Tropical Plant Biology最新文献

Pokkah boeng disease (PBD), a fungal disease of sugarcane, is caused by multiple species of Fusarium. To identify the pathogens causing PBD in Yunnan Province, China, we collected 87 leaf samples with typical PBD symptoms from the sugarcane-growing areas of Puer, Honghe, and Lincang, from which eight strains (FS1–FS8) were isolated and purified. The identities of the eight isolates were determined based on a combination of morphological observations and molecular analyses, using which we identified five Fusarium species as the causal agents of PBD in Yunnan, namely, F. incarnatum, F. andiyazi, F. sacchari, F. proliferatum, and F. verticillioides. Among these, F. incarnatum is a newly recorded species in Yunnan. Pathogenicity tests revealed that all five Fusarium species can infect sugarcane and cause PBD symptoms, with the severity of pathogenicity, ranked from strong to weak, being ordered as follows: F. proliferatum > F. andiyazi > F. incarnatum > F. verticillioides > F. sacchari. In this study, we identified the species and established the pathogenicity of the causal agents of PBD in Yunnan Province. Our findings will provide a scientific basis for the prevention and control of this disease.

RNA silencing plays a direct functional role in gene expression and defense against pathogens during various developmental stages in plants. This silencing process is regulated by the RNA interference (RNAi) pathway, which relies on double-stranded RNA (dsRNA) generated from small RNAs (sRNAs). Three important protein families regulate the functions of sRNAs: Dicer-like (DCLs), Argonautes (AGOs), and RNA-dependent RNA polymerases (RDRs). These major components have not been identified and characterized in papaya. In this study, we identified the RNAi gene families and comprehensively characterized their regulatory functions through a bioinformatics approach in papaya. The papaya genome contains 3 CaDCL, 8 CaAGO and 4 CaRDR genes, which comprise diverse functional regulatory elements compared to their corresponding Arabidopsis AtDCL, AtAGO, and AtRDR genes, indicating their pivotal roles in the RNA silencing mechanism. Phylogenetic tree and multiple sequence analyses reveal that each CaDCL, CaAGO and CaRDR protein clusters and aligns with the corresponding RNAi genes in Arabidopsis. The results from conserved domain, motif, and gene structure analyses indicate a higher level of similarity within the same gene family with some exceptions. The chromosomal and sub-cellular localization of the predicted proteins shows a well distributed pattern. Furthermore, the gene ontology (GO) analysis demonstrates that the candidate RNAi genes are associated with the RNAi silencing mechanism and related pathways. The network and sub-network analyses reveal interactions between various transcription factors (TFs), such as ERF, Dof, MIKC_MADS, NAC, and BBR-BPC families, and the identified RNAi gene families. Additionally, an analysis of cis-acting regulatory elements uncovers light-responsive (LR), stress-responsive (SR), hormone-responsive (HR), and other activities (OT) functions in the candidate CaDCL, CaAGO, and CaRDR genes. Tissue-specific expression patterns of papaya RNAi genes showed differential expression in various tissues. RNA-seq analysis revealed five candidates CpDCL1, CpAGO1, CpAGO5, CpAGO10a, and CpRDR6 that demonstrated potential in response to anthracnose-resistant in papaya. Over all, our findings provide useful information for the genetic improvement of papaya cultivars in breeding programs to overcome stress responses and offer a better understanding of these gene families in papaya.

Rice responds to individual N and P deficiencies through root traits’ modifications and characteristic starvation responses. The genomic regions associated with combined deficiencies of N and P are less reported, though the combinatorial regulation of N and P deficiencies is vital for seedling development. In this study, genome-wide association analysis (GWAS) using ~ 22 k SNPs was performed in one hundred and thirty rice genotypes for nine different traits at the seedling stage (21 days after sowing), and twenty-four statistically significant marker trait associations contributing to the phenotypic variation of 10–79% were identified. Further, except for 10% increase in root length, traits like shoot length, number of leaves, shoot area, shoot dry weight, and root dry weight decreased by 45%, 15%, 60%, 24%, and 45%, respectively, under N and P-deficient soils. Besides, candidate genes for root architecture remodeling (Dro1 and Sor1), P and N uptake (PTF1, PEPC), and amino acid transport and homeostasis (AAP7, BCAT2) were found within the genomic regions regulating the combined tolerance to low P and low N. Furthermore, three superior genotypes, namely ENT-62 (Root area, shoot area, and shoot dry weight), ENT-303 (shoot dry weight and root dry weight), and ENT-32 (no. of leaves and shoot area), were identified for regulating more than one trait under low P-low N conditions. Therefore, this study characterized the seedling stage trait response in rice genotypes and identified genomic regions regulating seedling traits for combined N and P deficient soils. The identified QTLs of these genes could be utilized in breeding programs for the combined improvement of nitrogen and phosphorus use efficiency under deficit soils.

This study delves into the comprehensive analysis of AQP genes in Eucalyptus grandis, providing insights into their genomic abundance, diversification, expression patterns across tissues, and responses to drought stress. We identified 48 AQP genes in the Eucalyptus grandis genome, categorized into four subfamilies: AQP-NIP, AQP-SIP, AQP-PIP, and AQP-TIP. This abundance of AQP genes is a reflection of gene duplications, both tandem and whole-genome, which have shaped their expansion. The chromosomal distribution of these genes reveals their widespread presence across the genome, with some subfamilies exhibiting more tandem duplications, suggesting distinct roles and evolutionary pressures. Sequence analysis uncovered characteristic motifs specific to different AQP subfamilies, demonstrating the diversification of protein and targeting. The expression profiles of AQP genes in various tissues in both Arabidopsis thaliana and Eucalyptus grandis showcased variations, with root tissues showing higher expression levels. Notably, AQP-PIP genes consistently exhibited robust expression across tissues, highlighting their importance in maintaining water regulation within plants. Furthermore, the study investigated the response of AQP genes to drought stress and rehydration, revealing differential expression patterns. EgAQP-NIP and EgAQP-TIP genes were up-regulated during drought stress, emphasizing their role in osmotic equilibrium and water transport. Conversely, EgAQP-PIP genes showed down-regulation during drought stress but were up-regulated upon rehydration, indicating their involvement in water movement across cell membranes. Overall, this research contributes to our understanding of AQP genes in Eucalyptus grandis, shedding light on their genomic evolution, expression patterns, and responses to environmental challenges, particularly drought stress. This information can be valuable for future studies aimed at enhancing the drought resilience of woody perennial plants like Eucalyptus grandis.

The WRKY gene family is an important class of transcription factors in higher plants that play key roles in secondary metabolism, phytohormone signaling, plant defense responses, and abiotic stress responses. The WRKY gene family has not been systematically studied in Passiflora edulis, a tropical fruit with edible and medicinal values. In this study, we performed a genome-wide analysis of passion fruit and identified 58 candidate PeWRKY genes distributed unevenly on nine chromosomes of passion fruit. Phylogenetic and gene structure analyses showed that members of the PeWRKY gene family could be categorized into three groups: class I (9), class II (40), and class III (9). Promoter and target gene prediction analyses indicated that the PeWRKY gene may be involved in various biological processes, including growth and development, metabolism, hormones, and stress responses, by regulating multiple target genes. The Ka/Ks ratios of PeWRKY indicated that PeWRKY may have undergone strong purification selection in the passion fruit genome. Tissue expression analysis showed that the PeWRKY gene was expressed in different tissues of Passiflora edulis, where the number and expression of the PeWRKY gene were more significant in the roots. Quantitative real-time polymerase chain reaction (qRT-PCR) showed that the relative expression of all 10 candidate PeWRKY genes was significantly up-regulated in leaf tissues after 48 h of drought stress compared with the control, and only PeWRKY55 and PeWRKY30 genes were down-regulated. In addition, at the time of biotic stress treatment up to 24 h, most PeWRKY genes were up-regulated after treatment, except the PeWRKY40 gene, which showed down-regulation. Three genes, PeWRKY02, PeWRKY30 and PeWRKY58, showed significant up-regulation of their expression after treatment up to 48 h. This study provides a valuable reference for the functional characterization of WRKY genes in passion fruit and other plants.

Banana bract mosaic virus (BBrMV), transmitted by aphids, is a major threat to banana cultivation, causing substantial economic losses. This study focuses on the development of BBrMV-resistant lines of banana cv. ‘Grand Naine’ by silencing viral coat protein (CP) gene using RNA interference (RNAi) strategy. To achieve this, an intron hairpin RNA (ihpRNA) construct containing a 326 bp fragment of the CP gene was designed using the pSTARLING vector. Identification of a Dicer substrate within the CP gene facilitated the prediction of small interfering RNAs (siRNAs) through Custom Dicer-Substrate siRNA analysis. The absence of viral silencing suppressors was validated using the VsupPred tool. Cloning of the sense and antisense fragments of the CP gene into the pSTARLING vector, flanking the cre intron, was confirmed through PCR analysis. Subsequently, the NotI fragment comprising the ubiquitin promoter, ubiquitin intron, sense fragment inserts, cre intron, antisense strand insert, and tumour morphology locus (tmL) terminator was transferred to the Agrobacterium tumefaciens binary vector pART27. Embryogenic calli were transformed with the ihpRNA-CP cassette, and regenerated plantlets were screened for complete cassette integration using PCR. Northern hybridization confirmed the production of siRNAs against coat protein mRNA. Upon exposure to virulent aphids carrying BBrMV, the transformed lines exhibited no disease symptoms. Additionally, reverse transcription quantitative PCR (RT-qPCR) demonstrated the absence of BBrMV, with transformed lines resembling healthy, non-inoculated controls both morphologically and in terms of coat protein gene expression. This RNAi-based approach showcases the successful creation of BBrMV-resistant banana lines, presenting a promising strategy for combating the virus's detrimental effects on banana cultivation.

Dynamin and dynamin-related proteins (DRPs) are large GTPases that are vital for cytokinesis, endocytosis and multiple biological processes. However, knowledge of the DRP gene family in soybean (Glycine max L.), an important leguminous crop plant, is still limited. In this study, 31 GmDRPs were identified from soybean genome, and were classified into five groups based on phylogenetic analysis. We observed that each group displayed specific conserved domain distribution and exon–intron structures. Collinearity analysis indicated that gene duplication events contribute largely to the expansion of GmDRP family. According to functional annotation, soybean dynamins were found implicated in cell division, endocytosis, and mitochondrion/peroxisome fission in GTP-dependent manner. Promoter analysis implied the potential roles of GmDRPs in mediating developmental processes, plant hormone signaling, and stress responses. Based on RNA-seq data, some of the GmDRPs were found ubiquitously expressed in various tissues/organs, some were barely expressed, while some showed obvious tissue/organ-preference. The expression analysis also revealed the involvement of GmDRPs in cold and/or drought stress response. In sum, we performed a systematic analysis of soybean dynamin family and our results provide a foundation for further researches on their functional roles.

Ascorbate peroxidases (APXs) are essential for plants as they act as hydrogen peroxide-scavenging enzymes, providing protection against oxidative damage. Using bioinformatic methods, five APX genes were discovered in the genome of Citrus sinensis in this study. APX genes of C. sinensis (CsAPXs) encode polypeptides between 250 and 436 residues in length, with molecular weights that range from 27.56 to 47.34 kDa. Additionally, the isoelectric point of CsAPXs varies from 5.64 to 8.63. The predicted locations of CsAPXs are peroxisome, chloroplast, and mitochondrion, with an uneven distribution across four chromosomes and eight orthologous gene pairs with Arabidopsis thaliana. A phylogenetic analysis revealed that the CsAPXs were divided into three clades. The CsAPXs all contained a conserved APX domain and six common motifs. Upon promoter analysis, it was found that CsAPXs could respond to abscisic acid, auxin, ethylene, gibberellin, methyl jasmonate, salicylic acid, and wounding stress treatments. In addition, the analysis of expression patterns revealed that the presence of Candidatus Liberibacter asiaticus (CLas) has a dynamic impact on the expression of CsAPXs, with CsAPX2 showing significant inhibition in response to CLas infection. These findings will provide novel insights for the forthcoming functional investigations of CsAPXs within the process of citrus-CLas interactions.

Plant endochitinases promote the cleavage of chitin, a polymer naturally found in the cell walls of fungi and insects. Although such enzymes are widely employed in plant genetic engineering to increase tolerance to pathogenic fungi, endochitinases from wild germplasm are poorly exploited for biotechnological purposes. Wild peanut species (Arachis spp.) have evolved under a range of environmental conditions and display distinct defensive adaptations, harboring high levels of genetic diversity and constituting an attractive source of resistance genes against pathogens. Arachis stenosperma shows broad resistance against various biotic stresses such as nematodes, fungi, and viruses. Previous transcriptome and proteomic studies on A. stenosperma challenged with fungi and nematodes identified differentially expressed genes (DEGs) involved in plant defense responses, including an upregulated endochitinase (AsECHI1). Here, we characterized endochitinases from 12 different legumes, including wild Arachis species, and evaluated the effects of overexpression of AsECHI1 for control of Sclerotinia sclerotiorum in tobacco, singly and in association with an expansin-like B defense-priming gene (AdEXLB8). Both singly and pyramided transgenic tobacco lines overexpressing AsECHI1 exhibited a delay in disease progression, and up to a 46% reduction in fungal lesions. Further analysis of transgenic plants showed that the overexpression of AsECHI1 led to an increased expression of defense-related genes in the jasmonic acid, auxin, and ethylene biosynthesis pathways, as well as a substantial accumulation of H₂O₂. These results suggest that the AsECHI1 gene isolated from wild Arachis has the potential to enhance resistance against this highly damaging necrotrophic fungal pathogen, reducing environmental damage related to the use of fungicides and increasing crop sustainability.