Seed oil accumulation is an important process affecting seed quality, and regulatory factors modulating this process remain less understood, especially in soybean. In this study, through RNA-seq and gene co-expression network analysis, we identified a single MYB (Myeloblastosis)-type transcription factor GmMYB331, which promotes seed oil accumulation in soybean seeds and enhances seed size/weight as well. Transgenic soybean plants with mild GmMYB331 overexpression showed higher total fatty acid contents in seeds and higher seed yield per plant compared to the control plants. In contrast, transgenic soybean plants with strong GmMYB331 overexpression showed only increased seed size/weight but much reduced seed yield per plant, along with an altered plant architecture. Knocking out GmMYB331 by CRISPR/Cas9 produced mutants with less total fatty acids, smaller seeds, and less seed weight, indicating that the gene is required for oil accumulation and seed size/weight control. GmMYB331 may achieve these functions by differential binding to the gene promoters and activation of the downstream genes, namely, GmOLEO1/2/4 for oil accumulation in mild overexpressing plants and GmCYCD2;2 for seed size/weight increase in strong overexpressing plants. Our study reveals a possible mechanism involving differential regulation by GmMYB331 toward oil accumulation and seed size/weight increase. Manipulation of the GmMYB331 gene may facilitate breeding for high-oil and/or -yield soybean cultivars.

Crop breeding technologies are vital for global food security. While traditional methods have improved yield, stress tolerance, and nutrition, rising challenges such as climate instability, land loss, and pest pressure now demand new solutions. This study introduces the Breeding 5.0 framework, driven by artificial intelligence (AI) and robotics, marking a shift from empirical selection to intelligent systems. Central to this transformation is AI's emerging ability to deeply “understand germplasm,” not merely by identifying genetic markers but also by decoding its architecture, plasticity, regulatory logic, and environmental interactions. This germplasm intelligence enables predictive trait modeling, optimized parental design, and targeted selection. We define four technical paradigms enabling this shift: (i) Multi-modal data integration to bridge genotype and phenotype; (ii) Omni‐simulated environments for virtual performance testing; (iii) Peopleless data capture for scalable precision; and (iv) Expert,explainable AI for biologically grounded decisions. Together, these technologies algorithmically convert germplasm into actionable breeding insights, accelerating the full cycle from ideal plant type design to elite line development. We further propose the “breeding flywheel,” a self‐reinforcing system that continuously amplifies phenotypic gains and refines breeding strategies, thereby enabling faster and smarter crop improvement to ensure a sustainable food future

Soybean is an important source of oil, protein, and feed. However, its yield is far below that of major cereal crops. The green revolution increased the yield of cereal crops partially through high-density planting of lodging-resistant semi-dwarf varieties, but required more nitrogen fertilizers, posing an environmental threat. Genes that can improve nitrogen use efficiency need to be integrated into semi-dwarf varieties to avoid the overuse of fertilizers without the loss of dwarfism. Unlike cereal crops, soybean can assimilate atmospheric nitrogen through symbiotic bacteria. Here, we created new alleles of GmGID1-2 (Glycine max GIBBERELLIN INSENSITIVE DWARF 1-2) using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) editing, which improved soybean architecture, yield, seed oil content, and nitrogen fixation, by regulation of important pathways and known genes related to branching, lipid metabolism, and nodule symbiosis. GmGID1-2 knockout reduced plant height, and increased stem diameter and strength, number of branches, nodes on the primary stem, pods, and seeds per plant, leading to an increase in seed weight per plant and yield in soybean. The nodule number, nodule weight, nitrogenase activity, and nitrogen content were also improved in GmGID1-2 knockout soybean lines, which is novel compared with the semi-dwarf genes in cereal crops. No loss-of-function allele for GmGID1-2 was identified in soybean germplasm and the edited GmGID1-2s are superior to the natural alleles, suggesting the GmGID1-2 knockout mutants generated in this study are valuable genetic resources to further improve soybean yield and seed oil content in future breeding programs. This study illustrates the pleiotropic functions of the GID1 knockout alleles with positive effects on plant architecture, yield, and nitrogen fixation in soybean, which provides a promising strategy toward sustainable agriculture.

The evolution of spermatophytes (seed plants) is relatively well known in their evolutionary relationships over temporal changes, but their spatial evolution is another critical yet often neglected lens, especially using a taxon-based approach. Here, by integrating geographic distributions and origin locations across 429 spermatophyte families worldwide with unsupervised machine learning approaches, we constructed a Spermatophyte Spatial Evolutionary System that classifies global spermatophytes into 18 distribution types and six distribution supertypes within three primary floristic elements: cosmopolitan, tropical, and temperate. We found that the three elements all primarily originated from Gondwana, with the cosmopolitan element being the youngest and the temperate element being the oldest in terms of origin. They primarily formed during the Tertiary, particularly between the Eocene and Miocene, driven mainly by climate, long-distance dispersal, and tectonic movement, while each exhibited distinct migration routes and formation models. Our results provide novel insights into the spatial evolution of global spermatophytes and highlight that similar distribution patterns of spermatophytes were driven by their comparable formation processes and mechanisms at the levels of floristic element, distribution supertype, and type.

Plants adapt to their local environments through natural or artificial selection of optimal phenotypes. Recent advances in genomics and computational biology, which integrate phenotypic and multi-omics data, have facilitated the rapid identification of key genes and allelic variations that underlie these adaptive evolutionary processes. Understanding the underlying molecular mechanisms has significantly enhanced our knowledge of how plants respond to changed habitats, including various biotic and abiotic stresses. In this review, we highlight recent progress in elucidating the genetic basis of phenotypic variation in morphological traits and stress responses, as well as the emergence of new ecotypes, subspecies, and species during adaptive evolution across varied environments. This occurs through allelic divergences in both coding and non-coding regions in both model and non-model plants. Furthermore, the terrestrialization and early diversification of land plants involved the acquisition of additional genes, primarily through horizontal gene transfer and whole-genome duplication, which facilitated the development of complex molecular pathways to adapt to increasingly diverse environments. Finally, we discuss emerging trends and prospects for exploring and utilizing beneficial alleles for environmental adaptation, to guide crop breeding efforts in response to global climate change.

Soybean (Glycine max) provides vegetable oils and proteins for human consumption. Its production depends on seeds and other production-related agronomic traits. How the seed traits are regulated in soybean remains largely unclear. In this study, we identified a miR172a-ERF416/413 module for the regulation of seed traits. The miR172a can cleave the targets ERF416 and ERF413 to affect the downstream gene expression for the reduction of soybean seed size and weight. Both the MIR172a-overexpressing transgenic soybean plants and the erf416/413 mutants produced smaller seeds than the control. Consistently, the ERF416-overexpressing transgenic soybean plants generated larger seeds. ERF416 and ERF413 were directly targeted to the promoter of GmKIX8-1 and GmSWEET10a to regulate their gene expression for seed size/weight control. Interestingly, the erf416/413 mutants showed higher seed yield per plant and higher total seed fatty acid (FA) content, whereas the MIR172a-transgenic soybean had lower total seed FA content compared with the control cultivar, suggesting that miR172a and ERF416/413 may function in FA accumulation through different pathways. Haplotypes of the ERF416 promoter region were further analyzed and Hap1 was correlated with higher gene expression and higher seed weight, while Hap3 was correlated with higher total seed lipid content. Our study revealed a new module for seed trait control. Manipulation of such alleles should facilitate breeding for high-oil and high-yield soybean cultivars.

Root nodules are specialized organs formed by the symbiotic relationship between legumes and soil-borne rhizobia, facilitating an exchange of energy and nutrients essential for both organisms. This process is accompanied by dynamic changes in genomic organization and gene expression. While the three-dimensional (3D) architecture of the genome is known to influence gene regulation, its role in nodulation and symbiotic nitrogen fixation remains largely unexplored. In this study, we present the first high-resolution (40 kb) 3D genomic map of peanut roots and root nodules, generated using a high-throughput/resolution chromosome conformation capture strategy. Compared to roots, ∼2.0% of chromosomal regions in nodules transition from a repressive (B) to an active (A) compartment and exhibit significant alterations in topologically associated domains (TADs). Peanut nodules also show more extensive cis-interactions, with 100s of differentially expressed genes enriched in symbiotic pathways and nitrate metabolism. Additionally, assay for transposase-accessible chromatin with high-throughput sequencing identifies 25,863 and 14,703 open chromatin regions (OCRs) in roots and nodules, respectively. By integrating OCR mapping with epigenomic modifications, we reveal dynamic local OCRs (LoOCRs) and histone modifications associated with nodulation-related genes. Notably, novel TADs and long-range chromatin loops are detected in peanut nodules, including an H3K27me3 modification-mediated loop that may regulate the expression of Nodule Inception. Another altered chromatin loop highlights the nodule highly expressed AhMsrA gene, which positively influences nodulation. Together, these findings shed new light on how chromatin architecture shapes gene expression during legume nodulation and nitrogen fixation.

Base editing technologies can improve crops, but their efficiency in maize remains suboptimal. This study attempts to overcome these limitations by examining optimized cytosine and adenine base editors (CBEs and ABEs), namely evoAPOBEC1, evoFERNY, evoCDA1, TadA8.20, and TadA8e, for precise genome editing in transient and stable expression maize cells. Employing a seed fluorescence reporter (SFR) system for rapid screening of BE transformants and transgene-free progenies, we enhanced editing efficiencies and heritability. Notably, TadA8.20 and evoCDA1 attained multiplexed editing efficiencies of up to 100.0% and 79.0% at the tested loci, respectively, with some homozygous and bi-allelic mutants exceeding 72.4% and 73.7%. Precise editing of ZmACC1/2 (acetyl-CoA carboxylase) improved herbicide resistance, with ZmACC2 mutants displaying improved performance. This study advances crop genetic engineering by facilitating robust, multi-locus modifications without altered agronomic performance, enhancing herbicide tolerance in maize. The successful utilization of these BE is a significant step forward in agricultural biotechnology and precision breeding.

INOSITOL-REQUIRING ENZYME 1 (IRE1) is conserved in plants and mammals to regulate stress responses. Here, we found that TaIRE1 is involved in the unconventional splicing of cell membrane-localized TabZIP60 messenger RNA (mRNA), which results in a nucleus resident protein form (TabZIP60s), and enhanced heat stress tolerance. Transcriptome analysis together with binding element prediction revealed 121 high-confidence targets of TabZIP60s responsive to heat stress in wheat (Triticum aestivum), including heat shock protein genes. Interestingly, we found that an asparagine to glutamic acid substitution, located next to DNA-binding domain of TabZIP60s, results in reduced binding affinity and transcriptional activity to downstream targets, and this heat stress tolerance inferior allele was positively selected during modern wheat breeding programs in China, possibly due to their negative effects on yield potential. Finally, we showed that TaIRE1 is also responsible for the mis-cleavage of miR172 precursors, and consequently contribute to heat stress tolerance. To the best of our knowledge, this represents the first report showing that, like in mammals, IRE1 also regulates miRNA cleavage in response to heat stress in plants. Together, this coordinate control of two signaling pathways provides new insights into heat stress tolerance regulation in wheat.

Bananas and plantains of the genus Musa constitute the most vital fruits and staple foods. Cultivated bananas may have originated from intraspecific and interspecific hybridizations of four wild species, namely Musa acuminata (A), M. balbisiana (B), M. schizocarpa (S), and the Australimusa species (T). Here, we appraise the advances made in banana genomics, genetics, and breeding over the past few decades. The sequencing of Musa genomes has been a major breakthrough in banana research programs, presenting unprecedented possibilities for gaining deeper insights into the evolution, domestication, breeding, and genetics of indispensable agronomic traits of bananas. Also, we delve into how these genetic facets, coupled with innovative genomic-assisted tools, including genomic selection and gene editing, propel advancements in banana breeding endeavors. Ultimately, we propose the forthcoming prospects within the domain of banana genetics and breeding.

Rubus (raspberries and blackberries) is a large genus of over 700 species well known for its taxonomic challenges. Many of its species hold significant economic value as important edible and medicinal plants. Here, near-complete genomes for four wild diploid raspberry species were assembled, including R. ellipticus, R. niveus, as well as the highly heterozygous diploid red raspberry (R. idaeus), and its closely related species R. sachalinensis. Pan-genome analysis of Rubus identified 10,243 core gene families (64% of total), and highlights expansions of flavonoid/terpenoid pathways in Rubus, correlating with fruit bioactive compound diversity. Our discovery of shared ancestral components between R. idaeus and R. sachalinensis subgenomes provides evidence for their homoploid hybrid origin. The centromere sequence characteristics could serve as markers for subgenome assignment in R. idaeus and R. sachalinensis. Moreover, population genomic studies of 125 accessions from ca. 80 species uncovered widespread genetic introgression, particularly in red raspberries, with centromeric haplotype signatures tracing ancestral contributions to cultivated varieties. By integrating metabolome and transcriptome data, we explore the fruit quality regulatory network of Chinese raspberries. We identified a glutathione S-transferase gene that may inhibit the successful transport of anthocyanins into the vacuole and appears to be a limiting factor for the anthocyanin pigmentation in R. ellipticus fruits. In summary, this research sheds new light on the genetic intricacies of raspberry species and their cultivars, and provides a robust foundation for horticultural improvement and genomic selection in raspberry breeding.

Phytopathogens, such as the rice blast fungus Magnaporthe oryzae, suppress plant immunity for reproduction by secreting effectors into plant cells. The M. oryzae effector AvrPib is known to be recognized by Pib, an intracellular nucleotide-binding, leucine-rich repeat receptor (NLR), in rice. However, how AvrPib manipulates blast resistance and its potential targets in rice remains unclear. In this study, we showed that AvrPib interacts with the rice MAP KINASE KINASE KINASE 72 (OsMAPKKK72), a previously uncharacterized Raf-like MAPKKK. The osmapkkk72 mutant shows enhanced susceptibility to the M. oryzae strain Guy11 and reduced mitogen-activated protein kinase (MAPK) activation after treatment with chitin. Furthermore, OsMAPKKK72 interacts with MAP KINASE KINASE 9 (OsMKK9) and increases the interaction between OsMKK9 and OsMPK3/6. Accordingly, OsMKK9 positively regulates rice blast resistance and increases MAPK activation in an OsMAPKKK72-dependent manner following chitin treatment in rice, suggesting that OsMAPKKK72 may serve as a scaffold in the MAPK cascade. AvrPib inhibits the interaction between OsMAPKKK72 and OsMKK9, leading to reduced MAPK activation, which is mediated by OsMKK9. Taken together, our results reveal the critical roles of OsMAPKKK72 in blast resistance and uncover a mechanism wherein AvrPib suppresses rice blast resistance by interference with MAPK activation by targeting a key component in the MAPK cascade.

Rice black-streaked dwarf virus (RBSDV) is a major viral pathogen threatening rice production worldwide. However, the molecular mechanisms underlying the arms race between RBSDV and its host remain largely elusive. Here, we demonstrate that RBSDV infection, or the expression of viral RNA-silencing suppressor protein P6, promotes the ubiquitination and degradation of rice small ubiquitin-like modifiers (SUMO) conjugating enzyme 1b (OsSCE1b). OsSCE1b catalyzes the SUMOylation of OsPelota, a protein involved in plant antiviral RNA decay. Furthermore, RBSDV P6 enhances the interaction between rice ubiquitin E3 ligases SINAT3/4/5 and OsSCE1b in the cytoplasm, leading to increased ubiquitination and degradation of OsSCE1b. Rice plants overexpressing OsSCE1b exhibited reduced susceptibility to RBSDV infection. Conversely, OsSCE1b knockdown and knockout lines, as well as OsPelota knockout lines, were more susceptible, indicating that both OsSCE1b and OsPelota negatively regulate RBSDV infection. Additionally, our findings show that OsSCE1b-catalyzed SUMOylated OsPelota interacts with the Hsp70 subfamily B suppressor OsHBS1, forming a complex that degrades RBSDV genomic RNAs containing one or more GA₆ motifs. Taken together, our data demonstrate that OsSCE1b negatively regulates RBSDV infection by promoting OsPelota SUMOylation and activating the antiviral RNA decay activity of the OsPelota–OsHBS1 complex. Conversely, RBSDV P6 promotes viral infection by enhancing OsSCE1b ubiquitination and degradation, thereby suppressing OsPelota SUMOylation and the rice antiviral RNA decay defense response.

Plants monitor daylength to synchronize their flowering time with their surroundings and thus maximize reproductive fitness. In Arabidopsis (Arabidopsis thaliana), CONSTANS (CO) activates the expression of FLOWERING LOCUS T (FT); this activation is a crucial aspect of the daylength-dependent regulation of flowering time. Here, we demonstrate that the basic leucine zipper 3 (bZIP3) transcription factor is important for CO-induced FT expression under long photoperiod conditions in Arabidopsis. We isolated bZIP3 as a CO-interacting protein by yeast two-hybrid screening and verified bZIP3–CO complex formation in Arabidopsis through co-immunoprecipitation assays. The temporal and spatial expression patterns of bZIP3 are very similar to those of CO, and bZIP3 protein levels fluctuate throughout the day, with high abundance in the late afternoon. The bzip3 mutant displayed delayed flowering under long photoperiods, whereas bZIP3 overexpression accelerated flowering regardless of daylength. bZIP3 directly binds to the FT promoter region containing CO-responsive elements in vivo. FT messenger RNA (mRNA) levels in the bzip3 mutant and bZIP3 overexpression lines correlated with their flowering times and changed only during the daytime. bZIP3 overexpression resulted in significantly lower FT transcript levels in the co mutant background than in the wild type. Furthermore, bZIP3 forms a complex with ASYMMETRIC LEAVES1 (AS1), a CO partner that helps CO induce FT expression. The bzip3 as1 double mutant flowered later than the two single mutants under longer daylengths, and FT mRNA levels were much lower in the double mutant than in the bzip3 single mutant. Collectively, our findings uncover a new layer of photoperiod-dependent FT regulation in which bZIP3 facilitates CO to activate FT transcription by forming a complex with AS1.

The highly transformable maize inbred line LH244 represents an attractive model for gene discovery and genome engineering. However, the lack of a high-quality genome assembly has limited its utility in functional genomics research. Here, we present a 2.29 Gb near-complete assembly of the LH244 maize genome, with an overall base accuracy of 99.998%. Except for five gaps associated with super-long thymine–adenine–guanine (TAG) repeat arrays, all the genome sequences were assembled from telomere to telomere (T2T). Comparative analysis revealed high genetic similarity between LH244 and B73, including 80.06% genome-wide synteny and 90.92% of genes nearly identical. The LH244 genome was also compared with the complete Mo17 genome and revealed extensive intraspecific genomic variations. A total of 14 megabase-scale structural variations (SVs) were identified, including a 3.15 Mb insertion, harboring 95 genes, within the 45S rDNA array of LH244 but not in the Mo17 genome. In addition, there were five knob arrays, with an average size of 21.76 Mb and the longest of 38.70 Mb, only existing in the LH244 genome. Despite the substantial variation in knob abundance, knob-6S and knob-8L were highly conserved between LH244 and Mo17, showing strong synteny and sequence identity, as well as consistent insertion patterns of genes and transposable elements (TEs). Overall, our study provides a near-complete reference genome of an important transformable maize germplasm, which will serve as a much-needed resource for functional genomics and genome editing of maize.

Bananas (Musa ssp.) are globally important staple crops increasingly constrained by biotic stressors, climatic instability, and the high labor demands of cultivation. The genetic improvement of dwarf phenotypes offers a strategic pathway to enhance mechanization and reduce production costs. In this study, we have carried out whole-genome resequencing of 300 Musa accessions to analyze genome-wide allelic diversity and identify loci associated with shoot architecture. Our analysis uncovered extensive genetic variation within the A subgenome, pivotal for environmental adaptability, and detected introgression from Musa itinerans (subgroup A) into cultivated varieties (subgroup F), suggesting a broadened genetic base amenable to breeding. A genome-wide association study (GWAS) pinpointed MabHLH30 as a crucial gene associated plant stature. Functional validation confirmed MabHLH30 as a critical regulator of plant stature and leaf morphology. Leveraging this finding, we developed molecular markers for MabHLH30, enabling marker-assisted selection (MAS) to accelerate the breeding of compact, high-yielding cultivars. Collectively, these results provide a genomic framework for the targeted improvement of banana architecture and represent a valuable resource for cultivar development under diverse agroecological conditions.

The pollen exine serves as a protective barrier and signaling interface essential for male fertility in flowering plants. Its precise patterning depends on coordinated interactions between microspores and tapetal cells. While the CLAVATA3/EMBRYO SURROUNDING REGION-related 19 (CLE19) peptide has been identified as a microspore-derived “brake” that restricts tapetal activity to maintain exine developmental homeostasis, how CLE19 integrates with hormonal signaling pathways remains poorly understood. Here, we demonstrate that CLE19 attenuates brassinosteroid (BR) signaling output by engaging a defined BSL–BIN2–BES1 signaling cascade. Through quantitative phosphoproteomic analysis, we identified that CLE19 affects the phosphorylation of multiple BR signaling components, including BSL-type phosphatases BSL1/2/3, the GSK3-like kinase BIN2, and the transcription factor BES1. We show that CLE19 is perceived by its receptor PXL1, which directly interacts with BSL-type phosphatases to activate the GSK3-like kinase BIN2, leading to phosphorylation of BES1 at serine residues S219 and S223. Functional analyses using phospho-dead and phospho-mimic BES1 variants confirm that CLE19-dependent phosphorylation controls BES1 nuclear export and degradation, ultimately suppressing BR-responsive transcriptional outputs required for pollen exine patterning. Together, our findings define a peptide–hormone signaling axis that regulates transcription factor activity through post-translational regulation, providing mechanistic insight into how developmental robustness is maintained via intercellular signal integration in plant reproduction.

Wild perennial sister species Medicago archiducis-nicolai (rhizomatous/alpine) and M. ruthenica (non-rhizomatous/xeric) constitute vital genetic resources for forage improvement. To decode the genomic basis of their contrasting trait and habitat adaptation, we generated chromosome-scale genome assemblies, resequenced 128 individuals, profiled transcriptomes under cold/heat stress, and functionally validated causal alleles. We demonstrate that structural variations (SVs)—particularly gene duplications—are primary drivers of rhizome formation and alpine/xeric adaptation. Further, pervasive presence–absence SVs (PAVs) in noncoding regulatory regions underpin divergent allele-specific expression governing rhizome development and stress responses. Crucially, these regulatory PAVs induce contrasting expression patterns during trait development and stress adaptation. Our findings reveal a dual mechanism whereby coding and regulatory SVs convergently orchestrate phenotypic innovation and ecological specialization in sister species, offering valuable genomic resources for legume evolution studies and alfalfa breeding.