Modifying the light formula is a central strategy for improving the yield and quality of fruits and vegetables in agriculture. While light signals have long been acknowledged as primary factors in regulating plant growth and development, their role in reprogramming metabolic networks is not well understood. Using tomato as a model, we demonstrate that supplementation with red or blue light induces metabolic shifts in tomato fruit. Through the creation of the Tomato Light-induced Expression Database (TomLED), we identified extensive transcriptomic and metabolic changes in tomato fruit under varying light conditions. Notably, the induction of key master regulators and metabolic genes is mediated by increased genome-wide DNA demethylation, facilitated by SlDML2. Additionally, we show that SlHY5, a central regulator in the light signaling pathway, directly induces the expression of SlDML2. This study reveals the molecular mechanisms by which light regulates the plant epigenome and establishes a direct link between light signals and plant metabolism.

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.

Soybean is a major crop that provides essential protein and oil for human consumption. Despite the increasing global demand, soybean yield has not experienced a “Green Revolution” comparable to that of rice, wheat, and maize. Here, we propose a pathway toward a soybean Green Revolution: enhancing soybean yield through the cultivation of dwarf soybeans optimized for ultra-high-density planting with a dwarf and dense-planting-tolerant soybean variety Dongsheng 89 as a paradigmatic case. We also suggest an ideal plant architecture and specific sowing and fertilization techniques. Furthermore, we discuss the prospective application of the rin1 gene in driving a global soybean Green Revolution, highlighting its potential to sustainably boost yields and address future food security challenges.

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.

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.

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.

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.

Dissecting quantitative traits into Mendelian factors is a great challenge in genetics. Apple fruit storability is a complex trait controlled by multi-genes with unequal effects. We previously identified 62 quantitative trait loci (QTLs) associated with apple fruit storability and genomics-assisted prediction (GAP) models were trained using 56 QTL-based markers. Here, three candidate genes, MdNAC83, MdBPM2, and MdRGLG3, were screened from the regions of QTLs with large G’ value and large genetic effects. Both a 216-bp deletion and an SNP934 T/C at the promoter of MdNAC83 were associated with higher MdNAC83 expression but an SNP388 G/A at the coding region significantly reduced the activity to activate the expression of the target genes MdACO1, MdMANA3, and MdXTH28. MdBPM2 and MdRGLG3 participated in the ubiquitination of MdNAC83. SNP657 T/A of MdBPM2 and SNP167 C/G of MdRGLG3 caused a reduction in the activity to ubiquitinate MdNAC83. By the addition of functional markers to the GenoBaits SNP array, the prediction accuracy of the updated GAP models increased to 0.7723/0.6231 and 0.5639/0.5345 for flesh firmness/crispness at harvest and flesh firmness/crispness retainability, respectively. The variation network involving eight simple Mendelian variations in six genes helps to gain insight into the molecular quantitative genetics, to improve breeding strategy, and to provide targets for future genome editing.

Chitin and its deacetylated derivative chitosan are the major components of fungal cell walls and are recognized by plant pattern-recognition receptors (PRRs) as pathogen-associated molecular patterns that induce innate immunity. Recognition of chitin oligosaccharide (CTOS) in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) requires the membrane-localized lysin-motif (LysM)-domain-containing receptors AtLYK5 and OsCEBiP, respectively. However, the mechanism underlying chitosan oligosaccharide (CSOS)-induced plant immunity remains unclear. In this study, we determined that CTOS and CSOS trigger immune responses and boost disease resistance in soybean (Glycine max) through the LysM-domain-containing protein GmNRF5a and its co-receptor GmCERK1. Surprisingly, both GmNFR5a and GmCERK1 bind directly to CTOS and CSOS, with distinct binding sites. The receptor-like kinase GmCAK1 acts downstream of GmCERK1 and is essential for CTOS/CSOS-mediated immune activation. Overall, these findings uncovered how soybean plants respond to CSOS and initiate immune signaling, demonstrating that soybean exploits shared immune sectors to transduce immune signals triggered by CTOS/CSOS, paving the way for the development of disease-resistant crops with broad-spectrum resistance.

Soil cadmium (Cd) contamination poses significant risks to human health and environmental sustainability. Despite advances in bioremediation, effective bioagents with clear mechanistic insights for Cd detoxification are lacking. We first deciphered the whole-genome sequence of a novel Cd-tolerant Trichoderma nigricans T32781 and its in vivo heavy metal tolerance. In five independent pot and field trials, we revealed the T32781-induced alleviation mechanisms of plant–microbe–soil interactions in wheat and barley in response to Cd toxicity using a combination of agronomic, physiological, microbiome and metabolome approaches. We discovered that T32781 inoculation in soil significantly increased grain yield and decreased grain Cd concentration in barley and wheat exposed to different soil Cd levels. T32781 predominantly colonized soils, mitigating Cd toxicity by reducing soil Cd availability and promoting beneficial soil microbial communities and metabolites. These beneficial effects were further validated in the field, where the exogenous application of key metabolites induced by T32781 inoculation in soils and plants significantly increased grain yield and reduced grain Cd concentration in barley. This work highlights the potential of T32781 to enhance plant‒microbe–soil interactions and support sustainable and safe crop production in Cd-contaminated soils, addressing the increasing global demand for cereal production for food and feed.

Lignified stone cells are a unique feature of pear fruit, significantly affecting fruit texture. Even though some research efforts have already been made, the stone cell formation mechanism is complex, with many aspects yet to be elucidated. Here, through a genome-wide association analysis of stone cell traits, we identified PbrMADS1, a member of the SEPALLATA3 (SEP3) subfamily, as a candidate gene specifically expressed in stone cells during early fruit development. Functional studies confirmed that PbrMADS1 promotes stone cell formation; however, it does not directly activate lignin-related genes. Instead, PbrMADS1 interacts with PbrMYB169, enhancing PbrMYB169's binding to AC elements and amplifying downstream gene activation. Notably, homologous MADS1 and MYB169 proteins from closely related species such as apple and loquat do not form a similar complex. Sequence analysis revealed that the protein sequence of PbrMADS1 contains methionine (M) at the 63^rd amino acid position, while apple and loquat homologs carry threonine (T) at the same site. Substituting M with T (PbrMADS1^M63T) weakened its interaction with PbrMYB169 and impaired its function in regulating stone cell formation. This study offers new insights into MADS gene-mediated stone cell formation and highlights functional divergence within the SEP3 subfamily among apple tribe species of the Rosaceae family.

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.

Symbiotic nitrogen fixation in legumes requires the exquisite regulation of the environment within the infected region of the nodule. The microaerobic environment critical for nitrogenase activity is maintained through the physical oxygen diffusion barrier of the cortex and locally the oxygen-binding protein leghemoglobin (Lb). Leghemoglobin binds and releases oxygen with heme moiety to maintain oxygen gradients inside the infected cell (IC) during nitrogen fixation. Heme binds to diverse proteins and plays critical roles in different redox reactions. However, the role and regulation of host-controlled heme production during symbiotic nitrogen fixation are not clear. Here, we identified coproporphyrinogen III oxidase plastid related 1 (CPOP1) as a key regulator of symbiotic heme biosynthesis in Lotus japonicus. CPOP1 is specifically highly expressed in nitrogen-fixing nodules, and knocking out CPOP1 alone causes leaf etiolation and dwarfism which could be recovered by the exogenous application of nitrogen source, indicating nitrogen fixation defect. The IC-specific expression of CPOP1 was directed by the −881 to −740 bp promoter region. The cpop1 mutant shows significantly increased nodule oxygen level and decreased nitrogen fixation activity compared to the wild-type. Intriguingly, bacteria proliferation is inhibited due to the down-regulation of cell division-related gene expression upon CPOP1 knockout. Our data showed that CPOP1 is essential for the microaerobic environment control of ICs and the activation of rhizobial nitrogenase required for symbiotic nitrogen fixation, through host-regulated nodule heme synthesis.

Multiple factors control primary seed dormancy established during seed maturation and secondary seed dormancy initiated when a non-dormant imbibed seed is exposed to adverse conditions. A key player in the control of primary and secondary dormancy in Arabidopsis thaliana is the Delay of Germination 1 (DOG1) gene, the expression of which is extensively regulated at the transcriptional and co-transcriptional levels. Despite its importance, the influence of post-transcriptional messenger RNA (mRNA) processing and mRNA storage of DOG1 on the determination of dormancy depth remains elusive. Here, we show that the UBA2A protein, a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family, negatively regulates primary and secondary seed dormancy through the regulation of the DOG1 gene expression at the post-transcriptional level. uba2a mutants show higher levels of the DOG1 mRNA. Surprisingly, DOG1 gene transcription is not affected, as demonstrated by single-molecule fluorescent in situ hybridization, chromatin-attached mRNA analysis and Pol II chromatin immunoprecipitation (ChIP). Instead, our results show that the UBA2A protein decreases the stability of both chromatin-bound and cytoplasmic DOG1 mRNA pools, and results in higher chromatin retention of DOG1 mRNA in the uba2a mutant. Our study highlights chromatin retention and mRNA stability as important features of DOG1 gene expression regulation with a profound impact on dormancy establishment and shows that UBA2A protein, like its human homolog hnRNPAB, is most likely implicated in mRNA transport in the cell.

Inositol pyrophosphates (PP-InsPs) are important signaling molecules that regulate diverse cellular processes in eukaryotes, including energy homeostasis, phosphate (P_i) signaling, and phytohormone perception. Yet, in plants, the enzymes responsible for their turnover remain largely unknown. Using a non-hydrolysable PP-InsP analog in a pull-down approach, we identified a family of Arabidopsis NUDIX-type hydrolases (NUDTs) that group into two closely related subclades. Through in vitro assays, heterologous expression systems, and higher order gene-edited mutants, we explored the substrate specificities and physiological roles of these hydrolases. Using a combination of strong anion exchange high-performance liquid chromatography (SAX-HPLC), polyacrylamide gel electrophoresis (PAGE), and capillary electrophoresis electrospray ionization mass spectrometry (CE-ESI-MS), we found that their PP-InsP pyrophosphatase activity is enantiomer selective and Mg²⁺ dependent. Specifically, Subclade I NUDTs preferentially hydrolyze 4-InsP₇, while Subclade II NUDTs target 3-InsP₇, with minor activity against other PP-InsPs, including 5-InsP₇. In higher order mutants of Subclade II NUDTs, we observed defects in both P_i and iron homeostasis, accompanied by increased levels of 1/3-InsP₇ and 5-InsP₇, with a markedly larger increase in 1/3-InsP₇. Ectopic expression of NUDTs from both subclades induced local Pi starvation responses (PSRs), while RNA-seq analysis comparing wild-type (WT) and Subclade II nudt12/13/16 loss-of-function plants indicates additional PSR-independent roles, potentially involving 1/3-InsP₇ in the regulation of plant defense. Consistently, nudt12/13/16 mutants displayed enhanced resistance to Pseudomonas syringae infection, indicating a role in bacterial pathogen susceptibility. Expanding beyond Subclade II NUDTs, we demonstrated susceptibility of the 3PP-position of PP-InsPs to enzymatic activities unrelated to NUDTs, and found that such activities are conserved across plants and humans. Additionally, we observed that NUDT effectors from pathogenic ascomycete fungi exhibit a substrate specificity similar to Subclade I NUDTs. Collectively, our findings reveal new roles for NUDTs in PP-InsP signaling, plant nutrient and immune responses, and highlight a cross-kingdom conservation of PP-InsP-metabolizing enzymes.

The phytohormone abscisic acid (ABA) regulates plant responses to environmental stresses, development, and immunity. Under unfavorable conditions, ABA forms a complex with its receptor proteins Pyrabactin Resistance 1 (PYR1)/PYR1-likes (PYLs)/Regulatory Component of ABA Receptors (RCARs), inhibiting Clade A Protein Phosphatases Type 2C (PP2Cs) and releasing Sucrose Non-Fermenting-1-Related Protein Kinase 2s (SnRK2s) from PP2C-mediated inhibition. Rapidly Accelerated Fibrosarcoma (RAF) kinases from the B1, B2, and B3 subgroups phosphorylate and reactivate SnRK2s, initiating ABA responses. While ABA does not significantly activate B-RAFs, their basal activity is essential for initiating ABA signaling. However, the mechanisms sustaining this basal B-RAF activity are not fully understood. In this study, we revealed that Clade A PP2Cs interact with and dephosphorylate a certain number of B3 subgroup RAFs at a conserved serine residue, corresponding to Ser619 in RAF3, within the phosphate-binding loop. A phosphomimicking mutation at this residue, RAF3^S619D, failed to bind ATP and exhibited diminished kinase activity in vitro and in vivo. Ser619 in RAF3 is an autophosphorylation site, phosphorylated by recombinant RAF3-KD but not by its substrate SnRK2.6. The RAF3^S619A mutant, abolishing Ser619 autophosphorylation, displayed increased kinase activity in vitro. The B-RAF high-order mutant OK¹⁰⁰-B3 carrying RAF3^S619A showed enhanced ABA sensitivity compared with those with wild-type RAF3. Thus, PP2C-mediated dephosphorylation and the autophosphorylation of this unique serine residue dynamically regulate ATP binding affinity and tightly control RAF3 activity during various ABA signaling phases. This intricate mechanism ensures rapid RAF–SnRK2 cascade activation during stress while promptly desensitizing RAFs once stress signaling commences.

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.

While many plant lineages display remarkable diversity in morphological form, our understanding of how phenotypic diversity, or disparity, arises in relation to genomic evolution over geologic scales remains poorly understood. Here, we investigated the relationship between phenotypic and genomic evolution in the Fagales, a lineage of woody plants that has been a dominant component of temperate and subtropical forests since the Late Cretaceous. We examine newly generated transcriptomic and trait datasets representing most extant genera and a rich diversity of Cretaceous fossil representatives. Our phylogenomic analyses identify recurrent hotspots of gene duplication and genomic conflict across the order. Our phenotypic analyses showed that the morphospace occupied by Fagales was largely filled by the early Cenozoic, and rates of evolution were highest during the early radiation of the Fagales crown and its major families. These results suggest that Fagales conforms to an “early-burst” model of disparification, with morphospace being filled early in the order's diversification history, and that elevated levels of phenotypic evolution also often correspond to hotspots of gene duplication. Species diversification appears decoupled from patterns of both phenotypic and genomic evolution, highlighting the multidimensional nature of the evolution of plant diversity across geological timescales.

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.

Rates of protein evolution (d_N/d_S) vary widely across the tree of life. In plants, both life-history traits and GC-biased gene conversion (gBGC) are thought to contribute to this variation, although disentangling their individual contributions remains a challenge. Using information on variation in life-history traits and molecular data in 148 species from Poaceae subfamilies Bambusoideae (mostly woody) and Pooideae (exclusively herbaceous), we investigated the relative importance of modes of reproduction and the non-selective forces of gBGC on protein evolutionary rates between the two subfamilies. Elevated rates of protein evolution associated with relaxed purifying selection were more evident in woody bamboos than in Pooideae and were better explained by reproductive modes than by traits that are likely proxies of effective population size. Although gBGC slightly reduced protein evolutionary rates in both subfamilies, its contribution had only a limited effect on molecular divergence between the groups. Forward simulations generally supported our empirical results on the influence of reproductive mode on selection and gBGC. Our findings from two sister lineages of the grass family provide evidence for association between protein evolution and life-history traits governing reproductive mode and enhance understanding of molecular evolution in plants with contrasting reproductive strategies.