Soybean seed composition is governed by an inverse correlation between protein and oil, a relationship complicated by environmental factors. In Canada, western grown soybeans consistently have lower seed protein than eastern grown soybeans, a pattern driven by genotype by environment interactions that modulate the protein-oil balance. To uncover the transcriptional networks behind these differences, a multi-year Weighted Gene Co-Expression Network Analysis (WGCNA) was performed on leaf transcriptomes from ten soybean genotypes cultivated in contrasting eastern and western environments. The analysis identified oil-associated co-expression modules preserved across years and environments; their eigengenes showed significant, consistent correlations with seed oil content each year. A core set of recurring hub genes formed the backbone of this network, many of which co-localize with major seed composition Quantitative Trait Loci. Notably, a key hub lies adjacent to the protein-oil trade-off regulator on chromosome 20, while additional hubs map within a QTL on chromosome 10 linked to a more favorable protein-oil balance. The relationship between module expression and oil content displayed a genotype by environment interaction, providing a molecular basis for phenotypic differences between eastern and western regions. These hub transcription factors are prime candidates for breeding soybean cultivars with improved seed composition.

Arabidopsis thaliana mitogen-activated protein kinase (MPK) signaling network plays a role in various cellular processes. This study integrated protein-protein interaction, genetic interaction, and co-expression data from the STRING, BioGRID, and ATTED-II databases to provide a comprehensive dataset of interactions within the network. The key MPK network components from this set were identified and subjected to functional enrichment analysis, which revealed their involvement in diverse biological processes and pathways. This integrative approach, combining multiple sources of evidence, provides a comprehensive approach for understanding Arabidopsis thaliana MPK signaling network. The findings demonstrate the complex regulatory mechanisms that play a role in plant stress responses and development.

Arabidopsis thaliana mitogen-activated protein kinase (MPK or MAPK) signaling network plays significant roles in various cellular processes. The three-dimensional structure of mitogen-activated protein kinase kinase 2 (MKK2), an upstream kinase in the MAP kinase cascade, was predicted using AlphaFold 2, and protein-protein docking simulations were performed between MPK6 and MKK2. The docking analysis identified important residues mediating their interaction. This structural prediction and protein docking analysis provide a further understanding at protein structure level.

There are a variety of conditions that regulate flowering time in Arabidopsis, but there are no reported instances mitogen-activated protein kinase pathways playing a decisive role in flowering time. Our work has indicated that when long-day plant Arabidopsis mitogen-activated protein kinase kinase 1 (AtMKK1) was knocked out, Arabidopsis plants flowered under short day conditions. Possible mechanisms are discussed.

The repair of damaged DNA is an essential function for living organisms. While great strides have been made in understanding this process in animal and yeast models, our knowledge in plant DNA repair is not as developed. Plants face many sources of DNA damage which they cannot so easily avoid: UV radiation from sunlight, reactive oxygen species produced endogenously by their mitochondria and chloroplasts, reactive oxygen species accumulated while under conditions of cold, heat, or salt stress. Understanding plant DNA repair is particularly relevant as the accumulation of DNA damage can negatively impact the growth and yield of agronomically important species. In this study, a broad classification of genes related to DNA repair in the model dicot Arabidopsis thaliana was conducted using gene ontology and gene enrichment analysis. The results of this broad classification serve to elucidate pathways for further study in plant DNA damage response and repair.

Electrical signals in plants were first documented in the mid-19th century. In response to insect attacks, plants generate electrical signals that spread throughout the plant body and trigger physiological, biochemical and molecular responses. Arabidopsis has been used as a model plant in the past several decades. In this mini review, we will address the current understanding of electrical signaling in Arabidopsis and its physiological and biochemical impacts during herbivore attacks.

Triticeae crops are major contributors to global food production and ensuring their capacity to reproduce and generate seeds is critical. However, despite their importance our knowledge of the proteins underlying Triticeae reproduction is severely lacking and this is not only true of pollen and stigma development, but also of their pivotal interaction. When the pollen grain and stigma are brought together they have each accumulated the proteins required for their intended meeting and accordingly studying their mature proteomes is bound to reveal proteins involved in their diverse and complex interactions. Using triticale as a Triticeae representative, gel-free shotgun proteomics was used to identify 11,533 and 2977 mature stigma and pollen proteins respectively. These datasets, by far the largest to date, provide unprecedented insights into the proteins participating in Triticeae pollen and stigma development and interactions. The study of the Triticeae stigma has been particularly neglected. To begin filling this knowledge gap, a developmental iTRAQ analysis was performed revealing 647 proteins displaying differential abundance as the stigma matures in preparation for pollination. An in-depth comparison to an equivalent Brassicaceae analysis divulged both conservation and diversification in the makeup and function of proteins involved in the pollen and stigma encounter. SIGNIFICANCE: Successful pollination brings together the mature pollen and stigma thus initiating an intricate series of molecular processes vital to crop reproduction. In the Triticeae crops (e.g. wheat, barley, rye, triticale) there persists a vast deficit in our knowledge of the proteins involved which needs to be addressed if we are to face the many upcoming challenges to crop production such as those associated with climate change. At maturity, both the pollen and stigma have acquired the protein complement necessary for their forthcoming encounter and investigating their proteomes will inevitably provide unprecedented insights into the proteins enabling their interactions. By combining the analysis of the most comprehensive Triticeae pollen and stigma global proteome datasets to date with developmental iTRAQ investigations, proteins implicated in the different phases of pollen-stigma interaction enabling pollen adhesion, recognition, hydration, germination and tube growth, as well as those underlying stigma development were revealed. Extensive comparisons between equivalent Triticeae and Brassiceae datasets highlighted both the conservation of biological processes in line with the shared goal of activating the pollen grain and promoting pollen tube invasion of the pistil to effect fertilization, as well as the significant distinctions in their proteomes consistent with the considerable differences in their biochemistry, physiology and morphology.

Mitogen-activated protein kinase cascades are one of the many systems that allow plants to survive and defend themselves against pathogens and other environmental stresses. Numerous scientific investigations rendered insights to molecular signaling pathways that take place in an event of a stress such as soil salinity. Despite the known functions and locations of proteins that play a role in these pathways, very little is known about upstream protein partners. In this paper, we elucidate biological functions and molecular locations of Arabidopsis thaliana MKK1 protein through data mining predominantly from STRING and BAR databases. Results revealed AtMEKK1 and CRLK1 as upstream protein partners. In addition, AtMKK2 was further analyzed as a redundant protein to AtMKK1.

Cell death occurs under various developmental and stress conditions. Its involvement in plant response to pathogen attacks has been well studied in model plant Arabidopsis thaliana. In our present work, Fumonisin B1, a toxin from Fusarium verticillioides, a major fungal pathogen of cereals, was used as a biotic stressor to trigger responses in two wheat cultivars. Fumonisin B1 induced cell death in both Fusarium head blight (FHB) resistant and FHB susceptible cultivars (Frontana and Roblin, respectively). The treatment also triggered DNA smearing in both. However, the expression of two DNA repairing genes was enhanced in Frontana but not in Roblin. Our results have suggested potential regulatory differences in the response to FB1 toxin in FHB resistant and FHB susceptible cultivars.

The successful existence of plants depends on their ability to coordinate complex developmental changes and to sense and respond to fluctuations in their surroundings. For decades, crop improvement through engineering of cell signaling mechanisms has been attempted. In this practice, it is critical that the complexity of cell signaling must be taken into consideration in order to enhance the performance of crops with minimum negative effects. With the generation of omics data and detailed delineation of transduction pathways up to date, it is time that we ask us once again what will be a rationale for a genetic manipulation approach and particularly whether we can predict the outcome of the manipulation. In this chapter, attempts to manipulate mitogen-activated protein (MAP) kinase pathways in crops will be primarily used as examples. We will review various outcomes in modification of MAP kinase cascades in crops, complexity of MAP kinase signaling at biochemical and cellular levels in crops and model plants, and the potential of network analysis of biological systems in genetic modification studies.

Successful pollination in Brassica brings together the mature pollen grain and stigma papilla, initiating an intricate series of molecular processes meant to eventually enable sperm cell delivery for fertilization and reproduction. At maturity, the pollen and stigma cells have acquired proteomes, comprising the primary molecular effectors required upon their meeting. Knowledge of the roles and global composition of these proteomes in Brassica species is largely lacking. To address this gap, gel-free shotgun proteomics was performed on the mature pollen and stigma of Brassica carinata, a representative of the Brassica family and its many crop species (e.g. Brassica napus, Brassica oleracea and Brassica rapa) that holds considerable potential as a bio-industrial crop. A total of 5608 and 7703 B. carinata mature pollen and stigma proteins were identified, respectively. The pollen and stigma proteomes were found to reflect not only their many common functional and developmental objectives, but also the important differences underlying their cellular specialization. Isobaric tag for relative and absolute quantification (iTRAQ) was exploited in the first analysis of a developing Brassicaceae stigma, and revealed 251 B. carinata proteins that were differentially abundant during stigma maturation, providing insight into proteins involved in the initial phases of pollination. Corresponding pollen and stigma transcriptomes were also generated, highlighting functional divergences between the proteome and transcriptome during different stages of pollen-stigma interaction. This study illustrates the investigative potential of combining the most comprehensive Brassicaceae pollen and stigma proteomes to date with iTRAQ and transcriptome data to provide a unique global perspective of pollen and stigma development and interaction.

During plant-microbe interactions, plant immune signaling relies significantly on post-translational modifications (PTMs) to induce rapid downstream changes. Organization at protein level is extensively complex and various forms of PTMs of transcript products provide a unique system in maintaining such an organization. With current proteomic research some detailed mechanisms of these PTMs have started to be uncovered. Pathogens also take PTMs as a virulence strategy to overturn host immunity through the activities of their effector proteins. In this review, we will address the importance of PTMs other than phosphorylation in plant defense response.

ATP-binding cassette-type (ABC) transporters are highly implicated in detoxification processes but not restricted to detoxification processes. Several ABC transporters including wheat Lr34 were shown to function in plant defense responses and secretion of plant antimicrobial compounds. Members of multidrug resistance (MDR) proteins and pleiotropic drug resistance (PDR) proteins were studied in wheat. MDR1 and PDR1 expression was relatively stable in all the developmental stages but responded differentially to salicylic acid and fumonisin B1. In silico analysis indicated that both MDR1 and PDR1 had expression levels in all analyzed parts of wheat.

Many uses of protoplasts, plant cells with the cell wall removed, have been explored. Many advantages of the system have been realized and proven in recent years in various physiological, biochemical, genetic, and molecular biological studies. Reliable methods to isolate viable protoplasts from a broad variety of plant species have been established. Regeneration of plants from protoplasts has become one of the options involved in crop gene manipulation and crop improvement. Here, we present how protoplast system may help crop gene editing and novel trait development, and discuss the potentials and challenges of this approach.

Wheat stripe rust pandemics have been recorded across all cereal growing regions. Lr34 provides an adult plant resistance and flag leaves of many wheat cultivars containing Lr34 develop a necrotic flag leaf tip. We studied cell death process in progressive necrotic and non-necrotic tissues of flag leaves in wheat cultivars Frontana (resistant to stripe rust) and Fielder (highly susceptible to stripe rust). Cleavage of the poly(ADP-ribose) polymerase (PARP) was detected in necrotic tissues of Frontana flag leaves but not in the non-necrotic tissues or in the corresponding leaf sections in Fielder flag leaves. DNA repairing genes were also studied but their expression was similar in the two different leaf sections for both cultivars. Our work may indicate that protein cleavage is involved in the cell death of flag leaf tips in Frontana.

Sugars regulate growth, development, and defense in trees. Sugars are also important signaling molecules and are transported over long distances via xylem and phloem. Sucrose loading to tracheids and vessels is associated with bulk xylem pressure and occurs seasonally in temperate broadleaf eudicot trees. Following restoration of xylem hydraulic conductivity in spring, sugars are unloaded from xylem sap at apical branches and deposited as starch before growth of shoot apical meristems. Growth of cambia and shoot apical meristems leads to starch catabolism that yields hexose-phosphates to fuel cell growth and regulate other signal networks. The contrast between cell molecular biology of Arabidopsis and physiology of temperate broadleaf eudicot trees indicates the importance of phosphorylation in long-distance sugar signaling. Hexokinase, acting as a hub for signal and hormone networks, is likely an important regulator of sugar signaling in response to stimuli such as energy status, sugar status, and environmental conditions. The comparative analysis suggested here could help bridge physiology and detailed molecular mechanisms regarding physiology of trees.

The rice Wsi18 promoter confers drought-induciblegene expression. This property makes it a useful candidate to drive relevantgenes for developing drought resistant traits for different monocot crops. In this study, we showed that the Bradi2G47700 gene, the closest homologue to rice Wsi18, was upregulated in Brachypodium distachyon plants exposed to ABA and mannitol. Wsi18: uidA transgenic B.distachyon plants were produced and then subjected to ABA or mannitol treatment. Theexpression of uidA in threetransgenic lines (line 10, 18 and 37) was significantly upregulated in plantsexposed to ABA (fold increases of 5.61 ± 0.98,2.88 ± 0.75 and 9.13 ± 1.96, respectively) compared to the same transgenic plant lines withouttreatment. The expression of uidA intwo transgenic lines (lines 18 and 37) also showed upregulationwhen treated with mannitol (fold increases of 4.43 ± 1.07 and 8.47 ± 2.90,respectively) compared to the same transgenic plant lines without mannitoltreatment. Moreover, GUS histochemical assay showed increased Wsi18 promoter activity in the leaves and stems of transgenic lines upon treatment with ABA or mannitol. This is the first report of thedrought inducible rice Wsi18 promoterbeing active in B. distachyon which is a model plant for molecular biologyresearch of various monocot plants. Taken together, the results indicate thatthe Wsi18 promoter and its homologue may be explored as a useful tool for drought stress-inducible gene expression in different monocot crops.

A protoplast is a plant cell from which the cell wall has been removed by enzyme treatment. Tremendous utilization of protoplast in molecular analysis of plant growth and development has been observed in the past decades and the system has paved its way to significantly facilitate the comprehensive understanding of the complexity of underlying mechanisms. However, it should be kept in mind that a plant, like all systems, is composed of networks of interdependent components that integrate the system into a unified whole. In this mini review, we will re-explore protoplast approach in answering plant physiology questions through discussion of its application in the study of (1) photosynthesis and chloroplast-related process; (2) pollen tube growth; (3) sieve tube element protoplast for long distance translocation; (4) new regulatory metabolites from guard cell protoplast. This in vitro approach may open the way to further meaningful results at organismal level.

Alfalfa (Medicago sativa L.) is an important leguminous crop worldwide and it has important roles in different aspects of the agriculture system, including livestock feed, crop soil conservation, and improvement of soil nitrogen supply. As a perennial crop, alfalfa breeding for trait improvement takes longer periods of time compared to many other crops, therefore, genetic engineering is a faster route for alfalfa trait modification and improvement. Alfalfa was a first crop in which somatic embryogenesis was developed. Alfalfa was also a pioneering crop in which transgenic technology was developed and applied for trait improvement. Transgenic technology in alfalfa has since advanced steadily in various areas. In this review, we update the recent research progress in alfalfa genetic engineering, focusing on genetic transformation and use of transgenic technology for trait improvement and new trait development.