Comparative Transcriptome and Expression Profiling of Resistant and Susceptible Banana Cultivars during Infection by Fusarium oxysporum

Plant biomarkers as early detection tools in stress management in food crops: a review

MAIN CONCLUSION

Plant Biomarkers are objective indicators of a plant's cellular state in response to abiotic and biotic stress factors. They can be explored in crop breeding and engineering to produce stress-tolerant crop species. Global food production safely and sustainably remains a top priority to feed the ever-growing human population, expected to reach 10 billion by 2050. However, abiotic and biotic stress factors negatively impact food production systems, causing between 70 and 100% reduction in crop yield. Understanding the plant stress responses is critical for developing novel crops that can adapt better to various adverse environmental conditions. Using plant biomarkers as measurable indicators of a plant's cellular response to external stimuli could serve as early warning signals to detect stresses before severe damage occurs. Plant biomarkers have received considerable attention in the last decade as pre-stress indicators for various economically important food crops. This review discusses some biomarkers associated with abiotic and biotic stress conditions and highlights their importance in developing stress-resilient crops. In addition, we highlighted some factors influencing the expression of biomarkers in crop plants under stress. The information presented in this review would educate plant researchers, breeders, and agronomists on the significance of plant biomarkers in stress biology research, which is essential for improving plant growth and yield toward sustainable food production.

S. A, Raveendran AP, Chaudhary A, Shanmugam A, Arunachalam A. Comparative transcriptomic and weighted gene co-expression network analysis to identify the core genes in the cultivars of Musa acuminata under both infected and chemical perturbated conditions

Banana is a high nutrient crop, which ranks fourth in terms of gross value production. Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense tropical race 4 (FocTR4), is considered the most destructive disease leading to the complete loss of production of the Cavendish cultivars Berangan, Brazilian and Williams, which are vulnerable to the infection of FocTR4. However, the treatment with benzothiadiazole, a synthetic salicylic analog, is aimed to induce resistance in plants. Thus, the treatments pertaining to the banana plants subjected to the Foc infection within the chosen cultivars were compared with chemically treated samples obtained at different time intervals for a short duration (0-4 days). The integrated omics analyses considering the parameters of WGCNA, functional annotation, and protein-protein interactions revealed that many pathways have been negatively influenced in Cavendish bananas under FocTR4 infections and the number of genes influenced also increased over time in Williams cultivar. Furthermore, elevation in immune response and resistance genes were also observed in the roots of the Cavendish banana.

Comprehensive transcriptome analyses of Fusarium-infected root xylem tissues to decipher genes involved in chickpea wilt resistance

Fusarium wilt is the most destructive soil-borne disease that poses a major threat to chickpea production. To comprehensively understand the interaction between chickpea and Fusarium oxysporum, the xylem-specific transcriptome analysis of wilt-resistant (WR315) and wilt-susceptible (JG62) genotypes at an early timepoint (4DPI) was investigated. Differential expression analysis showed that 1368 and 348 DEGs responded to pathogen infection in resistant and susceptible genotypes, respectively. Both genotypes showed transcriptional reprogramming in response to Foc2, but the responses in WR315 were more severe than in JG62. Results of the KEGG pathway analysis revealed that most of the DEGS in both genotypes with enrichment in metabolic pathways, secondary metabolite biosynthesis, plant hormone signal transduction, and carbon metabolism. Genes associated with defense-related metabolites synthesis such as thaumatin-like protein 1b, cysteine-rich receptor-like protein kinases, MLP-like proteins, polygalacturonase inhibitor 2-like, ethylene-responsive transcription factors, glycine-rich cell wall structural protein-like, beta-galactosidase-like, subtilisin-like protease, thioredoxin-like protein, chitin elicitor receptor kinase-like, proline transporter-like, non-specific lipid transfer protein and sugar transporter were mostly up-regulated in resistant as compared to susceptible genotypes. The results of this study provide disease resistance genes, which would be helpful in understanding the Foc resistance mechanism in chickpea.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03803-9.

Resistant cumin cultivar, GC-4 counters Fusarium oxysporum f. sp. cumini infection through up-regulation of steroid biosynthesis, limonene and pinene degradation and butanoate metabolism pathways

Cumin (Cuminum cyminum L.), an important spice crop belonging to the Apiaceae family is infected by Fusarium oxysporum f. sp. cumini (Foc) to cause wilt disease, one of the most devastating diseases of cumin adversely affects its production. As immune responses of cumin plants against the infection of Foc are not well studied, this research aimed to identify the genes and pathways involved in responses of cumin (cv. GC-2, GC-3, GC-4, and GC-5) to the wilt pathogen. Differential gene expression analysis revealed a total of 2048, 1576, 1987, and 1174 differentially expressed genes (DEGs) in GC-2, GC-3, GC-4, and GC-5, respectively. In the resistant cultivar GC-4 (resistant against Foc), several important transcripts were identified. These included receptors, transcription factors, reactive oxygen species (ROS) generating and scavenging enzymes, non-enzymatic compounds, calcium ion (Ca2+) transporters and receptors, R-proteins, and PR-proteins. The expression of these genes is believed to play crucial roles in conferring resistance against Foc. Gene ontology (GO) analysis of the up-regulated DEGs showed significant enrichment of 19, 91, 227, and 55 biological processes in GC-2, GC-3, GC-4, and GC-5, respectively. Notably, the resistant cultivar GC-4 exhibited enrichment in key GO terms such as 'secondary metabolic process', 'response to reactive oxygen species', 'phenylpropanoid metabolic process', and 'hormone-mediated signaling pathway'. Furthermore, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed the enrichment of 28, 57, 65, and 30 pathways in GC-2, GC-3, GC-4, and GC-5, respectively, focusing on the up-regulated DEGs. The cultivar GC-4 showed enrichment in pathways related to steroid biosynthesis, starch and sucrose metabolism, fatty acid biosynthesis, butanoate metabolism, limonene and pinene degradation, and carotenoid biosynthesis. The activation or up-regulation of various genes and pathways associated with stress resistance demonstrated that the resistant cultivar GC-4 displayed enhanced defense mechanisms against Foc. These findings provide valuable insights into the defense responses of cumin that could contribute to the development of cumin cultivars with improved resistance against Foc.

The Signal Peptidase FoSpc2 Is Required for Normal Growth, Conidiation, Virulence, Stress Response, and Regulation of Light Sensitivity in Fusarium odoratissimum

Signal peptidase (SPase) is responsible for cleavage of N-terminal signal peptides in most secretory precursor proteins and many membrane proteins during maturation. In this study, we identified four components of the SPase complex (FoSec11, FoSpc1, FoSpc2, and FoSpc3) in the banana wilt fungal pathogen Fusarium odoratissimum. We proved that interactions exist among the four SPase subunits by bimolecular fluorescence complementation (BiFC) and affinity purification and mass spectrometry (AP-MS) assays. Among the four SPase genes, FoSPC2 was successfully deleted. FoSPC2 deletion caused defects in vegetative growth, conidiation, and virulence. Loss of FoSPC2 also affected the secretion of some pathogenicity-related extracellular enzymes, suggesting that SPase without FoSpc2 may have a lower efficiency in managing the maturation of the extracellular enzymes in F. odoratissimum. In addition, we found that the ΔFoSPC2 mutant had increased sensitivity to light, and the colonies of the mutant grew faster under all-dark conditions than under all-light conditions. We further observed that deletion of FoSPC2 affected expression of the blue light photoreceptor gene FoWC2, leading to cytoplasmic accumulation of FoWc2 under all-light conditions. Since FoWc2 has signal peptides, FoSpc2 may regulate the expression and subcellular localization of FoWc2 indirectly. Contrary to its response to light, the ΔFoSPC2 mutant displayed a significant decreased sensitivity to osmotic stress, and culturing the mutant under osmotic stress conditions restored both the localization of FoWc2 and light sensitivity of the ΔFoSPC2, suggesting that a cross talk between osmotic stress and light response pathways in F. odoratissimum and FoSpc2 takes part in these processes. IMPORTANCE In this study, we identified four components of SPase in the banana wilt pathogen Fusarium odoratissimum and characterized the SPase FoSpc2. Loss of FoSPC2 affected the secretion of extracellular enzymes, suggesting that SPase without FoSpc2 may have a lower efficiency in managing the maturation of the extracellular enzymes in F. odoratissimum. In addition, this is the first time that we have found a relationship between the SPase and fungal light response. Deletion of FoSPC2 resulted in decreased sensitivity to the osmotic stresses but with increased sensitivity to light. Continuous light inhibited the growth rate of the ΔFoSPC2 mutant and affected the cellular localization of the blue light photoreceptor FoWc2 in this mutant, but culturing the mutant under osmotic stress both restored the localization of FoWc2 and eliminated the light sensitivity of the ΔFoSPC2 mutant, suggesting that loss of FoSPC2 may affect a cross talk between the osmotic stress and light response pathways in F. odoratissimum.

miR164-NAC21/22 module regulates the resistance of Malus hupehensis against Alternaria alternata by controlling jasmonic acid signaling

Apple leaf spot disease caused by Alternaria alternata apple pathotype (A. alternata AP) is one of the most severe fungal diseases affecting apple cultivation. Transcription factors are involved in various disease-resistance responses, and many of them are regulated by miRNAs. Here, we performed RNA-Seq to investigate gene expression changes during the defense response of Malus hupehensis against A. alternata AP. NAC21/22 was induced upon A. alternata AP infection and silenced by miR164 via direct mRNA cleavage. Contrasting expression patterns were noted between mature miR164 and NAC21/22 during infection. Contrary to NAC21/22 silencing, transiently overexpressing NAC21/22 in M. hupehensis alleviated disease symptoms on 'gala' leaves, impeded A. alternata AP growth, and promoted jasmonic acid (JA) signaling-related gene expression. Importantly, transient miR164f overexpression in 'gala' leaves enhanced A. alternata AP sensitivity, due perhaps to NAC21/22 downregulation, whereas miR164 suppression produced an opposite effect. In summary, the miR164-NAC21/22 module plays a pivotal role in apple resistance against A. alternata AP by regulating JA signaling.

Characterization of microRNAs and Target Genes in Musa acuminata subsp. burmannicoides, var. Calcutta 4 during Interaction with Pseudocercospora musae

Endogenous microRNAs (miRNAs) are small non-coding RNAs that perform post-transcriptional regulatory roles across diverse cellular processes, including defence responses to biotic stresses. Pseudocercospora musae, the causal agent of Sigatoka leaf spot disease in banana (Musa spp.), is an important fungal pathogen of the plant. Illumina HiSeq 2500 sequencing of small RNA libraries derived from leaf material in Musa acuminata subsp. burmannicoides, var. Calcutta 4 (resistant) after inoculation with fungal conidiospores and equivalent non-inoculated controls revealed 202 conserved miRNAs from 30 miR-families together with 24 predicted novel miRNAs. Conserved members included those from families miRNA156, miRNA166, miRNA171, miRNA396, miRNA167, miRNA172, miRNA160, miRNA164, miRNA168, miRNA159, miRNA169, miRNA393, miRNA535, miRNA482, miRNA2118, and miRNA397, all known to be involved in plant immune responses. Gene ontology (GO) analysis of gene targets indicated molecular activity terms related to defence responses that included nucleotide binding, oxidoreductase activity, and protein kinase activity. Biological process terms associated with defence included response to hormone and response to oxidative stress. DNA binding and transcription factor activity also indicated the involvement of miRNA target genes in the regulation of gene expression during defence responses. sRNA-seq expression data for miRNAs and RNAseq data for target genes were validated using stem-loop quantitative real-time PCR (qRT-PCR). For the 11 conserved miRNAs selected based on family abundance and known involvement in plant defence responses, the data revealed a frequent negative correlation of expression between miRNAs and target host genes. This examination provides novel information on miRNA-mediated host defence responses, applicable in genetic engineering for the control of Sigatoka leaf spot disease.

Comparative Analysis of Alternative Splicing in Two Contrasting Apple Cultivars Defense against Alternaria alternata Apple Pathotype Infection

Alternaria blotch disease, caused by the Alternaria alternata apple pathotype (A. alternata AP), is one of the most serious fungal diseases in apples. Alternative splicing (AS), one of the pivotal post-transcriptional regulatory mechanisms, plays essential roles in various disease resistance responses. Here, we performed RNA-Seq for two apple cultivars (resistant cultivar 'Jonathan' (J) and susceptible cultivar 'Starking Delicious' (SD)) infected by A. alternata AP to further investigate their AS divergence. In total, 1454, 1780, 1367 and 1698 specifically regulated differential alternative splicing (DAS) events were detected in J36, J72, SD36 and SD72 groups, respectively. Retained intron (RI) was the dominant AS pattern. Conformably, 642, 764, 585 and 742 uniquely regulated differentially spliced genes (DSGs) were found during A. alternata AP infection. Comparative analysis of AS genes in differential splicing and expression levels suggested that only a small proportion of DSGs overlapped with differentially expressed genes (DEGs). Gene ontology (GO) enrichment analysis demonstrated that the DSGs were significantly enriched at multiple levels of gene expression regulation. Briefly, the specific AS was triggered in apple defense against A. alternata AP. Therefore, this study facilitates our understanding on the roles of AS regulation in response to A. alternata AP infection in apples.

Comparative transcriptome profiling reveals the role of phytohormones and phenylpropanoid pathway in early-stage resistance against powdery mildew in watermelon (Citrullus lanatus L.)

Yield and fruit quality loss by powdery mildew (PM) fungus is a major concern in cucurbits, but early-stage resistance mechanisms remain elusive in the majority of cucurbits. Here, we explored the comparative transcriptomic dynamics profiling of resistant line ZXG1755 (R) and susceptible line ZXG1996 (S) 48 h post-inoculation in watermelon seedlings to check precise expression changes induced by Podosphaera. xanthii race '2F'. Phenotypic responses were confirmed by microscopy and endogenous levels of defense and signaling related phytochromes were detected higher in resistant lines. In total, 7642 differently expressed genes (DEGs) were detected, and 57.27% of genes were upregulated in four combinations. DEGs were predominantly abundant in the KEGG pathway linked with phenylpropanoid biosynthesis, plant hormone and transduction, and phenylalanine metabolism, whereas GO terms of defense response, response to fungus, and chitin response were predominant in resistant lines, evidencing significant defense mechanisms and differences in the basal gene expression levels between these contrasting lines. The expression of selected DEGs from major pathways (hormonal, lignin, peroxidase, sugar) were validated via qRT-PCR. Detailed analysis of DEGs evidenced that along with other DEGs, genes including PR1 (Cla97C02G034020) and PRX (Cla97C11G207220/30, Cla97C02G045100 and Cla97C02G049950) should be studied for their potential role. In short, our study portrayed strong evidence indicating the important role of a complex network associated with lignin biosynthesis and phytohormone related downstream mechanisms that are responsible for incompatible interaction between PM and watermelon resistance line.

Subterranean Microbiome Affiliations of Plantain (Musa spp.) Under Diverse Agroecologies of Western and Central Africa

Plantain (Musa spp.) is a staple food crop and an important source of income for millions of smallholder farmers in sub-Saharan Africa (SSA). However, there is a paucity of knowledge on soil microbial diversity in agroecologies where plantains are grown. Microbial diversity that increases plant performance with multi-trophic interactions involving resiliency to environmental constraints is greatly needed. For this purpose, the bacterial and fungal communities of plantain fields in high rainfall forests (HR) and derived savannas (SV) were studied using Illumina MiSeq for 16S rDNA and ITS amplicon deep sequencing. Microbial richness (α- and β-diversity), operational taxonomic units, and Simpson and Shannon-Wiener indexes (observed species (Sobs), Chao, ACE; P < 0.05) suggested that there were significant differences between HR and SV agroecologies among the most abundant bacterial communities, and some specific dynamic response observed from fungal communities. Proteobacteria formed the predominant bacterial phylum (43.7%) succeeded by Firmicutes (24.7%), and Bacteroidetes (17.6%). Ascomycota, Basidiomycota, and Zygomycota were the three most dominant fungal phyla in both agroecologies. The results also revealed an immense array of beneficial microbes in the roots and rhizosphere of plantain, including Acinetobacter, Bacillus, and Pseudomonas spp. COG and KEGG Orthology database depicted significant variations in the functional attributes of microbes found in the rhizosphere to roots. This result indicates that the different agroecologies and host habitats differentially support the dynamic microbial profile and that helps in altering the structure in the rhizosphere zone for the sake of promoting synergistic host-microbe interactions particularly under resource-poor conditions of SSA.

Compositional Shifts in Microbial Diversity under Traditional Banana Cropping Systems of Sub-Saharan Africa

Simple Summary

In soil, the connection between microbial diversity and plant health is vital in terms of achieving the food security. Here, we suggested the study on soil microbial diversity in diverse cropping systems of banana adopted and followed by small holder farmers over the years. We tracked down the bacterial and fungal diversity in mono cropping and intercropping systems using advanced molecular techniques. Our outcomes likewise uncovered that the impact of cropping systems on bacterial and fungal increments in plant roots and rhizosphere soil. Hence, safeguarding of soil microbial diversity is profoundly significant taking into consideration of the contributions for plant buildups and rhizodeposits into the soil.

Abstract

Improvements in the crop productivity, soil health, and sustainable intensification should be premised on the better understanding of interactions between the cropping systems and soil microbial diversity. In this study, we assessed variations in the microbial communities across the traditional banana-based cropping systems of contrasting monocrop vigor (vigorous or V vs. non-vigorous or NV) and the cropping system (monocrop or MC vs. intercropped or IC) using 16S rDNA (V3–V4) and ITS2 amplicon deep sequencing via Illumina platform. Sequencing results of the bacterial and fungal communities showed high variability among MC and V cropping systems. The abundances of Proteobacteria, Firmicutes, and Actinobacteria were significantly higher in NV (non-vigorous) and V (vigorous) cropping systems; and the abundances of Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes in the MC (monocropping) than IC (intercropping). There were high relative abundances of Pseudomonas (6.1–37.43%), Bacillus (4.5–20.4%), Rhizobium (1.4–6.5%), and Devosia (1.5–6.7%) in the cropping systems. The dominant family of fungal class Incertae_sedis was Mortierellales, which accounted for 8.79–41.12% of total taxa. This result indicated that the cropping systems are vital for supporting the dynamic microbial diversity specifically beneficial for bacterial communities that helps in promoting synergistic plant-soil interactions and total productivity under resource poor conditions of smallholder farmers in sub-Saharan Africa (SSA).

Single-Molecule Real-Time and Illumina Sequencing to Analyze Transcriptional Regulation of Flavonoid Synthesis in Blueberry

Blueberries (Vaccinium corymbosum) contain large amounts of flavonoids, which play important roles in the plant's ability to resist stress and can also have beneficial effects on human health when the fruits are eaten. However, the molecular mechanisms that regulate flavonoid synthesis in blueberries are still unclear. In this study, we combined two different transcriptome sequencing platforms, single-molecule real-time (SMRT) and Illumina sequencing, to elucidate the flavonoid synthetic pathways in blueberries. We analyzed transcript quantity, length, and the number of annotated genes. We mined genes associated with flavonoid synthesis (such as anthocyanins, flavonols, and proanthocyanidins) and employed fluorescence quantitative PCR to analyze the expression of these genes and their correlation with flavonoid synthesis. We discovered one R2R3 MYB transcription factor from the sequencing library, VcMYB1, that can positively regulate anthocyanin synthesis in blueberries. VcMYB1 is mainly expressed in colored (mature) fruits. Experiments showed that overexpression and transient expression of VcMYB1 promoted anthocyanin synthesis in Arabidopsis, tobacco (Nicotiana benthamiana) plants and green blueberry fruits. Yeast one-hybrid (Y1H) assay, electrophoretic mobility shift assay, and transient expression experiments showed that VcMYB1 binds to the MYB binding site on the promoter of the structural gene for anthocyanin synthesis, VcMYB1 to positively regulate the transcription of VcDFR, thereby promoting anthocyanin synthesis. We also performed an in-depth investigation of transcriptional regulation of anthocyanin synthesis. This study provides background information and data for studying the synthetic pathways of flavonoids and other secondary metabolites in blueberries.

Metabolomics analysis of grains of wheat infected and noninfected with Tilletia controversa Kühn

Dwarf bunt caused by the pathogen Tilletia controversa Kühn is one of the most serious quarantine diseases of winter wheat. Metabolomics studies provide detailed information about the biochemical changes at the cell and tissue levels of plants. In the present study, a liquid chromatography/mass spectrometry (LC/MS) metabolomics approach was used to investigate the changes in the grain metabolomics of infected and noninfected with T. controversa samples. PCA suggested that T. controversa-infected and noninfected samples were separated during the interaction. LC/MS analysis showed that 62 different metabolites were recorded in the grains, among which a total of 34 metabolites were upregulated and 28 metabolites were downregulated. Prostaglandins (PGs) and 9-hydroxyoctadecadienoic acids (9-HODEs) are fungal toxin-related substances, and their expression significantly increased in T. controversa-infected grains. Additionally, the concentrations of cucurbic acid and octadecatrienoic acid changed significantly after pathogen infection, which play a large role in plant defense. The eight different metabolic pathways activated during T. controversa and wheat plant interactions included phenylalanine metabolism, isoquinoline alkaloid biosynthesis, starch and sucrose metabolism, tyrosine metabolism, sphingolipid metabolism, arginine and proline metabolism, alanine, aspartate, and glutamate metabolism, and tryptophan metabolism. In conclusion, we found differences in the metabolic profiles of wheat grains after T. controversa infection. To our knowledge, this is the first study to evaluate the metabolites in wheat grains after T. controversa infection.