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<jats:p>The <jats:italic>Cellulose synthase</jats:italic> (<jats:italic>CesA</jats:italic>) and <jats:italic>Cellulose synthase-like</jats:italic> (<jats:italic>Csl</jats:italic>) gene superfamilies encode key enzymes involved in the synthesis of cellulose and hemicellulose, which are major components of plant cell walls, and play important roles in the regulation of fruit ripening. However, genome-wide identification and functional analysis of the <jats:italic>CesA</jats:italic> and <jats:italic>Csl</jats:italic> gene families in strawberry remain limited. In this study, eight <jats:italic>CesA</jats:italic> genes and 25 <jats:italic>Csl</jats:italic> genes were identified in the genome of diploid woodland strawberry (<jats:italic>Fragaria vesca</jats:italic>). The protein structures, evolutionary relationships, and <jats:italic>cis</jats:italic>-acting elements of the promoter for each gene were investigated. Transcriptome analysis and quantitative real-time PCR (qRT-PCR) results showed that the transcript levels of many <jats:italic>FveCesA</jats:italic> and <jats:italic>FveCsl</jats:italic> genes were significantly decreased during fruit ripening. Moreover, based on the transcriptome analysis, we found that the expression levels of many <jats:italic>FveCesA/Csl</jats:italic> genes were changed after nordihydroguaiaretic acid (NDGA) treatment. Transient overexpression of <jats:italic>FveCesA4</jats:italic> in immature strawberry fruit increased fruit firmness and reduced fresh fruit weight, thereby delaying ripening. In contrast, transient expression of <jats:italic>FveCesA4</jats:italic>-RNAi resulted in the opposite phenotypes. These findings provide fundamental information on strawberry <jats:italic>CesA</jats:italic> and <jats:italic>Csl</jats:italic> genes and may contribute to the elucidation of the molecular mechanism by which <jats:italic>FveCesA</jats:italic>/<jats:italic>Csl</jats:italic>-mediated cell wall synthesis regulates fruit ripening. In addition, these results may be useful in strawberry breeding programs focused on the development of new cultivars with increased fruit shelf-life.</jats:p>

<jats:p>Green and blue mold of citrus are threatening diseases that continuously inflict economic post-harvest loss. The suppressive effect of salicylic (SA) and <jats:italic>Cinnamomum verum</jats:italic> (CV) on green and blue mold of sweet oranges was investigated in this study. Among five tested plant extracts methanolic extract of Cinnamon caused the highest colony growth inhibition of <jats:italic>P. digitatum</jats:italic> and <jats:italic>P. italicum</jats:italic> in an <jats:italic>in vitro</jats:italic> antifungal assay. The methanolic extract of Cinnamon in combination with SA showed the lowest disease incidence and severity of green and blue mold on citrus fruit without affecting the fruit quality. Transcriptional profiling of defense enzymes revealed that the polyphenol oxidase (<jats:italic>PPO</jats:italic>), phenylalanine ammonia-lyase (<jats:italic>PAL</jats:italic>), and peroxidase (<jats:italic>POD</jats:italic>) genes were upregulated in fruit treated with CV, SA, and their combination compared to the control. The treatment SA+CV caused the highest upsurge in <jats:italic>PPO</jats:italic>, <jats:italic>POD</jats:italic>, and <jats:italic>PAL</jats:italic> gene expression than the control. Furthermore, the biochemical quantification of PPO, POD and PAL also revealed a similar pattern of activity. The present findings unravel the fact that the escalation in the activity of tested defense enzymes is possibly associated with the reduced incidence of blue and green molds. In conclusion, the study unveils the promising suppressive potential of SA+CV against green and blue mold by regulating the expression of <jats:italic>PPO</jats:italic>, <jats:italic>POD</jats:italic>, and <jats:italic>PAL</jats:italic> genes. Therefore, these treatments can find a role as safer alternatives to chemicals in the management of post-harvest green and blue mold.</jats:p>

<jats:p>Heat shock factors (HSFs) play a crucial role in the environmental stress responses of numerous plant species, including defense responses to pathogens; however, their role in cotton resistance to <jats:italic>Verticillium dahliae</jats:italic> remains unclear. We have previously identified several differentially expressed genes (DEGs) in <jats:italic>Arabidopsis thaliana</jats:italic> after inoculation with <jats:italic>V. dahliae</jats:italic>. Here, we discovered that <jats:italic>GhHSFA4a</jats:italic> in <jats:italic>Gossypium hirsutum</jats:italic> (cotton) after inoculation with <jats:italic>V. dahliae</jats:italic> shares a high identity with a DEG in <jats:italic>A. thaliana</jats:italic> in response to <jats:italic>V. dahliae</jats:italic> infection. Quantitative real-time PCR (qRT-PCR) analysis indicated that <jats:italic>GhHSFA4a</jats:italic> expression was rapidly induced by <jats:italic>V. dahliae</jats:italic> and ubiquitous in cotton roots, stems, and leaves. In a localization analysis using transient expression, GhHSFA4a was shown to be localized to the nucleus. Virus-induced gene silencing (VIGS) revealed that downregulation of <jats:italic>GhHSFA4a</jats:italic> significantly increased cotton susceptibility to <jats:italic>V. dahliae.</jats:italic> To investigate <jats:italic>GhHSFA4a-</jats:italic>mediated defense, 814 DEGs were identified between <jats:italic>GhHSFA4a-</jats:italic>silenced plants and controls using comparative RNA-seq analysis. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that DEGs were enriched in “flavonoid biosynthesis”, “sesquiterpenoid and triterpenoid biosynthesis”, “linoleic acid metabolism” and “alpha-linolenic acid metabolism”. The expression levels of marker genes for these four pathways were triggered after inoculation with <jats:italic>V. dahliae</jats:italic>. Moreover, <jats:italic>GhHSFA4a</jats:italic>-overexpressing lines of <jats:italic>A. thaliana</jats:italic> displayed enhanced resistance against <jats:italic>V. dahliae</jats:italic> compared to that of the wild type. These results indicate that <jats:italic>GhHSFA4a</jats:italic> is involved in the synthesis of secondary metabolites and signal transduction, which are indispensable for innate immunity against <jats:italic>V. dahliae</jats:italic> in cotton.</jats:p>

<jats:p>The efficient induction of peony embryogenic callus is of great significance to the improvement and establishment of its regeneration technology system. In this study, the <jats:italic>in vitro</jats:italic> embryos of ‘Fengdanbai’ at different developmental stages were selected as explants, the effects of different concentrations and types of plant growth regulator combinations on the induction and proliferation of embryonic callus at different developmental stages were investigated, and comparative transcriptome analysis of callus with different differentiation potentials were performed to explore the molecular mechanisms affecting callus differentiation. The results showed that the germination rate of 90d seed embryo was the best, which was 94.17%; the 70d and 80d cotyledon callus induction effect was the best, both reaching 100%, but the 80d callus proliferation rate was higher, the proliferation rate reached 5.31, and the optimal induction medium was MS+0.1 mg·L<jats:sup>–1</jats:sup>NAA+0.3 mg·L<jats:sup>–1</jats:sup>TDZ+3 mg·L<jats:sup>–1</jats:sup>2,4-D, the callus proliferation multiple was 4.77. Based on the comparative transcriptomic analysis, we identified 3470 differentially expressed genes (DEGs) in the callus with high differentiation rate and low differentiation rate, including 1767 up-regulated genes and 1703 down-regulated genes. Pathway enrichment analysis showed that the “Phenylpropanoid biosynthesis” metabolic pathway was significantly enriched, which is associated with promoting further development of callus shoots and roots. This study can provide reference for genetic improvement and the improvement of regeneration technology system of peony.</jats:p>

<jats:p>Changes in temperature and nitrogen (N) deposition determine the growth and competitive dominance of both invasive and native plants. However, a paucity of experimental evidence limits understanding of how these changes influence plant invasion. Therefore, we conducted a greenhouse experiment in which invasive <jats:italic>Solidago canadensis</jats:italic> L. was planted in mixed culture with native <jats:italic>Artemisia argyi</jats:italic> Levl. et Van under combined conditions of warming and N addition. Our results show that due to the strong positive effect of nitrogen addition, the temperature increases and nitrogen deposition interaction resulted in greatly enhanced species performance. Most of the relative change ratios (RCR) of phenotypic traits differences between <jats:italic>S. canadensis</jats:italic> and <jats:italic>A. argyi</jats:italic> occur in the low invasion stage, and six of eight traits had higher RCR in response to N addition and/or warming in native <jats:italic>A. argyi</jats:italic> than in invasive <jats:italic>S. canadensis</jats:italic>. Our results also demonstrate that the effects of the warming and nitrogen interaction on growth-related traits and competitiveness of <jats:italic>S. canadensis</jats:italic> and <jats:italic>A. argyi</jats:italic> were usually additive rather than synergistic or antagonistic. This conclusion suggests that the impact of warming and nitrogen deposition on <jats:italic>S. canadensis</jats:italic> can be inferred from single factor studies. Further, environmental changes did not modify the competitive relationship between invasive <jats:italic>S. canadensis</jats:italic> and native <jats:italic>A. argyi</jats:italic> but the relative yield of <jats:italic>S. canadensis</jats:italic> was significantly greater than <jats:italic>A. argyi</jats:italic>. This finding indicated that we can rule out the influence of environmental changes such as N addition and warming which makes <jats:italic>S. canadensis</jats:italic> successfully invade new habitats through competition. Correlation analysis showed that invasive <jats:italic>S. canadensis</jats:italic> may be more inclined to mobilize various characteristics to strengthen competition during the invasion process, which will facilitate <jats:italic>S. canadensis</jats:italic> becoming the superior competitor in <jats:italic>S. canadensis-A. argyi</jats:italic> interactions. These findings contribute to our understanding of the spreading of invasive plants such as <jats:italic>S. canadensis</jats:italic> under climate change and help identify potential precautionary measures that could prevent biological invasions.</jats:p>

<jats:p>Arbuscular mycorrhizal fungi (AMF) play various important roles in promoting plant growth. Numerous environmental and evolutionary factors influence the response of plants to AMF. However, the importance of the individual factors on the effects of AMF on plant biomass is not clearly understood. In this study, a meta-analysis using 1,640 observations from 639 published articles related to the influence of AMF on the plant shoot, root, and total biomass was performed; 13 different experimental setting factors that had an impact on the influence of AMF and their importance were quantitatively synthesized. The meta-analysis showed that AMF had positive effects on the plant shoot, root, and total biomass; moreover, the experimental duration, plant root-to-shoot ratio (R/S), AMF root length colonization, plant family, pot size, soil texture, and the soil pH all influenced the effects of AMF on the shoot, root, and total biomass. In addition, the plant root system and plant functional type had impacts on the effect of AMF on shoot biomass; AMF guild also impacted the effect of AMF on root biomass. Of these factors, the experimental duration, plant R/S, and pot size were the three most important predicting the effects of AMF on the plant shoot, root, and total biomass. This study comprehensively assessed the importance of the different factors that influenced the response of plants to AMF, highlighting that the experimental duration, plant R/S, and pot size should be taken into consideration in pot experiments in studies of the functions of AMF. Multiple unfavorable factors that may obscure or confound the observed functions of AMF should be excluded.</jats:p>

<jats:p>Genome-wide association studies (GWAS) of fiber quality traits of upland cotton were conducted to identify the single-nucleotide polymorphic (SNP) loci associated with cotton fiber quality, which lays the foundation for the mining of elite] cotton fiber gene resources and its application in molecular breeding. A total of 612 upland cotton accessions were genotyped using the ZJU Cotton Chip No. 1 40K chip array <jats:italic>via</jats:italic> the liquid-phase probe hybridization-based genotyping-by-target-sequencing (GBTS) technology. In the present study, five fiber quality traits, namely fiber length, fiber strength, micronaire, uniformity and elongation, showed different degrees of variation in different environments. The average coefficient of variation of fiber strength was the greatest, whereas the average coefficient of variation of uniformity was the least. Significant or extremely significant correlations existed among the five fiber quality traits, especially fiber length, strength, uniformity and elongation all being significantly negative correlated with micronaire. Population cluster analysis divided the 612 accessions into four groups: 73 assigned to group I, 226 to group II, 220 to group III and 93 to group IV. Genome-wide association studies of five fiber quality traits in five environments was performed and a total of 42 SNP loci associated with target traits was detected, distributed on 19 chromosomes, with eight loci associated with fiber length, five loci associated with fiber strength, four loci associated with micronaire, twelve loci associated with fiber uniformity and thirteen loci associated with fiber elongation. Of them, seven loci were detected in more than two environments. Nine SNP loci related to fiber length, fiber strength, uniformity and elongation were found on chromosome A07, seven loci related to fiber length, fiber strength, micronaire and elongation were detected on chromosome D01, and five loci associated with fiber length, uniformity and micronaire were detected on chromosome D11. The results from this study could provide more precise molecular markers and genetic resources for cotton breeding for better fiber quality in the future.</jats:p>

<jats:p><jats:italic>Zoysia matrella</jats:italic> is a salt-tolerant turfgrass grown in areas with high soil salinity irrigated with effluent water. Previous studies focused on explaining the regulatory mechanism of <jats:italic>Z. matrella</jats:italic> salt-tolerance at phenotypic and physiological levels. However, the molecular mechanism associated with salt tolerance of <jats:italic>Z. matrella</jats:italic> remained unclear. In this study, a high-efficient method named FOX (full-length cDNA overexpression) hunting system was used to search for salt-tolerant genes in <jats:italic>Z. matrella</jats:italic>. Eleven candidate genes, including several known or novel salt-tolerant genes involved in different metabolism pathways, were identified. These genes exhibited inducible expression under salt stress condition. Furthermore, a novel salt-inducible candidate gene <jats:italic>ZmGnTL</jats:italic> was transformed into <jats:italic>Arabidopsis</jats:italic> for functional analysis. <jats:italic>ZmGnTL</jats:italic> improved salt-tolerance through regulating ion homeostasis, reactive oxygen species scavenging, and osmotic adjustment. In summary, we demonstrated that FOX is a reliable system for discovering novel genes relevant to salt tolerance and several candidate genes were identified from <jats:italic>Z. matrella</jats:italic> that can assist molecular breeding for plant salt-tolerance improvement.</jats:p>

<jats:p>Both plant- and rhizobia-derived small RNAs play an essential role in regulating the root nodule symbiosis in legumes. Small RNAs, in association with Argonaute proteins, tune the expression of genes participating in nodule development and rhizobial infection. However, the role of Argonaute proteins in this symbiosis has been overlooked. In this study, we provide transcriptional evidence showing that Argonaute5 (AGO5) is a determinant genetic component in the root nodule symbiosis in <jats:italic>Phaseolus vulgaris</jats:italic>. A spatio-temporal transcriptional analysis revealed that the promoter of <jats:italic>PvAGO5</jats:italic> is active in lateral root primordia, root hairs from rhizobia-inoculated roots, nodule primordia, and mature nodules. Transcriptional analysis by RNA sequencing revealed that gene silencing of <jats:italic>PvAGO5</jats:italic> affected the expression of genes involved in the biosynthesis of the cell wall and phytohormones participating in the rhizobial infection process and nodule development. PvAGO5 immunoprecipitation coupled to small RNA sequencing revealed the small RNAs bound to PvAGO5 during the root nodule symbiosis. Identification of small RNAs associated to PvAGO5 revealed miRNAs previously known to participate in this symbiotic process, further supporting a role for AGO5 in this process. Overall, the data presented shed light on the roles that PvAGO5 plays during the root nodule symbiosis in <jats:italic>P. vulgaris</jats:italic>.</jats:p>

<jats:p>The natural environment of plants comprises a complex set of biotic and abiotic stresses, and plant responses to these stresses are complex as well. Plant proteomics approaches have significantly revealed dynamic changes in plant proteome responses to stress and developmental processes. Thus, we reviewed the recent advances in cotton proteomics research under changing environmental conditions, considering the progress and challenging factors. Finally, we highlight how single-cell proteomics is revolutionizing plant research at the proteomics level. We envision that future cotton proteomics research at the single-cell level will provide a more complete understanding of cotton’s response to stresses.</jats:p>