Jasmonic acid (JA) is a critical signal controlling ripening and trait development in non-climacteric (NC) fruit. However, the mechanisms governing the JA biosynthesis remain unclear. Here, the signaling mechanisms for the JA biosynthesis are explored in strawberry (Fragaria vesca), a model NC fruit. The JA biosynthesis is demonstrated to be tightly coupled with the signaling of ABA, a pivotal signal controlling NC fruit ripening. When overexpressed or knocked out by CRISPR/Cas9 editing, FvSnRK2.6, a gene encoding a component of ABA signaling, promotes or inhibits JA production and aroma production, respectively. Moreover, FvSnRK2.6 phosphorylates FvJAZ12, a jasmonate ZIM-domain repressor, at the S142 residue, thereby promoting its degradation. Transforming the FvJAZ12 knockout mutant with FvJAZ12^S142A inhibits the production of ABA-induced aroma and JA. Furthermore, our current study reveals that FvMYC2, a transcription factor directly repressed by FvJAZ12, binds to cis-acting elements in the promoters of FvAOC3, FvAOS, FvLOX3, and FvOPR3, thus directly regulating JA biosynthesis. Thus, this study reveals an ABA signaling cascade that leads to JA biosynthesis, thereby elucidating the signaling mechanism governing the JA production during strawberry fruit ripening.

Numerous members of the Nepeta genus (family Lamiaceae, subfamily Nepetoideae) are medicinal herbs and sources of important bioactive compounds. Most Nepeta species produce iridoids, which are monoterpenoids that deter herbivores and pathogens and are potential biopesticides. In Nepeta, some species produce iridoid aglycones and glycosylated iridoids (referred to as chemotype A), some produce only glycosylated iridoids (chemotype B), and some produce neither iridoid aglycones nor glycosylated iridoids (chemotype C). Here, we show that the observed diversity in iridoids is, at least partially, attributed to evolutionary gains and losses of key biosynthetic genes. Based on reconstructed phylogenetic relationships, we propose a scenario in which partial or complete loss of the ability to synthesize iridoids with specific stereochemistries in the taxa with chemotypes B and C resulted from independent evolutionary events. These observations improve our understanding of metabolic diversity in the Nepeta genus and may inform efforts to produce specific iridoids in plants.

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.