ABSTRACTHormonal signaling shapes plant architecture and salt stress responses, but its effects on root architecture and ion accumulation remain unclear. Here, we conducted a detailed analysis of how individual hormone treatments affect root architecture and ion accumulation under salt stress in tomato. The study focused on three tomato accessions with varying responses to salt stress. Our findings revealed distinct, species‐specific hormonal effects. Auxin, ethylene, and gibberellin promoted lateral root development, yet their impacts on ion accumulation, particularly in Na+/K+ ratio, varied considerably. To explore the molecular basis of these differences, we examined Arabidopsis mutants for ethylene‐ and auxin‐related genes, revealing novel components of hormone signaling involved in the salt stress response. Further, analysis of tomato mutants with impaired ethylene perception demonstrated that the nr mutant exhibits increased root growth and a higher shoot Na+/K+ ratio, largely due to reduced K+ retention. Our integrated physiological and genetic analysis reveals species‐specific hormonal strategies can boost crop performance under salt stress.

Upstream open reading frames (uORFs) are regulatory elements present in the 5' leaders of mRNA that can significantly impact downstream gene expression in eukaryotes. In crop engineering, editing of uORFs can provide an avenue to upregulate expression of native genes without the need to add persistent transgenic copies. Even with genome-wide methods to identify translated uORFs such as ribosome profiling, their functional characterization depends on validation through reporter gene assays and mutagenesis studies. Current screening methods for plants use luciferases or protoplasts to measure differential gene expression between wild-type and mutated transcript leaders, which requires tissue processing and/or substrate addition. Here, we present a time- and cost-efficient alternative to investigate transcript leaders by co-expression of two fluorescent proteins in Nicotiana benthamiana leaf tissue and test our assay on genes involved in photoprotection, editing of which could provide a pathway to increase CO2 assimilation during sun-shade transitions.

ABSTRACT To reduce the environmental burden associated with excessive nitrogen fertilizer use in rice cultivation, we developed NR160E, an early heading isogenic line derived from the high‐yielding variety NSIC Rc 160 (NR160). Although early heading is often considered unfavorable for yield and excluded from high‐yield breeding programs, our results challenge this assumption. In field trials conducted under natural long‐day conditions in Tsukuba, Japan (planting density of 18.5 plants m −2 ), heading occurred ~8–10 days earlier in NR160E than in NR160 across all nitrogen fertilization levels (0, 4.8, and 9.6 g N m −2 ). In NR160E, early heading was associated with reduced plant height and a marked increase in harvest index (HI). Specifically, plant height decreased by ~15%, whereas HI increased by 20% compared with NR160, indicating efficient biomass partitioning and suggesting its potential within this genetic and environmental context. Fine‐mapping identified a 33.3‐kbp region on chromosome 3 containing four annotated genes ( Os03G0122600 , Os03g0123100 , Os03g0123200 , and Os03g0123300 ) among which OsMADS50 ( Os03G0122600 ) was upregulated in NR160E under long‐day conditions, accompanied by elevated Ehd1 and RFT1 expression, consistent with the early heading phenotype. Photoperiod experiments revealed that heading occurred significantly earlier in NR160E than in NR160 under long‐day conditions (13.0–14.5 h), whereas no significant difference was observed under short‐day conditions (10.0–11.5 h), indicating that the expression of early heading in NR160E depends strongly on photoperiodic conditions. Field trials across 12 cultivation regimes varying in nitrogen input and planting density consistently showed that NR160E outperformed NR160 in grain yield. At 18.5 plants m −2 , NR160E produced grain yields of 649.0, 797.7, and 922.9 g m −2 under 0‐, 4.8‐, and 9.6‐g N m −2 fertilization, respectively, whereas NR160 yielded 513.0, 666.4, and 692.3 g m −2 under the same conditions. Within each nitrogen–field condition, NR160E produced higher yield than NR160. Seed fertility was consistently higher in NR160E across nitrogen–field conditions (e.g., 0.815 under zero nitrogen input), and NR160E also exhibited a consistently higher agronomical HI, consistent with more efficient assimilate allocation to grain. Growth analysis showed that NR160E maintained dry matter production during grain filling, coinciding with its higher HI and physiological nitrogen‐use efficiency. Although these relationships are observational and the physiological basis remains unclear, the trend was consistent across conditions. Regression analysis also revealed a steeper slope between nitrogen uptake and grain yield in NR160E than in NR160, consistent with higher physiological nitrogen‐use efficiency (as defined in this study). Collectively, these results suggest that earlier heading may be associated with sustained productivity under the long‐day field conditions examined here. However, determining how this trait could inform fertilizer management or nitrogen‐input strategies will require multienvironment and multibackground validation.

Cassava production in sub-Saharan Africa is severely impacted by diseases. Most pathogens require interaction with host susceptibility factors to complete their life cycles and cause disease. Targeted DNA methylation is an epigenetic strategy to alter gene expression in plants, and we previously reported that a zinc-finger fused to DMS3 could establish methylation at the promoter of MeSWEET10a, a bacterial susceptibility gene, and this resulted in decreased disease. Here, we attempt a similar strategy for cassava brown streak disease. This disease is caused by the ipomoviruses CBSV and UCBSV. These viruses belong to the family Potyviridae, which has been shown extensively to require host eIF4E-family proteins to infect plants and cause disease. We previously found that cassava plants with simultaneous knockout mutations in two eIF4E genes, nCBP-1 and nCBP-2, resulted in decreased susceptibility to CBSD. Here, we report successful simultaneous targeting of both promoters with methylation using a dCas9-DRMcd-SunTag system. However, in contrast to our previous work with MeSWEET10a, controls indicate that CRISPR interference is occurring in these lines and is sufficient for the reduction of gene expression. Future research will use genetic crosses to segregate away the DNA methylation reagents and, if DNA methylation proves heritable, assess whether methylation alone is sufficient to increase resistance to CBSD.

ABSTRACTDespite being one of the few bona fide plant tyrosine phosphatases, the Arabidopsis thalianaRhizobiales‐like phosphatase 2 (RLPH2) has no known substrates. Utilizing phospho‐proteomics, we identified the activation loop phospho‐tyrosine of several A. thaliana D‐group mitogen‐activated protein kinases (MPKs) as potential RLPH2 substrates. All Arabidopsis D‐group MPKs possess a TDY activation loop phosphorylation motif, whereas other MPKs (Groups A, B, and C) contain a TEY motif. Our findings reveal that RLPH2 has a strong preference for aspartate (D) in the TXY motif, providing specificity for RLPH2 to exclusively target and dephosphorylate the D‐group MPKs. Additionally, D‐group MPKs contain a unique activation loop insertion that conforms to a protein phosphatase one (PP1) binding motif, with findings presented here confirming Arabidopsis PP1 phosphatases dock at this site. Intriguingly, only D‐group MPKs among all identified Arabidopsis protein kinases possess this PP1 recruiting motif. Using multiple RLPH2‐deficient plant lines, we demonstrate that RLPH2 represses seed dormancy release. Overall, this work highlights the power of phospho‐proteomics in identifying substrates of this novel plant tyrosine phosphatase while also revealing new complexities in the interactions between MPK activation loops and multiple phospho‐mediated cell signaling events.

ABSTRACTDrought stress, which is exacerbated by climate change, is a major contributor to crop production losses in rainfed agriculture. Two genotypes of cowpea (Vigna unguiculata, (L.) Walp.) with determinate (IT‐16) and indeterminate (IT‐96D‐610) growth patterns were grown either well‐watered or subjected to drought stress at vegetative and flowering stages in a pot experiment in a glasshouse. Stomatal conductance (gs) and soil moisture were measured daily during the drought stress periods, while chlorophyll fluorescence data were collected every third day. Both genotypes maintained relatively high‐water content (RWC > 80%), indicating dehydration avoidance; however, IT‐96D‐610 consistently maintained a higher RWC than IT‐16. Under drought stress, IT‐96D‐610 exhibited lower gs and less sensitive stomata, greater total root length, root surface area and a higher root‐to‐shoot ratio compared to IT‐16. These traits were associated with higher seed yield and water productivity in IT‐96D‐610 than in IT‐16. In contrast to IT‐96D‐610, genotype IT‐16 showed higher photosynthetic efficiency, indicated by higher Fq′/Fm′ and qP, and produced more biomass, but with reduced grain yield. This study underscores the importance of selecting traits for dehydration avoidance, such as RWC, deep‐fine roots and moderated stomatal conductance, in cowpea breeding programs aimed at improving productivity under drought conditions.

ABSTRACTCrossover recombination is a pivotal event that takes place during meiosis of germinal cells, leading to the rearrangement of parental chromosomes and generating novel allele combinations, thereby enhancing genetic diversity. This process holds significant importance for plant breeders as it enables the transfer of gene variants from one variety to another. Recent studies have explored diverse strategies to predict recombination events along chromosomes in key plant species, employing various types of genome features. In this study, the relationship between genome structure, quantified using k‐mers, and crossover recombination is investigated. To facilitate this analysis, the Python package kmerExtractor is introduced; it uses frequency chaos game representation (FCGR) to count k‐mers from genome fasta files and adds them as column features for subsequent analysis. This package is used to explore the genomes of one model and five crop plant species, namely, Arabidopsis, bean, maize, rice, sorghum, and tomato. The investigation reveals both positive and negative trends between 3‐mers, 2‐mers, and recombination rates. Furthermore, the information derived from k‐mers was used to train regression‐based machine learning models for predicting recombination rates along chromosomes. The results demonstrate the efficacy of using k‐mer for predicting purposes, particularly for sorghum and tomato datasets, highlighting linear relationships between several k‐mers and recombination events. We hope that this predictive strategy based on genomic sequence information can be useful for the development of new plant crosses.

ABSTRACTDavidia involucrata Baill. is a species that thrives in warm, humid climates with consistently moist soil conditions. With rising global temperatures and an increasing frequency of droughts, the natural habitat of Davidia involucrata Baill. is facing severe threats. In‐depth investigation of the molecular mechanisms underlying Davidia involucrata Baill.'s response to drought stress is crucial for the conservation of this rare species and the enhancement of its environmental adaptability. This study systematically analyzed the drought stress response of Davidia involucrata Baill. under varying light conditions through transcriptome data analysis. The results showed that under different light conditions, Davidia involucrata Baill. responded to drought stress by regulating its internal osmotic balance via the “response to mannitol” pathway. Notably, the molecular mechanisms by which Davidia involucrata Baill. responds to drought stress vary significantly under different light conditions. Compared with high light intensity, Davidia involucrata Baill. under shaded conditions responded to drought stress by upregulating glycosyltransferase‐related pathways. In addition, three soil drought–related pathway genes (SDRPGs) (Dinv08247, Dinv34952, and Dinv00865) involved in the regulation of drought stress in Davidia involucrata Baill. were identified, and both ABA and SA were found to influence their expression. As a key environmental factor, air humidification may enhance the drought stress adaptability of Davidia involucrata Baill. by modulating ABA biosynthesis. The SDRPGs and signaling pathways identified in this study may serve as important candidate targets, providing theoretical guidance and scientific reference for the genetic improvement of drought resistance in Davidia involucrata Baill. and the long‐term conservation of rare plant resources.

[This corrects the article DOI: 10.1002/pld3.70081.].

ABSTRACTPlant diseases caused by pathogenic microorganisms result in significant damage to agriculture. Lactic acid bacteria (LAB), in particular strains of Lactiplantibacillus plantarum (L. plantarum), are used as one of the biocontrol methods against plant pathogenic bacteria due to high antagonistic activity associated with their metabolic potential. We have investigated the influence of nutrient medium components (various carbon and nitrogen sources) and cultivation conditions (temperature, duration, and pH) of L. plantarum strains on the level of their antagonistic activity against the test strains of plant pathogenic bacteria. The antimicrobial activity of LAB supernatants was maximal in the presence of 3% (30 g/L) sucrose as the main carbon source and 1% (10 g/L) tyrosine as the main nitrogen source in the nutrient medium against all investigated test strains of PPB. However, the use of such a carbon source as galactose or arabinose led to a decrease or even absence of antimicrobial properties of LAB against phytopathogenic bacteria. The optimal conditions for cultivation of lactobacilli were determined: cultivation temperature +30 ± 1°C, pH 7.8, and duration 72 h. Strains of L. plantarum13c and 21c caused zones of inhibition in test pathogens from 298 to 291 mm. Whereas during 24‐h cultivation of LAB strains, their antagonistic activity was significantly lower, and the zones of inhibition decreased by 30%. The duration and temperature had a significant effect on increasing the antagonistic activity of L. plantarum strains, in contrast to the pH of the medium (p ≥ 0.05).