9ac enrichment was observed in the promoter regions of key starch synthesis genes and the SSP regulator NAC019 during endosperm development. This reduction leads to lower expression levels, resulting in decreased starch content, smaller grains, reduced yield, and poor gluten quality. We also found that ADA2 contains an intrinsically disordered region 2 (IDR2) that undergoes liquid-liquid phase separation (LLPS) and forms nuclear condensates. In vitro assays, the LLPS of ADA2 is affected by GCN5 through direct interaction with IDR2, and the ratio of their concentrations determines the behavior of phase-separated condensates and HAT activity. High levels of GCN5 can dissolve ADA2 aggregates, while excessive ADA2 recruits and sequesters GCN5 into co-aggregated droplets, with lower HAT activity. This potential dynamic regulatory mechanism may facilitate the efficient promotion of transcription by the ADA2-GCN5 complex in wheat. Finally, we identified an elite haplotype of ADA2-B Hap2, which is significantly associated with grain size and weight, highlighting its potential as a candidate gene for genetic improvement of wheat yield.
The high-efficiency multiplex gene editing technology based CRISPR-Cas12i3-5M is capable of simultaneously editing 13 target sites in soybean, and was used to generate germplasm with high oleic acid content and no beany...The high-efficiency multiplex gene editing technology based CRISPR-Cas12i3-5M is capable of simultaneously editing 13 target sites in soybean, and was used to generate germplasm with high oleic acid content and no beany flavor.
Hao X, Hu X, Pan Y
… +9 more, Zhang Q, Ou R, Jiang F, Liu F, Zhang J, Wang W, Xing G, Gai J, He J
J Integr Plant Biol
· 2026 Jul · PMID 41840828
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The subgenus Soja, including annual wild (Glycine soja) and cultivated soybean (Glycine max), is the primary germplasm source of soybeans. We analyzed the genome constitution of 750 wild and cultivated accessions from th...The subgenus Soja, including annual wild (Glycine soja) and cultivated soybean (Glycine max), is the primary germplasm source of soybeans. We analyzed the genome constitution of 750 wild and cultivated accessions from the Chinese Soybean Germplasm Population (CSGP), covering ~20.42% genic and ~79.58% intergenic regions. Most previous genomic studies focused on gene compositions and functions, with intergenic regions being non-emphasized yet. Our results showed: (i) We defined 48,465 gene blocks (2-23 alleles/gene block) in the genic region. For intergenic region partitioning, the linkage-disequilibrium (LD) confidence interval (CI) method performed the best, identifying 137,104 SNP LD blocks (SNPLDBs, 2-24 haplotypes/SNPLDB). (ii) Wild and cultivated accessions shared 98.5%/80.9% genes/alleles and 88.0%/80.8% SNPLDBs/haplotypes, indicating high wild genomic contribution to the cultivated genome; genic and intergenic regions exhibit distinct allele/haplotype dynamics during domestication. (iii) We proposed the three-case restricted two-stage multi-locus multi-allele genome-wide association study (three-case RTM-GWAS), identifying 82 day-to-flowering (DTF) main-effect genes and 47 intergenic-SNPLDB-impacted genes (by 34 SNPLDBs) (total 129 genes, 746 alleles). These explained 98.87% of phenotypic variance (PV), with main-effect and SNPLDB-impacted genes accounting for 68.61% and 30.26% PV, respectively; gene-allele(s) impacted by SNPLDB-haplotype (one/both sides) were also identified. (iv) Domestication process excluded more large-effect positive alleles that shorten DTF in cultivated accessions, enhancing DTF's transgressive recombination potential in earliness. This study provides insights into genic/intergenic genome regions, offering a novel understanding of soybean functional genomics.
Liao S, Wei Y, Zhu Y
… +11 more, Li K, Chen T, Zhao S, Wu F, Wang J, Yu P, Xie H, Chen L, Cai Q, Xie H, Zhang J
J Integr Plant Biol
· 2026 Jul · PMID 41840826
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Seed storability is crucial for maintaining vigor at the sowing stage and ensuring agricultural sustainability. Although molecular chaperones are well characterized in protein homeostasis, their roles in regulating ABA r...Seed storability is crucial for maintaining vigor at the sowing stage and ensuring agricultural sustainability. Although molecular chaperones are well characterized in protein homeostasis, their roles in regulating ABA receptor stability and starch integrity during seed aging remain unclear. Here, we demonstrate that OsCPN10a enhances storability by maintaining ABA homeostasis, suppressing ROS accumulation, and preserving starch granule structure. Genetic and biochemical analyses reveal that OsCPN10a functions upstream of the OsCPN20-OsHSP60-3B cascade, directly interacts with both partners to promote complex assembly, and negatively regulates ABA signaling. The resulting trimeric complex interacts with OsPYL10, facilitating receptor dissociation and high-affinity association with the PP2C phosphatase OsABIL1 to attenuate signaling. This study reveals a non-canonical function of molecular chaperones in directly modulating hormone receptor signaling, establishing a mechanistic link between protein homeostasis and ABA sensitivity in seeds.
GLYCOGEN SYNTHASE KINASE 3 (GSK3), a negative regulator of brassinosteroid signaling, phosphorylates and stabilizes the seed dormancy protein DOG1L4, which in turn activates ABSCISIC ACID INSENSITIVE 5 (ABI5) to enhance...GLYCOGEN SYNTHASE KINASE 3 (GSK3), a negative regulator of brassinosteroid signaling, phosphorylates and stabilizes the seed dormancy protein DOG1L4, which in turn activates ABSCISIC ACID INSENSITIVE 5 (ABI5) to enhance seed dormancy. GSK3 also phosphorylates ABI5. This dual-target mechanism suggests a strategy for controlling seed dormancy and germination in crops.
Phillyrin, a unique antiviral lignan exclusive to Forsythia suspensa, shows potent anti-influenza activity. However, its broad pharmaceutical application is hindered by low and variable natural accumulation, underscoring...Phillyrin, a unique antiviral lignan exclusive to Forsythia suspensa, shows potent anti-influenza activity. However, its broad pharmaceutical application is hindered by low and variable natural accumulation, underscoring the need to elucidate its biosynthetic pathway for sustainable production. In this study, we used an integrated metabolomic and transcriptomic approach to investigate tissue-specific phillyrin biosynthesis in F. suspensa. We identified two O-methyltransferases (FsE4MT01 and FsE4MT02) that catalyze the methylation of (+)-epipinoresinol to form phillygenin and a UDP-glycosyltransferase (FsP4'GT) that glucosylates phillygenin to yield phillyrin. Using recombinant proteins expressed in Escherichia coli, we validated their in vitro catalytic activities and determined their kinetic parameters. Molecular docking and site-directed mutagenesis of key residues further revealed the structural basis of their catalytic mechanisms. The in vivo functions of these enzymes were confirmed through heterologous expression in Nicotiana benthamiana and F. suspensa leaves. Importantly, by developing a transient leaf-expression system in F. suspensa, we demonstrated that overexpression of FsE4MTs and FsP4'GT substantially increased the production of phillygenin and phillyrin, respectively, whereas virus-induced gene silencing (VIGS) of these genes reduced the accumulation of the corresponding products. Notably, enhanced phillyrin production was also achieved by expressing FsE4MTs and FsP4'GT in the related species Forsythia × intermedia, highlighting the potential of these key enzymes for metabolic engineering. Our findings elucidate the terminal steps of phillyrin biosynthesis and provide a strategic foundation for engineering the sustainable production of this pharmaceutically valuable compound.
Casδ is a recently identified evolutionary transitional CRISPR system characterized by its compact size (~900 amino acids), broad temperature tolerance, and guidance with a short crRNA without the requirement of a tracrR...Casδ is a recently identified evolutionary transitional CRISPR system characterized by its compact size (~900 amino acids), broad temperature tolerance, and guidance with a short crRNA without the requirement of a tracrRNA. However, the low editing efficiency of Casδ in eukaryotic cells limits its application. Here, we have developed a hierarchical engineering strategy to improve the genome editing activity of Casδ-1, with optimization focused on enhancing its interactions with the crRNA, the protospacer adjacent motif (PAM) duplex, the single-stranded DNA substrate, and the RNA-DNA heteroduplex. Through this strategy, we successfully generated an activity-enhanced Casδ-1 variant, designated enCasδ, which harbors 9 amino acid substitutions that synergistically augment its editing efficiency. In human cell lines, enCasδ showed 1.3- to 29.3-fold higher editing activity than the wild-type Casδ-1 across ten tested genomic loci, with an average editing efficiency of 54.6%. In addition, enCasδ also mediated robust genome editing in maize; its editing efficiency increased by an average of 5.3-fold relative to Casδ-1, and reached up to an average of 80% at the TS4 and PSY1 loci in stable transgenic lines. The overall editing performance of enCasδ was comparable to that of Streptococcus pyogenes Cas9 (SpCas9) and other Cas12 nucleases. Collectively, enCasδ represents a highly optimized Casδ-1 variant that broadens the applicability of the Casδ CRISPR system and facilitates robust genome editing in both animal cells and plants.
Xu Y, Xie Y, Jia H
… +5 more, Li Q, Liu X, Ma T, Lang Z, Niu Q
J Integr Plant Biol
· 2026 Jul · PMID 41834248
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Many dicotyledonous plants exhibit considerable developmental plasticity and are capable of regenerating new organs upon wounding. Leveraging this wound-induced cellular pluripotency, a simple, efficient, and genotype-in...Many dicotyledonous plants exhibit considerable developmental plasticity and are capable of regenerating new organs upon wounding. Leveraging this wound-induced cellular pluripotency, a simple, efficient, and genotype-independent "cut-dip-budding" transformation system has been developed in recent years. Although genetic transformation in dicotyledonous crops like tomato is still largely based on tissue culture methods, and research into their molecular regulatory mechanisms and regeneration factors is extensive, the mechanisms underlying cut-induced shoot regeneration (cut-budding) remain poorly understood. This study investigated the molecular basis of cut-budding in tomato, focusing on the role of GROWTH-REGULATING FACTOR1 (GRF1) and its association with gibberellin (GA) signaling. By combining single-cell RNA sequencing, time-course transcriptome analysis, and genetic validation, we elucidated the key stages of shoot regeneration and identified SlGRF1 as a critical regulator. SlGRF1 was revealed to be essential for shoot initiation, with its expression significantly upregulated during cut-budding. Functional characterization using CRISPR/Cas9 knockout mutants (grf1-cr) demonstrated that SlGRF1 is required for pluripotency acquisition and shoot formation. Additionally, GA signaling negatively regulated shoot initiation by repressing SlGRF1 expression. An exogenous GA treatment inhibited shoot regeneration, while a paclobutrazol (GA biosynthesis inhibitor) treatment had the opposite effect. Moreover, grf1-cr mutants were similar to GA1-treated samples in terms of transcriptional changes and phenotypes, further indicating that GA signaling represses SlGRF1 expression. A ChIP-seq analysis showed that SlGRF1 controls cut-budding by activating the expression of shoot apical meristem regulator-encoding genes, including NAM1, EPF4, and ER2. NAM1 overexpression rescued the defective regeneration of grf1-cr1 mutants, highlighting the role of NAM1 as a downstream effector of SlGRF1. The study findings further clarify the molecular mechanisms governing cut-budding in tomato.
Auxin response factor (ARF) and brassinosteroid (BR) play significant roles in plant growth and development, such as determining leaf angle. However, the relationship between ARFs and BR signaling in regulating tomato le...Auxin response factor (ARF) and brassinosteroid (BR) play significant roles in plant growth and development, such as determining leaf angle. However, the relationship between ARFs and BR signaling in regulating tomato leaf angle remains unclear. Here, we report that auxin-responsive factor 11 (SlARF11) positively regulates tomato leaf angle and exhibits hypersensitivity to BR. SlARF11 is a non-canonical ARF that is highly expressed at the adaxial side of petiole bases. SlARF11 interacts with and acts upstream of SlGATA5, a GATA transcription factor that negatively regulates BR signaling by directly binding to the promoter of its downstream gene BRASINOSTEROID-INSENSITIVE 2 (SlBIN2.1), thereby inhibiting its expression in tomato. SlARF11-mediated regulation of leaf angle involves cell elongation at the petiole base, and lignin deposition, significantly facilitating the expression of U-type cyclin (SlCYCU2;1) and phenylalanine ammonia-lyase 4 (SlPAL4) mediated by SlGATA5. In addition, SlBIN2.1 is located upstream of SlARF11 and phosphorylates SlARF11, thereby enhancing the interaction between SlARF11 and SlGATA5. Some BRASSINOSTERIOD INSENSITIVE1-EMS-SUPPRESSOR 1 (SlBES1), located downstream of SlBIN2.1, could inhibit the expression of SlARF11. Briefly, these findings validate the SlARF11-mediated signaling pathway as linking auxin response factors to the traditional BR signaling pathway, ensuring effective crosstalk between tomato leaf angle and BR signaling.
Most land plants have evolved both a direct root uptake pathway and a symbiotic pathway, via association with arbuscular mycorrhizal (AM) fungi, to facilitate nutrient acquisition, particularly of phosphorus (P) and nitr...Most land plants have evolved both a direct root uptake pathway and a symbiotic pathway, via association with arbuscular mycorrhizal (AM) fungi, to facilitate nutrient acquisition, particularly of phosphorus (P) and nitrogen (N), from soil. Recently, we revealed a highly efficient symbiotic pathway for nitrate uptake, mediated by an AM-specific NPF/NRT1 transporter, OsNPF4.5, in rice. However, the regulatory mechanism controlling the AM-specialized expression of OsNPF4.5 remains unclear. Here, we demonstrate that two cis-acting elements, the CArG and GCC box, are essential for activating the expression of OsNPF4.5 in rice mycorrhizal roots. Deletion of either of the two motifs in its promoter caused almost complete abolition of the promoter activity of OsNPF4.5. An AM-responsive MADS (MCM1, AG, DEFA, and SRF) transcript factor, OsMADS61, could positively regulate OsNPF4.5 and another nitrate transporter gene, OsNRT2.2, involved in direct nitrate uptake. Knockout of OsMADS61 decreased root biomass, N accumulation, and mycorrhization efficiency in its mutants. OsMADS61 could be directly regulated by another AM-upregulated OsMADS paralog, OsMADS26, which itself can also activate OsNPF4.5, OsNRT2.2, and OsNAR2.1, encoding a nitrate transporter-activating protein. Together, our results reveal a dual regulatory role for OsMADS61 and OsMADS26 in governing both direct and symbiotic nitrate uptake pathways.
Leaf color is an important trait for the quality and ornamental value of turfgrass. As an essential component of chlorophyll molecules and related pigments, nitrogen is pivotal for leaf coloration. However, the mechanism...Leaf color is an important trait for the quality and ornamental value of turfgrass. As an essential component of chlorophyll molecules and related pigments, nitrogen is pivotal for leaf coloration. However, the mechanisms underlying nitrogen-mediated leaf color regulation in perennial turfgrass species remain unclear. In this study, we demonstrate that mitogen-activated protein kinase 6 (LpMPK6) regulates leaf color in perennial ryegrass by phosphorylating LpMYBR1. LpMPK6 overexpression (OE) plants showed leaf chlorosis under soil conditions without nutrient supplementation or in low-nitrogen hydroponic cultivation, accompanied by reduced chlorophyll and nitrogen content. Conversely, LpMPK6 RNAi lines maintained less chlorotic leaves and higher levels of chlorophyll and nitrogen under nitrogen-deficient conditions. Yeast two-hybrid, pull-down, co-immunoprecipitation, and luciferase complementation imaging indicated that LpMPK6 interacted with transcription factor LpMYBR1. Phenotypic analysis revealed that LpMYBR1 functionally antagonized LpMPK6, with more chlorotic leaves and lower levels of chlorophyll and nitrogen in LpMYBR1 RNAi lines, whereas LpMYBR1 OE plants retained more green leaves under nitrogen-deficient conditions. DNA affinity purification, yeast one-hybrid, electrophoretic mobility shift, and dual-luciferase assays demonstrated that LpMYBR1 bound to the promoter of LpNRT1.5 and activated its transcription. Furthermore, LpNRT1.5 regulated leaf color by mediating NO root-to-shoot transport. Notably, LpMPK6 negatively regulated this transport process by phosphorylating LpMYBR1 and suppressing its transactivation of LpNRT1.5. Taken together, our results revealed a mechanism whereby LpMPK6 suppresses LpMYBR1-mediated transcriptional activation of LpNRT1.5 via phosphorylation, thereby regulating NO transport and leaf coloration in perennial ryegrass. These findings provide insights and offer candidate genes for turfgrass quality improvement.
The root system is a crucial determinant of maize yield and stress resilience, particularly under drought stress. However, the complex genetic basis governing root system architecture remains largely elusive. To dissect...The root system is a crucial determinant of maize yield and stress resilience, particularly under drought stress. However, the complex genetic basis governing root system architecture remains largely elusive. To dissect the genetic architecture of the maize root, a transcriptome-wide association study (TWAS) was performed for 16 root traits in a panel of 357 diverse maize inbred lines. TWAS identified 2,978 significantly associated genes, of which 530 showed root-preferential expression patterns, representing high-confidence candidates for root development. Among these candidates, ZmSAUR21, a member of the Small Auxin-Up RNA gene family, was functionally characterized. Both CRISPR-Cas9-mediated knockout and overexpression analyses demonstrated that ZmSAUR21 acts as a key positive regulator of root growth by promoting cell elongation. Furthermore, the transcription factor ZmbZIP89 was identified as a direct upstream activator that binds to the ZmSAUR21 promoter to enhance its transcription, establishing a novel ZmbZIP89-ZmSAUR21 regulatory module. Crucially, ZmSAUR21-overexpressing plants showed substantially enhanced survival rates, improved water use efficiency, and a more vigorous root system under drought conditions. Collectively, this study uncovered a key regulatory pathway controlling maize root development and demonstrates that ZmSAUR21 is a valuable target gene for improving root systems and enhancing drought tolerance in maize breeding programs.
The CRISPR-Cas12 family nucleases, particularly the Cas12i subtypes, are considered promising alternatives to Cas9 for genome editing in plants. We previously developed a new Cas12i variant, CasY7, which has been success...The CRISPR-Cas12 family nucleases, particularly the Cas12i subtypes, are considered promising alternatives to Cas9 for genome editing in plants. We previously developed a new Cas12i variant, CasY7, which has been successfully applied in clinical trials; its performance in plants remains to be investigated. Initial testing in stable transgenic maize and rice showed that the codon-optimized CasY7 (pCasY7e1) achieved average editing efficiencies of 58.7% and 62.3% across five target sites, respectively, outperforming the typical Cpf1 (pCpf1) control that targets the same sites. To further enhance activity, we fused T5 exonuclease to CasY7 (pCasY7e2), which shifted mutation profiles toward larger deletions, and subsequently integrated an MS2 aptamer into the crRNA scaffold (pCasY7e3). The optimized pCasY7e3 system increased editing efficiencies to 87.7% in maize and 82.9% in rice-approximately 2.7-fold higher than pCpf1. We further demonstrated multiplexed editing in maize, generating biallelic dwarf mutants, and validated functionality in hexaploid wheat with editing efficiencies up to 58.8%. Overall, our comprehensive validation across 942 transgenic plants confirmed robust editing in maize, rice, and wheat, establishing CasY7 as a high-efficiency addition to the CRISPR toolkit.
Unlike Arabidopsis, Nicotiana benthamiana uses the SENESCENCE ASSOCIATED GENE 101-N REQUIREMENT GENE 1 branch of TIR signaling to activate salicylic acid biosynthesis, illustrating evolutionary divergence in how conserve...Unlike Arabidopsis, Nicotiana benthamiana uses the SENESCENCE ASSOCIATED GENE 101-N REQUIREMENT GENE 1 branch of TIR signaling to activate salicylic acid biosynthesis, illustrating evolutionary divergence in how conserved immune signaling modules are deployed to control salicylic acid production across plant lineages.
Cao L, Huang W, Yu H
… +5 more, Liu S, Yin J, Lu Z, Wu J, Liu X
J Integr Plant Biol
· 2026 Jul · PMID 41814559
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A novel allelic variant of the heat shock protein 101, designated neo-tetraploid rice fertility gene 1 (NTRF1), has been identified and is implicated in regulating fertility in neo-tetraploid rice (NTR); however, its reg...A novel allelic variant of the heat shock protein 101, designated neo-tetraploid rice fertility gene 1 (NTRF1), has been identified and is implicated in regulating fertility in neo-tetraploid rice (NTR); however, its regulatory mechanism remains unclear. In this study, we identified the ntrf1 mutant and demonstrated that its significantly reduced seed-setting rate was due to pollen developmental defects. Mechanistically, NTRF1 deficiency disrupts reactive oxygen species (ROS) homeostasis in anthers, thereby delaying the progression of programmed cell death (PCD) in tapetal cells. RNA-seq analysis of mutant anthers revealed dysregulated expression of abscisic acid (ABA) signaling components (OsPP2C49, OsbZIP23) and ROS-related genes (OsRBOH1, OsRBOH8), along with a significant downregulation of key tapetal developmental regulators (OsGAmyb, CYP703A3). Integrated multi-omics analysis showed that the reduced pollen viability in the ntrf1 mutant is associated with the pyruvate metabolic pathway. Protein interaction assays confirmed that NTRF1 directly binds SAPK2, a core kinase in ABA signaling transduction. This interaction explained how exogenous ABA application partially restored the reduced seed-setting rate in ntrf1 mutants. Collectively, our findings elucidated an NTRF1-centered regulatory network that coordinates ABA signaling with ROS homeostasis to ensure timely tapetal PCD and subsequent pollen maturation. This study provides valuable molecular targets for advancing the genetic improvement of polyploid rice.