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<jats:p>Dormancy and heteromorphism are innate seed properties that control germination timing through adaptation to the prevailing environment. The degree of variation in dormancy depth within a seed population differs considerably depending on the genotype and maternal environment. Dormancy is therefore a key trait of annual weeds to time seedling emergence across seasons. Seed heteromorphism, the production of distinct seed morphs (in color, mass or other morphological characteristics) on the same individual plant, is considered to be a bet-hedging strategy in unpredictable environments. Heteromorphic species evolved independently in several plant families and the distinct seed morphs provide an additional degree of variation. Here we conducted a comparative morphological and molecular analysis of the dimorphic seeds (black and brown) of the Amaranthaceae weed <jats:italic>Chenopodium album</jats:italic>. Freshly harvested black and brown seeds differed in their dormancy and germination responses to ambient temperature. The black seed morph of seedlot #1 was dormant and 2/3<jats:sup>rd</jats:sup> of the seed population had non-deep physiological dormancy which was released by after-ripening (AR) or gibberellin (GA) treatment. The deeper dormancy of the remaining 1/3<jats:sup>rd</jats:sup> non-germinating seeds required in addition ethylene and nitrate for its release. The black seeds of seedlot #2 and the brown seed morphs of both seedlots were non-dormant with 2/3<jats:sup>rd</jats:sup> of the seeds germinating in the fresh mature state. The dimorphic seeds and seedlots differed in testa (outer seed coat) thickness in that thick testas of black seeds of seedlot #1 conferred coat-imposed dormancy. The dimorphic seeds and seedlots differed in their abscisic acid (ABA) and GA contents in the dry state and during imbibition in that GA biosynthesis was highest in brown seeds and ABA degradation was faster in seedlot #2. <jats:italic>Chenopodium</jats:italic> genes for GA and ABA metabolism were identified and their distinct transcript expression patterns were quantified in dry and imbibed <jats:italic>C. album</jats:italic> seeds. Phylogenetic analyses of the Amaranthaceae sequences revealed a high proportion of expanded gene families within the <jats:italic>Chenopodium</jats:italic> genus. The identified hormonal, molecular and morphological mechanisms and dormancy variation of the dimorphic seeds of <jats:italic>C. album</jats:italic> and other Amaranthaceae are compared and discussed as adaptations to variable and stressful environments.</jats:p>

<jats:p>Tomato yellow leaf curl virus (TYLCV) is a global spreading begomovirus that is exerting a major restraint on global tomato production. In this transgenic approach, an RNA interference (RNAi)-based construct consisting of sequences of an artificial microRNA (amiRNA), a group of small RNA molecules necessary for plant cell development, signal transduction, and stimulus to biotic and abiotic disease was engineered targeting the AC1/Rep gene of the Oman strain of TYLCV-OM. The Rep-amiRNA constructs presented an effective approach in regulating the expression of the Rep gene against TYLCV as a silencing target to create transgenic <jats:italic>Solanum lycopersicum</jats:italic> L. plant tolerance against TYLCV infection. Molecular diagnosis by PCR followed by a Southern hybridization analysis were performed to confirm the effectiveness of agrobacterium-mediated transformation in T0/T1-transformed plants. A substantial decrease in virus replication was observed when T1 transgenic tomato plants were challenged with the TYLCV-OM infectious construct. Although natural resistance options against TYLCV infection are not accessible, the current study proposes that genetically transformed tomato plants expressing amiRNA could be a potential approach for engineering tolerance in plants against TYLCV infection and conceivably for the inhibition of viral diseases against different strains of whitefly-transmitted begomoviruses in Oman.</jats:p>

<jats:sec><jats:title>Introduction</jats:title><jats:p>The increasing use of cerium nanoparticles (CeO<jats:sub>2</jats:sub>-NPs) has made their influx in agroecosystems imminent through air and soil deposition or untreated wastewater irrigation. Another major pollutant associated with anthropogenic activities is Cd, which has adverse effects on plants, animals, and humans. The major source of the influx of Cd and Ce metals in the human food chain is contaminated food, making it an alarming issue; thus, there is a need to understand the factors that can reduce the potential damage of these heavy metals.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>The present investigation was conducted to evaluate the effect of CeO<jats:sub>2</jats:sub>-10-nm-NPs and Cd (alone and in combination) on <jats:italic>Zea mays</jats:italic> growth. A pot experiment (in sand) was conducted to check the effect of 0, 200, 400, 600, 1,000, and 2,000 mg of CeO<jats:sub>2</jats:sub>-10 nm-NPs/kg<jats:sup>-1</jats:sup> dry sand alone and in combination with 0 and 0.5 mg Cd/kg<jats:sup>-1</jats:sup> dry sand on maize seedlings grown in a partially controlled greenhouse environment, making a total of 12 treatments applied in four replicates under a factorial design. Maize seedling biomass, shoot and root growth, nutrient content, and root anatomy were measured.</jats:p></jats:sec><jats:sec><jats:title>Results and discussion</jats:title><jats:p>The NPs were toxic to plant biomass (shoot and root dry weight), and growth at 2,000 ppm was the most toxic in Cd-0 sets. For Cd-0.5 sets, NPs applied at 1,000 ppm somewhat reverted Cd toxicity compared with the contaminated control (CC). Additionally, CeO<jats:sub>2</jats:sub>-NPs affected Cd translocation, and variable Ce uptake was observed in the presence of Cd compared with non-Cd applied sets. Furthermore, CeO<jats:sub>2</jats:sub>-NPs partially controlled the elemental content of roots and shoots (micronutrients such as B, Mn, Ni, Cu, Zn, Mo, and Fe and the elements Co and Si) and affected root anatomy.</jats:p></jats:sec>

<jats:sec><jats:title>Introduction</jats:title><jats:p>Low selenium (Se) concentrations in soils and plants pose a health risk for ruminants consuming locally-grown forages. Previous studies have shown that Se concentrations in forages can be increased using soil-applied selenate amendments. However, the effects of foliar selenate amendments applied with traditional nitrogen-phosphorus-potassium-sulfur (NPKS) fertilizers on forage yields, and nutrient contents, and agronomic efficiencies are unknown.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>Using a split plot design, we determined the effects of springtime sodium selenate foliar amendment rates (0, 45, and 90 g Se ha<jats:sup>-1</jats:sup>) and NPKS application (none, NPK for grasses/PK for alfalfa, and NPKS/PKS fertilization at amounts adapted to meet local forage and soil requirements) on forage growth and N, S, and Se concentrations, yields, and agronomic efficiencies. This 2-year study was conducted across Oregon on four representative forage fields: orchardgrass (<jats:italic>Dactylis glomerata</jats:italic> L.) in Terrebonne (central Oregon), grass-clover mixture in Roseburg (southwestern Oregon), and both grass mixture and alfalfa (<jats:italic>Medicago sativa</jats:italic> L.) fields in Union (eastern Oregon).</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>Grasses grew poorly and were low in N content without NPK fertilization. Fertilization with NPK/PK promoted forage growth, increased forage N concentrations, and had to be co-applied with S when plant available S was low. Without Se amendment, forage Se concentrations were low and further decreased with NPKS/PKS fertilization. Selenate amendment linearly increased forage Se concentration without adversely affecting forage yields, N and S concentrations, or N and S agronomic efficiencies.</jats:p></jats:sec><jats:sec><jats:title>Discussion</jats:title><jats:p>Importantly, S fertilization did not interfere with Se uptake in Se amended plots. In conclusion, co-application of NPKS/PKS fertilizers and foliar sodium selenate in springtime is an effective strategy to increase forage total Se concentrations, while maintaining optimal growth and quality of Oregon forages.</jats:p></jats:sec>

<jats:p><jats:italic>Growth-regulating factors</jats:italic> (<jats:italic>GRFs</jats:italic>) are plant-specific transcription factors that contain two highly conserved QLQ and WRC domains, which control a range of biological functions, including leaf growth, floral organ development, and phytohormone signaling. However, knowledge of the evolutionary patterns and driving forces of <jats:italic>GRFs</jats:italic> in <jats:italic>Gramineae</jats:italic> crops is limited and poorly characterized. In this study, a total of 96 <jats:italic>GRFs</jats:italic> were identified from eight crops of <jats:italic>Brachypodium distachyon</jats:italic>, <jats:italic>Hordeum vulgare</jats:italic>, <jats:italic>Oryza sativa</jats:italic> L. ssp. <jats:italic>indica</jats:italic>, <jats:italic>Oryza rufipogon</jats:italic>, <jats:italic>Oryza sativa</jats:italic> L. ssp. <jats:italic>japonica</jats:italic>, <jats:italic>Setaria italic</jats:italic>, <jats:italic>Sorghum bicolor</jats:italic> and <jats:italic>Zea mays</jats:italic>. Based on their protein sequences, the <jats:italic>GRFs</jats:italic> were classified into three groups. Evolutionary analysis indicated that the whole-genome or segmental duplication plays an essential role in the <jats:italic>GRFs</jats:italic> expansion, and the <jats:italic>GRF</jats:italic>s were negatively selected during the evolution of <jats:italic>Gramineae</jats:italic> crops. The GRFs protein function as transcriptional activators with distinctive structural motifs in different groups. In addition, the expression of <jats:italic>GRFs</jats:italic> was induced under multiple hormonal stress, including IAA, BR, GA3, 6BA, ABA, and MeJ treatments. Specifically, <jats:italic>OjGRF11</jats:italic> was significantly induced by IAA at 6 h after phytohormone treatment. Transgenic experiments showed that roots overexpressing <jats:italic>OjGRF11</jats:italic> were more sensitive to IAA and affect root elongation. This study will broaden our insights into the origin and evolution of the GRF family in <jats:italic>Gramineae</jats:italic> crops and will facilitate further research on <jats:italic>GRF</jats:italic> function.</jats:p>

<jats:p><jats:italic>Eucommia ulmoides</jats:italic> Oliver is a typical dioecious plant endemic to China that has great medicinal and economic value. Here, we report a high-quality chromosome-level female genome of <jats:italic>E. ulmoides</jats:italic> obtained by PacBio and Hi-C technologies. The size of the female genome assembly was 1.01 Gb with 17 pseudochromosomes and 31,665 protein coding genes. In addition, Hi-C technology was used to reassemble the male genome released in 2018. The reassembled male genome was 1.24 Gb with the superscaffold N50 (48.30 Mb), which was increased 25.69 times, and the number of predicted genes increased by 11,266. Genome evolution analysis indicated that <jats:italic>E. ulmoides</jats:italic> has undergone two whole-genome duplication events before the divergence of female and male, including core eudicot γ whole-genome triplication event (γ-WGT) and a recent whole genome duplication (WGD) at approximately 27.3 million years ago (Mya). Based on transcriptome analysis, <jats:italic>EuAP3</jats:italic> and <jats:italic>EuAG</jats:italic> may be the key genes involved in regulating the sex differentiation of <jats:italic>E. ulmoides</jats:italic>. Pathway analysis showed that the high expression of ω-3 fatty acid desaturase coding gene <jats:italic>EU0103017</jats:italic> was an important reason for the high α-linolenic acid content in <jats:italic>E. ulmoides</jats:italic>. The genome of female and male <jats:italic>E. ulmoides</jats:italic> presented here is a valuable resource for the molecular biological study of sex differentiation of <jats:italic>E. ulmoides</jats:italic> and also will provide assistance for the breeding of superior varieties.</jats:p>

<jats:p>Chloroplasts have important roles in photosynthesis, stress sensing and retrograde signaling. However, the relationship between chloroplast peptide chain release factor and ROS-mediated plant growth is still unclear. In the present study, we obtained a loss-of-function mutant <jats:italic>dig8</jats:italic> by EMS mutation. The <jats:italic>dig8</jats:italic> mutant has few lateral roots and a pale green leaf phenotype. By map-based cloning, the <jats:italic>DIG8</jats:italic> gene was located on AT3G62910, with a point mutation leading to amino acid substitution in functional release factor domain. Using yeast-two-hybrid and BiFC, we confirmed <jats:italic>DIG8</jats:italic> protein was characterized locating in chloroplast by co-localization with plastid marker and interacting with ribosome-related proteins. Through observing by transmission electron microscopy, quantifying ROS content and measuring the transport efficiency of plasmodesmata in dig8 mutant, we found that abnormal thylakoid stack formation and chloroplast dysfunction in the <jats:italic>dig8</jats:italic> mutant caused increased ROS activity leading to callose deposition and lower PD permeability. A local sugar supplement partially alleviated the growth retardation phenotype of the mutant. These findings shed light on chloroplast peptide chain release factor-affected plant growth by ROS stress.</jats:p>

<jats:sec><jats:title>Introduction</jats:title><jats:p>Starch metabolism is involved in the stress response. Starch synthase (SS) is the key enzyme in plant starch synthesis, which plays an indispensable role in the conversion of pyrophosphoric acid to starch. However, the SS gene family in cotton has not been comprehensively identified and systematically analyzed.</jats:p></jats:sec><jats:sec><jats:title>Result</jats:title><jats:p>In our study, a total of 76 SS genes were identified from four cotton genomes and divided into five subfamilies through phylogenetic analysis. Genetic structure analysis proved that SS genes from the same subfamily had similar genetic structure and conserved sequences. A cis-element analysis of the SS gene promoter showed that it mainly contains light response elements, plant hormone response elements, and abiotic stress elements, which indicated that the SS gene played key roles not only in starch synthesis but also in abiotic stress response. Furthermore, we also conducted a gene interaction network for SS proteins. Silencing <jats:italic>GhSS9</jats:italic> expression decreased the resistance of cotton to drought stress. These findings suggested that SS genes could be related to drought stress in cotton, which provided theoretical support for further research on the regulation mechanism of SS genes on abiotic starch synthesis and sugar levels.</jats:p></jats:sec>

<jats:p>This review is a compilation of proteomic studies on forest tree species published in the last decade (2012-2022), mostly focused on the most investigated species, including <jats:italic>Eucalyptus, Pinus</jats:italic>, and <jats:italic>Quercus</jats:italic>. Improvements in equipment, platforms, and methods in addition to the increasing availability of genomic data have favored the biological knowledge of these species at the molecular, organismal, and community levels. Integration of proteomics with physiological, biochemical and other large-scale omics in the direction of the Systems Biology, will provide a comprehensive understanding of different biological processes, from growth and development to responses to biotic and abiotic stresses. As main issue we envisage that proteomics in long-living plants will thrive light on the plant responses and resilience to global climate change, contributing to climate mitigation strategies and molecular breeding programs. Proteomics not only will provide a molecular knowledge of the mechanisms of resilience to either biotic or abiotic stresses, but also will allow the identification on key gene products and its interaction. Proteomics research has also a translational character being applied to the characterization of the variability and biodiversity, as well as to wood and non-wood derived products, traceability, allergen and bioactive peptides identification, among others. Even thought, the full potential of proteomics is far from being fully exploited in forest tree research, with PTMs and interactomics being reserved to plant model systems. The most outstanding achievements in forest tree proteomics in the last decade as well as prospects are discussed.</jats:p>