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<jats:sec><jats:title>Introduction</jats:title><jats:p>Bacteria of genus <jats:italic>Pectobacterium</jats:italic>, encompassing economically significant pathogens affecting various plants, includes the species <jats:italic>P. betavasculorum</jats:italic>, initially associated with beetroot infection. However, its host range is much broader. It causes diseases of sunflower, potato, tomato, carrots, sweet potato, radish, squash, cucumber, and chrysanthemum. To explain this phenomenon, a comprehensive pathogenomic and phenomic characterisation of <jats:italic>P. betavasculorum</jats:italic> species was performed.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>Genomes of <jats:italic>P. betavasculorum</jats:italic> strains isolated from potato, sunflower, and artichoke were sequenced and compared with those from sugar beet isolates. Metabolic profiling and pathogenomic analyses were conducted to assess virulence determinants and adaptation potential. Pathogenicity assays were performed on potato tubers and chicory leaves to confirm <jats:italic>in silico</jats:italic> predictions of disease symptoms. Phenotypic assays were also conducted to assess the strains ability to synthesise homoserine lactones and siderophores.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>The genome size ranged from 4.675 to 4.931 kbp, and GC % was between 51.0% and 51.2%. The pangenome of <jats:italic>P. betavasculorum</jats:italic> is open and comprises, on average, 4,220 gene families. Of these, 83% of genes are the core genome, and 2% of the entire pangenome are unique genes. Strains isolated from sugar beet have a smaller pangenome size and a higher number of unique genes than those from other plants. Interestingly, genomes of strains from artichoke and sunflower share 391 common CDS that are not present in the genomes of other strains from sugar beet or potato. Those strains have only one unique gene. All strains could use numerous sugars as building materials and energy sources and possessed a high repertoire of virulence determinants in the genomes. <jats:italic>P. betavasculorum</jats:italic> strains were able to cause disease symptoms on potato tubers and chicory leaves. They were also able to synthesise homoserine lactones and siderophores.</jats:p></jats:sec><jats:sec><jats:title>Discussion</jats:title><jats:p>The findings underscore the adaptability of <jats:italic>P. betavasculorum</jats:italic> to diverse hosts and environments. Strains adapted to plants with high sugar content in tissues have a different composition of fatty acids in membranes and a different mechanism of replenishing nitrogen in case of deficiency of this compound than strains derived from other plant species. Extensive phenomics and genomic analyses performed in this study have shown that <jats:italic>P. betavasculorum</jats:italic> species is an agronomically relevant pathogen.</jats:p></jats:sec>

<jats:p>Mungbean [<jats:italic>Vigna radiata</jats:italic> var. <jats:italic>radiata</jats:italic> (L.) Wilczek] production in Asia is detrimentally affected by transient soil waterlogging caused by unseasonal and increasingly frequent extreme precipitation events. While mungbean exhibits sensitivity to waterlogging, there has been insufficient exploration of germplasm for waterlogging tolerance, as well as limited investigation into the genetic basis for tolerance to identify valuable loci. This research investigated the diversity of transient waterlogging tolerance in a mini−core germplasm collection of mungbean and identified candidate genes for adaptive traits of interest using genome−wide association studies (GWAS) at two critical stages of growth: germination and seedling stage (i.e., once the first trifoliate leaf had fully−expanded). In a temperature−controlled glasshouse, 292 genotypes were screened for tolerance after (i) 4 days of waterlogging followed by 7 days of recovery at the germination stage and (ii) 8 days of waterlogging followed by 7 days of recovery at the seedling stage. Tolerance was measured against drained controls. GWAS was conducted using 3,522 high−quality DArTseq−derived SNPs, revealing five significant associations with five phenotypic traits indicating improved tolerance. Waterlogging tolerance was positively correlated with the formation of adventitious roots and higher dry masses. FGGY carbohydrate kinase domain−containing protein was identified as a candidate gene for adventitious rooting and mRNA-uncharacterized LOC111241851, Caffeoyl-CoA O-methyltransferase At4g26220 and MORC family CW-type zinc finger protein 3 and zinc finger protein 2B genes for shoot, root, and total dry matter production. Moderate to high broad−sense heritability was exhibited for all phenotypic traits, including seed emergence (81%), adventitious rooting (56%), shoot dry mass (81%), root dry mass (79%) and SPAD chlorophyll content (70%). The heritability estimates, marker−trait associations, and identification of sources of waterlogging tolerant germplasm from this study demonstrate high potential for marker−assisted selection of tolerance traits to accelerate breeding of climate−resilient mungbean varieties.</jats:p>

<jats:p>Proanthocyanidins (PAs) and anthocyanins are flavonoids that contribute to the quality and health benefits of grapes and wine. Salinity affects their biosynthesis, but the underlying mechanism is still unclear. We studied the effects of NaCl stress on PA and anthocyanin biosynthesis in grape suspension cells derived from berry skins of <jats:italic>Vitis vinifera</jats:italic> L. Cabernet Sauvignon using metabolite profiling and transcriptome analysis. We treated the cells with low (75 mM NaCl) and high (150 mM NaCl) salinity for 4 and 7 days. High salinity inhibited cell growth and enhanced PA and anthocyanin accumulation more than low salinity. The salinity-induced PAs and anthocyanins lacked C5’-hydroxylation modification, suggesting the biological significance of delphinidin- and epigallocatechin-derivatives in coping with stress. The genes up-regulated by salinity stress indicated that the anthocyanin pathway was more sensitive to salt concentration than the PA pathway, and WGCNA analysis revealed the coordination between flavonoid biosynthesis and cell wall metabolism under salinity stress. We identified transcription factors potentially involved in regulating NaCl dose- and time-dependent PA and anthocyanin accumulation, showing the dynamic remodeling of flavonoid regulation network under different salinity levels and durations. Our study provides new insights into regulator candidates for tailoring flavonoid composition and molecular indicators of salt stress in grape cells.</jats:p>

<jats:p>MADS-domain transcription factors play pivotal roles in numerous developmental processes in <jats:italic>Arabidopsis thaliana.</jats:italic> While their involvement in flowering transition and floral development has been extensively examined, their functions in root development remain relatively unexplored. Here, we explored the function and genetic interaction of three MADS-box genes (<jats:italic>XAL2</jats:italic>, <jats:italic>SOC1</jats:italic> and <jats:italic>AGL24</jats:italic>) in primary root development. By analyzing loss-of-function and overexpression lines, we found that <jats:italic>SOC1</jats:italic> and <jats:italic>AGL24</jats:italic>, both critical components in flowering transition, redundantly act as repressors of primary root growth as the loss of function of either <jats:italic>SOC1</jats:italic> or <jats:italic>AGL24</jats:italic> partially recovers the primary root growth, meristem cell number, cell production rate, and the length of fully elongated cells of the short-root mutant <jats:italic>xal2-2</jats:italic>. Furthermore, we observed that the simultaneous overexpression of <jats:italic>AGL24</jats:italic> and <jats:italic>SOC1</jats:italic> leads to short-root phenotypes, affecting meristem cell number and fully elongated cell size, whereas <jats:italic>SOC1</jats:italic> overexpression is sufficient to affect columella stem cell differentiation. Additionally, qPCR analyses revealed that these genes exhibit distinct modes of transcriptional regulation in roots compared to what has been previously reported for aerial tissues. We identified 100 differentially expressed genes in <jats:italic>xal2-2</jats:italic> roots by RNA-seq. Moreover, our findings revealed that the expression of certain genes involved in cell differentiation, as well as stress responses, which are either upregulated or downregulated in the <jats:italic>xal2-2</jats:italic> mutant, reverted to WT levels in the absence of <jats:italic>SOC1</jats:italic> or <jats:italic>AGL24</jats:italic>.</jats:p>

<jats:sec><jats:title>Introduction</jats:title><jats:p>The components of nighttime sap flux (En), which include transpiration (Qn) and stem water recharge (Rn), play important roles in water balance and drought adaptation in plant communities in water-limited regions. However, the quantitative and controlling factors of En components are unclear.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>This study used the heat balance method to measure sap flow density in <jats:italic>Vitex negundo</jats:italic> on the Loess Plateau for a normal precipitation year (2021) and a wetter year (2022).</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>The results showed that the mean values were 1.04 and 2.34 g h<jats:sup>-1</jats:sup> cm<jats:sup>-2</jats:sup> for Qn, 0.19 and 0.45 g h<jats:sup>-1</jats:sup> cm<jats:sup>-2</jats:sup> for Rn in 2021 and 2022, respectively, and both variables were greater in the wetter year. The mean contributions of Qn to En were 79.76% and 83.91% in 2021 and 2022, respectively, indicating that the En was mostly used for Qn. Although the vapor pressure deficit (VPD), air temperature (Ta) and soil water content (SWC) were significantly correlated with Qn and Rn on an hourly time scale, they explained a small fraction of the variance in Qn on a daily time scale. The main driving factor was SWC between 40-200 cm on a monthly time scale for the Qn and Rn variations. Rn was little affected by meteorological and SWC factors on a daily scale. During the diurnal course, Qn and Rn initially both declined after sundown because of decreasing VPD and Ta, and Qn was significantly greater than Rn, whereas the two variables increased when VPD was nearly zero and Ta decreased, and Rn was greater than Qn.</jats:p></jats:sec><jats:sec><jats:title>Discussion</jats:title><jats:p>These results provided a new understanding of ecophysiological responses and adaptation of <jats:italic>V. negundo</jats:italic> plantations to increasing drought severity and duration under climate changes.</jats:p></jats:sec>

<jats:p>The GATA gene family belongs to a kind of transcriptional regulatory protein featuring a zinc finger motif, which is essential for plant growth and development. However, the identification of the GATA gene family in tetraploid potato is still not performed. In the present research, a total of 88 <jats:italic>GATA</jats:italic> genes in the tetraploid potato C88.v1 genome were identified by bioinformatics methods. These <jats:italic>StGATA</jats:italic> genes had an uneven distribution on 44 chromosomes, and the corresponding StGATA proteins were divided into four subfamilies (I-IV) based on phylogenetic analysis. The <jats:italic>cis</jats:italic>-elements of <jats:italic>StGATA</jats:italic> genes were identified, including multiple <jats:italic>cis</jats:italic>-elements related to light-responsive and hormone-responsive. The collinearity analysis indicates that segmental duplication is a key driving force for the expansion of GATA gene family in tetraploid potato, and that the GATA gene families of tetraploid potato and <jats:italic>Arabidopsis</jats:italic> share a closer evolutionary relationship than rice. The transcript profiling analysis showed that all 88 <jats:italic>StGATA</jats:italic> genes had tissue-specific expression, indicating that the StGATA gene family members participate in the development of multiple potato tissues. The RNA-seq analysis was also performed on the tuber flesh of two potato varieties with different color, and 18 differentially expressed <jats:italic>GATA</jats:italic> transcription factor genes were screened, of which eight genes were validated through qRT-PCR. In this study, we identified and characterized StGATA transcription factors in tetraploid potato for the first time, and screened differentially expressed genes in potato flesh with different color. It provides a theoretical basis for further understanding the StGATA gene family and its function in anthocyanin biosynthesis.</jats:p>

<jats:p>The eIF6 proteins are distributed extensively in eukaryotes and play diverse and essential roles. The bona fide eIF6 protein in <jats:italic>Arabidopsis</jats:italic>, At-eIF6;1, is essential for embryogenesis. However, the role of eIF6 proteins in rice growth and development remains elusive and requires further investigation. Here, we characterized the functions of OseIF6.1, which is homologous to At-eIF6;1. <jats:italic>OseIF6.1</jats:italic> encodes an eukaryotic translation initiation factor with a conserved eIF6 domain. The knockdown of <jats:italic>OseIF6.1</jats:italic> resulted in a decrease in grain length and pollen sterility, whereas the overexpression of <jats:italic>OseIF6.1</jats:italic> displayed opposite phenotypes. Further studies revealed that <jats:italic>OseIF6.1</jats:italic> regulates grain shape by influencing cell expansion and proliferation. In addition, OseIF6.1 interacts with OsNMD3, which is a nuclear export adaptor for the 60S ribosomal subunit. The knockdown of <jats:italic>OsNMD3</jats:italic> in plants exhibited reduced fertility and seed setting. Therefore, our findings have significantly enriched the current understanding of the role of <jats:italic>OseIF6.1</jats:italic> in rice growth and development.</jats:p>

<jats:p>Rice blast is a destructive fungal disease affecting rice plants at various growth stages, significantly threatening global yield stability. Development of resistant rice cultivars stands as a practical means of disease control. Generally, association mapping with a diversity panel powerfully identifies new alleles controlling trait of interest. On the other hand, utilization of a breeding panel has its advantage that can be directly applied in a breeding program. In this study, we conducted a genome-wide association study (GWAS) for blast resistance using 296 commercial rice cultivars with low population structure but large phenotypic diversity. We attempt to answer the genetic basis behind rice blast resistance among early maturing cultivars by subdividing the population based on its <jats:italic>Heading date 1</jats:italic> (<jats:italic>Hd1</jats:italic>) functionality. Subpopulation-specific GWAS using the mixed linear model (MLM) based on blast nursery screening conducted in three years revealed a total of 26 significant signals, including three nucleotide-binding site leucine-rich repeat (NBS-LRR) genes (<jats:italic>Os06g0286500</jats:italic>, <jats:italic>Os06g0286700</jats:italic>, and <jats:italic>Os06g0287500</jats:italic>) located at <jats:italic>Piz</jats:italic> locus on chromosome 6, and one at the <jats:italic>Pi-ta</jats:italic> locus (<jats:italic>Os12g0281300</jats:italic>) on chromosome 12. Haplotype analysis revealed blast resistance associated with <jats:italic>Piz</jats:italic> locus was exclusively specific to Type 14 <jats:italic>hd1</jats:italic> among <jats:italic>japonica</jats:italic> rice. Our findings provide valuable insights for breeding blast resistant rice and highlight the applicability of our elite cultivar panel to detect superior alleles associated with important agronomic traits.</jats:p>

<jats:p>Pyramiding resistance genes may expand the efficacy and scope of a canola variety against clubroot (<jats:italic>Plasmodiophora brassicae</jats:italic>), a serious threat to canola production in western Canada. However, the mechanism(s) of multigenic resistance, especially the potential interaction among clubroot resistance (CR) genes, are not well understood. In this study, transcriptome was compared over three canola (<jats:italic>Brassica napus</jats:italic> L.) inbred/hybrid lines carrying a single CR gene in chromosome A03 (<jats:italic>CRa<jats:sup>M</jats:sup></jats:italic>, Line 16) or A08 (<jats:italic>Crr1<jats:sup>rutb</jats:sup></jats:italic>, Line 20), and both genes (<jats:italic>CRa<jats:sup>M</jats:sup></jats:italic>+<jats:italic>Crr1<jats:sup>rutb</jats:sup></jats:italic>, Line 15) inoculated with a field population (L-G2) of <jats:italic>P. brassicae</jats:italic> pathotype X, a new variant found in western Canada recently. The line16 was susceptible, while lines 15 and 20 were partially resistant. Functional annotation identified differential expression of genes (DEGs) involved in biosynthetic processes responsive to stress and regulation of cellular process; The Venn diagram showed that the partially resistant lines 15 and 20 shared 1,896 differentially expressed genes relative to the susceptible line 16, and many of these DEGs are involved in defense responses, activation of innate immunity, hormone biosynthesis and programmed cell death. The transcription of genes involved in Pathogen-Associated Molecular Pattern (PAMP)-Triggered and Effector-Triggered Immunity (PTI and ETI) was particularly up-regulated, and the transcription level was higher in line 15 (<jats:italic>CRa<jats:sup>M</jats:sup></jats:italic> + <jats:italic>Crr1<jats:sup>rutb</jats:sup></jats:italic>) than in line 20 (<jats:italic>Crr1<jats:sup>rutb</jats:sup></jats:italic> only) for most of the DEGs. These results indicated that the partial resistance to the pathotype X was likely conferred by the CR gene <jats:italic>Crr1<jats:sup>rutb</jats:sup></jats:italic> for both lines 15 and 20 that functioned via the activation of both PTI and ETI signaling pathways. Additionally, these two CR genes might have synergistic effects against the pathotype X, based on the higher transcription levels of defense-related DEGs expressed by inoculated line 15, highlighting the benefit of gene stacking for improved canola resistance as opposed to a single CR gene alone.</jats:p>