Jin He

Basic leucine zipper (bZIP) transcription factors represent one of the largest and most conserved transcription factor families in plants, yet their evolutionary origin, expansion dynamics, and regulatory diversification across the plant kingdom remain incompletely understood. Here, we identified 22,378 bZIP genes from 321 representative plant species spanning major lineages from red algae to angiosperms and integrated phylogenomic reconstruction, duplication-mode analysis, evolutionary constraint assessment, comparative transcriptomics, regulatory-network inference, pangenome analysis, and functional validation. Phylogenetic analyses revealed that plant bZIP proteins are organized into four major clades comprising 13 conserved subgroups, and that the core subgroup architecture was established before the emergence of land plants. Family expansion showed strong lineage dependence, with dispersed duplication predominating in early-diverging lineages and whole-genome/segmental duplication becoming the major expansion mode in angiosperms. Despite extensive expansion during plant evolution, pervasive purifying selection maintained the structural conservation of bZIP proteins, particularly within the conserved bZIP domain. Comparative expression and regulatory network analyses revealed substantial divergence in bZIP regulatory programs across plant lineages. AtbZIP27 and MsbZIP26 activated their corresponding MIOX promoters, whereas SlbZIP70 did not, indicating that the bZIP–MIOX regulatory relationship is conserved in some lineages but has diverged in others. Functional assays under aluminum stress further supported the biological relevance of this regulatory relationship, while tomato pan-genome analysis revealed that such regulatory divergence can occur against a largely conserved genomic background. Collectively, these findings reveal that plant bZIP evolution combines duplication-driven expansion and strong selective constraint with progressive diversification of regulatory relationships and functions.

Flavonoids are central to abiotic stress responses, yet the specific signaling roles and evolutionary dynamics of flavonoid biosynthetic intermediates in crop drought adaptation remain elusive. Here, we demonstrate that dihydrokaempferol (DHK) and dihydroquercetin (DHQ), specific intermediate products of the soybean flavanone 3-hydroxylases GmF3H1/2, function as potent signaling molecules that mitigate drought stress. Exogenous DHK/DHQ promoted abscisic acid-dependent stomatal closure and enhanced drought tolerance across diverse dicot species, including soybean and tobacco, highlighting a broadly conserved stress-mitigating signaling mechanism. CRISPR/Cas9-generated gmf3hs double mutants exhibited severe drought hypersensitivity due to compromised redox homeostasis and defective stomatal regulation, which could be specifically rescued by DHK/DHQ application. Furthermore, the loss of GmF3H triggered a distinct reproductive trade-off under stress, leading to increased pod initiation but severe filling defects. Multiomics network analysis revealed extensive rewiring of broader stress-responsive pathways and identified upstream transcription factors, among which GmPHL11 directly binds to and activates the GmF3H1 promoter; overexpression of GmPHL11 promoted DHK accumulation and enhanced drought stress tolerance in soybean hairy roots. Finally, population genomic analyses demonstrated that the GmF3H1H1 haplotype, which confers superior enzymatic activity and robust root growth under drought stress, might have undergone positive selection during soybean domestication. Collectively, our findings redefine the role of GmF3H-derived specific intermediates as potent signaling molecules, providing comprehensive mechanistic and evolutionary insights into flavonoid-mediated drought resilience, developmental trade-offs, and molecular breeding in crops.

Disrupting starch biosynthesis in soybeans redirects seed carbon partitioning toward soluble sugars, offering a genetic strategy to breed sweeter crops.

Phosphorus (P) acquisition in plants involves a range of strategies, with differences between legume and non-legume crop species. We studied 11 legume and 11 non-legume crop species under two P levels for P acquisition strategies related to root morphological and physiological traits and their roles in biomass accumulation and P content. We hypothesise that the legume crops species used a P-mining strategy related to carboxylates and non-legume crop species used a P-scavenging strategy related to root morphological trait, contributing to differences in P-acquisition strategies between legume and non-legume crop species. Legume crop species demonstrated higher P concentrations and greater biomass than non-legume under both P conditions. Legume crop species relied on root morphological traits and carboxylate release, while non-legume crop species relied on arbuscular mycorrhizal (AM) colonisation and acid phosphatase activity. Legume crop species exhibited a lower response ratio for AM colonisation and acid phosphatase activity but a higher response ratio for rhizosheath carboxylate release than non-legume crop species. Legume crop species utilised a P-scavenging strategy, characterised by enhanced root length and a P-mining strategy through carboxylate release; legume crop species exhibited greater plasticity in carboxylate release but lower plasticity in AM colonisation and acid phosphatase activity than non-legume crop species did, indicating a trade-off between different P-acquisition strategies. These results provide insights into the P-acquisition strategies of crop species adapted to low soil P conditions, offering valuable ecological insights for sustainable intercropping systems and strategies to enhance P-use efficiency in low-input agricultural system.

Nuclear factor Y (NF-Y), evolutionarily conserved heterotrimeric transcription factors (TFs), are found throughout eukaryotic organisms. Comprising the NF-YA, NF-YB, and NF-YC subfamilies, this family is established as playing critical roles in plant growth and development. While earlier research has mainly centered on the functional and evolutionary characteristics of NF-Y within individual plant species, large-scale analyses and evolutionary patterns of these genes across major plant lineages remain largely unexplored. Here, we systematically identified 15 392 nonredundant genes of NF-Y family from 320 horticultural and representative plant species. Our findings showed that this gene family originated from charophytes. In bryophytes, pteridophytes, and gymnosperms, dispersed duplication served as the predominant mode of NF-Y gene expansion, whereas in angiosperms, their expansion was driven by whole genome duplication/segmental, dispersed, and tandem duplication. Conserved motif analysis revealed that highly conserved motifs are present within each NF-Y subfamily across eight representative plant species. However, some NF-Y genes in higher plants exhibited motif loss, indicating sequence variations during their evolutionary history. Transcriptomic profiling analysis of NF-Y genes in Arabidopsis thaliana under various conditions, including hormonal treatments, abiotic/biotic stresses, as well as various developmental stages, revealed their functional versatility. Furthermore, an interaction network comprising 36 NF-Y genes along with 2473 downstream and 261 upstream genes was constructed in A. thaliana. Enrichment analysis revealed interactions between NF-Y genes and other TFs, particularly those from the Myb_DNA-binding and APETALA2 (AP2) families, which were consistently enriched among both upstream and downstream regulatory genes. This work provides the first comprehensive and large-scale investigation into the evolutionary dynamics of NF-Y genes, encompassing taxa from basal algae to advanced horticultural plants, thereby offering novel insights into their evolutionary and lineage-specific expansion.

The roles of leaf phosphorus (P) fractions in leaf photosynthetic P‐use‐efficiency (PPUE) under low soil P, and differences, if any, between legume and non‐legume species are largely unknown. We investigated 24 crop species, 13 legumes and 11 non‐legumes, for leaf PPUE and P acquisition strategies under low plant‐available soil P. Legume species had a lower PPUE (38%), photosynthetic rate per area (A _area ; 38%) and per mass (A _mass ; 32%), but higher leaf P concentration (19%) than non‐legume species. Legume species had a significantly higher nucleic acid P concentration, while percentage of nucleic acid P was higher, but percentage of inorganic P and metabolite P were lower in legumes than in non‐legumes. Legume species had significantly greater total root length and carboxylate release than non‐legume species. PPUE showed a positive correlation with A _area , A _mass , percentage of lipid P and metabolite P, but a negative correlation with concentrations of inorganic P, nucleic acid P, and leaf P. There was contrasting P‐use‐efficiency and P acquisition capacities between legume and non‐legume species; high photosynthesis rate was associated with a high metabolite P concentration, but low nucleic acid P concentrations were related to a high PPUE. A P mining strategy was associated with a high leaf P concentration and low PPUE. This study provides insight into P use and P acquisition strategies and their correlations among 24 crop species grown under low plant‐available soil P conditions.