Wheat Thioredoxin (TaTrxh1) Associates With RD19-Like Cysteine Protease TaCP1 to Defend Against Stripe Rust Fungus Through Modulation of Programmed Cell Death

Genetic dissection of leaf rust resistance in a diversity panel of tetraploid wheat (Triticum turgidum)

BACKGROUND

Leaf rust, caused by Puccinia triticina Eriks (Pt) is a major threat to wheat cultivation worldwide. The rapid evolution of this pathogen has led to the emergence of new virulent strains that can overcome the resistance of commonly cultivated wheat varieties. To address this threat, continuous monitoring of leaf rust pathotypes is conducted in wheat-growing regions across the world. This approach helps prioritize the development and deployment of resistant cultivars, as well as the implementation of other effective control measures against the prevailing races. The key wheat leaf rust pathotypes in India include 77-5 (121R63-1), 77-6 (121R55-1), 77-9 (121R60-1), 12-5 (29R45), and 104 (17R23). Among these pathotypes, 77-5 (121R63-1) and 77-9 (121R60-1) are the most prevalent since 2016. As virulent pathotypes continue to evolve and adapt, there is an urgent need to continually explore the vast germplasm repositories of wheat and its related species to identify novel genetic resources and genes that confer resistance to these evolving leaf rust pathotypes. Therefore, the present study aims to identify genes and genomic regions responsible for leaf rust resistance against prevalent pathotypes in India, focusing on a subset of the Global Durum Wheat Panel, which includes genotypes from various tetraploid wheat species.

RESULTS

This study revealed wide variation in seedling-stage resistance among 189 tetraploid wheat accessions against five prevalent leaf rust pathotypes in India namely, 77-5 (121R63-1), 77-6 (121R55-1), 77-9 (121R60-1), 12-5 (29R45) and 104 (17R23). Approximately 45% of the population exhibited immune/highly resistant to moderately resistant responses to pathotypes 77-5, 77-6 and 104, while around 23-27% showed similar levels of resistance to pathotypes 77-9 and 12-5. A genome-wide association study using six multi-locus models identified 88 significantly associated quantitative trait nucleotides (QTNs) across the five leaf rust pathotypes. Among these, 22 QTNs were considered reliable, including four for pathotype 77-5, six for 12-5, three for 77-9, seven for 104, and two for 77-6. Among the 22 reliable QTNs, 10 coincided with the rust resistance regions reported in previous studies, whereas 12 appeared to be novel. Further investigations of the regions flanking all 88 QTNs revealed 300 genes, including 62 associated with disease resistance or defense responses. In silico expression analysis of these defense-related genes revealed two nucleotide-binding site-leucine-rich repeat genes: one on chromosome 6B (TRITD6Bv1G224600) near QTN RAC875_c35430_373, and another on chromosome 6A (TRITD6Av1G225060) in the vicinity of QTN Excalibur_c77841_224 with significantly higher levels of expression in the leaf-resistant genotype during the early hours of Pt infection. Therefore, these two genes could be potential candidates for resistance to leaf rust in tetraploid wheat germplasm.

CONCLUSIONS

Our study provides a comprehensive understanding of the genetic basis underlying leaf rust resistance in a diverse tetraploid wheat germplasm panel. It has also revealed novel candidate genomic regions for leaf rust resistance. These genomic regions represent important targets for inclusion in marker-assisted breeding initiatives, aimed at fostering durable resistance against leaf rust disease.

Genome-wide identification and characterization of the thioredoxin (TRX) gene family in tomato (Solanum lycopersicum) and a functional analysis of SlTRX2 under salt stress

Thioredoxin is a multifunctional acidic protein widely presented in organisms that regulates intracellular redox processes, participating in a series of biochemical reactions in cells to affect the growth and development of plants. Although the thioredoxin (TRX) gene family has been widespread recognized across various plant species, and the tomato genome has been sequenced for years now, of tomato (Solanum lycopersicum) has remained largely uncharted in terms of identifying and unraveling the functional intricacies of is TRX genes. In this study, 53 SlTRX genes were identified, unevenly distributed across 11 of the 12 tomato chromosomes. These 53 SlTRX genes were categorized into 4 distinct subfamilies based on their evolutionary kinship and phylogenetic development. Expression profiling reveals that most of SlTRX genes exhibited distinct expression patterns across various tissues and developmental stages. In addition, the gene structure, conserved protein motifs and cis-elements of 53 SlTRX genes were analyzed simultaneously. In our rigorous in silico expression analysis, 8 SlTRX genes were meticulously selected for subsequent experiments. Subcellular localization indicated that these 8 SlTRX genes were localized in chloroplasts. Furthermore, these 8 SlTRX genes were responsive to abiotic stress (salt, drought and cold stress) under the qRT-PCR analysis, and their different expression patterns under diverse types of treatments indicated their possible roles in stress tolerance in tomato. Based on these results, SlTRX2, whose expression level continued to increase under salt stress, was selected for silencing to further investigate its function, and furthermore, silencing SlTRX2 inhibited plant growth and led to a significant reduction in photosynthesis under salt stress. Yeast two-hybrid and luciferase complementation imaging assays demonstrated that SlTRX2 may regulate tomato salt resistance by affecting related photosynthetic genes. Thus, our study establishes a valuable resource for further analysis on biological functions of SlTRX genes and will provide important insights in the mechanism of action under stress.

TRX h2-PP2AC2 module serves as a convergence node for aluminum stress and leaf senescence signals, regulating cell death via ABA-mediated ROS pathway

ROS/redox signaling plays an important role in the regulation of signal transduction and acclimation pathways activated by multiple abiotic stresses and leaf senescence. However, the regulatory events that produce ROS under different stimuli are far from clear. Here, we report the elucidation of the molecular mechanism of an h type thioredoxin, AhTRX h2, positively regulates Al sensitivity and leaf senescence by promoting ROS. AhTRX h2 transcript levels increased greatly during both natural senescence and Al stress condition in peanut. Ectopic expression of AhTRX h2 in Arabidopsis conferred Al sensitivity as well as premature leaf senescence, manifested by multiple indices, including inhibiting root elongation, severe cell death, and accelerated expression of MC1 and CEX17. AhTRX h2 exhibited similar functions to AtTRX h2, as AhTRX h2 was able to restore the phenotypes of the AtTRX h2 defective mutant (trxh2-4) which showed Al tolerant and late senescence phenotypes. The knock down of AhTRX h2 markedly suppressed Al- and senescence-induced cell death in peanut. AhTRX h2 could recruit catalytic subunit of protein phosphatase 2A (PP2AC2) to form a stable complex. The interaction between AhTRX h2 and AtPP2AC2, as well as AhPP2AC2 and AtTRX h2 was also proved. Overexpression of AhPP2AC2 significantly enhanced Al sensitivity and leaf senescence in Arabidopsis. Protein stability assay revealed that AhTRX h2 was more stable during aging or aluminum stress. Moreover, PP2AC2 could greatly enhance the stability of AhTRX h2 in vivo. Consistent with these observations, overexpression of AhPP2AC2 effectively enhanced AhTRX h2-induced Al sensitivity and precocious leaf senescence. AhTRX h2 and AhPP2AC2 required ABA and ROS in response to cell death under Al stress and senescence, and it was evidence to suggest that ABA acted upstream of ROS in this process. Together, AhTRX h2 and AhPP2AC2 constitute a stable complex that promotes the accumulation of ABA and ROS, effectively regulate cell death. These findings suggest that TRX h2-PP2AC2-mediated pathway may be a widespread mechanism in regulating Al stress and leaf senescence.

The Wheat Annexin TaAnn12 Plays Positive Roles in Plant Disease Resistance by Regulating the Accumulation of Reactive Oxygen Species and Callose

(1) Annexins are proteins that bind phospholipids and calcium ions in cell membranes and mediate signal transduction between Ca2+ and cell membranes. They play key roles in plant immunity. (2) In this study, virus mediated gene silencing and the heterologous overexpression of TaAnn12 in Arabidopsis thaliana Col-0 trials were used to determine whether the wheat annexin TaAnn12 plays a positive role in plant disease resistance. (3) During the incompatible interaction between wheat cv. Suwon 11 and the Puccinia striiformis f. sp. tritici (Pst) race CYR23, the expression of TaAnn12 was significantly upregulated at 24 h post inoculation (hpi). Silencing TaAnn12 in wheat enhanced the susceptibility to Pst. The salicylic acid hormone contents in the TaAnn12-silenced plants were significantly reduced. The overexpression of TaAnn12 in A. thaliana significantly increased resistance to Pseudomonas syringae pv. tomato DC3000, and the symptoms of the wild-type plants were more serious than those of the transgenic plants; the amounts of bacteria were significantly lower than those in the control group, the accumulation of Reactive Oxygen Species (ROS)and callose deposition increased, and the expression of resistance-related genes (AtPR1, AtPR2, and AtPR5) significantly increased. (4) Our results suggest that wheat TaAnn12 resisted the invasion of pathogens by inducing the production and accumulation of ROS and callose.

Characterization of thioredoxin gene TaTrxh9 associated with heading-time regulation in wheat

Thioredoxins (Trxs) are thiol-disulfide oxidoreductase proteins that play important roles in a spectrum of processes linking redox regulation and signaling in plants. However, little is known about Trxs and their biological functions in wheat, one of the most important food crops worldwide. This study reports the identification and functional characterization of an h-type Trx gene, TaTrxh9, in wheat. Three homoeologs of TaTrxh9 were identified and the sequences in the coding region were highly consistent among the homoeologs. Protein characterization showed that a conserved Trx_family domain, as well as a typical active site with a dithiol signature (WCGPC), was included in TaTrxh9. Structural modeling demonstrated that TaTrxh9 could fold into a canonical thioredoxin structure consisting of five-stranded antiparallel beta sheets sandwiched between four alpha helices. The insulin disulfide reduction assay demonstrated that TaTrxh9 was catalytically active in vitro. TaTrxh9 overexpression in the Arabidopsis mutant trxh9 complemented the abnormal growth phenotypes of the mutant, suggesting is functionality in vivo. The transcription level of TaTrxh9 was higher in leaf tissues and it was differentially expressed during the development of wheat plants. Interestingly, barley stripe mosaic virus-mediated suppression of TaTrxh9 shortened the seedling-heading period of wheat. Furthermore, CRISPR-Cas9 mediated gene knockout confirmed that the TaTrxh9 mutation resulted in early heading of wheat. To our knowledge, this study is the first to report that Trxh is associated with heading-time regulation, which lays a foundation for further exploring the biological function of TaTrxh9 and provides new ideas for molecular breeding focusing on early heading in wheat.

The transcription factor VaNAC72-regulated expression of the VaCP17 gene from Chinese wild Vitis amurensis enhances cold tolerance in transgenic grape (V. vinifera)

Papain-like cysteine proteases (PLCP) play diverse roles in plant biology. In our previous studies, a VaCP17 gene from the cold-tolerant Vitis amurensis accession 'Shuangyou' was isolated and its role in cold tolerance was preliminarily verified in Arabidopsis. Here, we confirmed the function of VaCP17 in cold tolerance by stably overexpressing VaCP17 in the cold-sensitive Vitis vinifera cultivar 'Thompson Seedless' and transiently silencing VaCP17 in 'Shuangyou' leaves. The results showed that overexpression of VaCP17 improved the cold tolerance in 'Thompson Seedless' as manifested by reduced electrolyte leakage and malondialdehyde accumulation, chlorophyll homeostasis, increased antioxidant enzymes (superoxide dismutase, peroxidase, and catalase) activitiy, and rapid up-regulation of stress-related genes (VvKIN2, VvRD29B, and VvNCED1) compared with wild-type line. Conversely, RNA interfere-mediated knockdown of VaCP17 in 'Shuangyou' leaves resulted in opposite physiological and biochemical responses and exacerbated leaves wilting compared with control. Subsequently, by yeast one-hybrid, dual-luciferase assays, and transient overexpression of VaNAC72 in 'Shuangyou' leaves, a VaCP17-interacting protein VaNAC72 was confirmed to promote the expression of VaCP17 under cold stress, which depends on abscisic acid, methyl jasmonate, and salicylic acid signaling. By yeast two-hybrids, bimolecular fluorescence complementation and luciferase complementation assays, it was found that VaNAC72 could form homodimers or heterodimers with VaCBF2. Furthermore, co-expression analysis confirmed that VaNAC72 works synergistically with VaCBF2 or VaCP17 to up-regulate the expression of VaCP17. In conclusion, the study revealed that the VaNAC72-VaCP17 module positively regulated cold tolerance in grapevine, and this knowledge is useful for further revealing the cold-tolerance mechanism of V. amurensis and grape molecular breeding.

Transcriptome analysis reveals differential transcription in tomato (Solanum lycopersicum) following inoculation with Ralstonia solanacearum

Tomato (Solanum lycopersicum L.) is a major Solanaceae crop worldwide and is vulnerable to bacterial wilt (BW) caused by Ralstonia solanacearum during the production process. BW has become a growing concern that could enormously deplete the tomato yield from 50 to 100% and decrease the quality. Research on the molecular mechanism of tomato regulating BW resistance is still limited. In this study, two tomato inbred lines (Hm 2-2, resistant to BW; and BY 1-2, susceptible to BW) were used to explore the molecular mechanism of tomato in response to R. solanacearum infection by RNA-sequencing (RNA-seq) technology. We identified 1923 differentially expressed genes (DEGs) between Hm 2-2 and BY 1-2 after R. solanacearum inoculation. Among these DEGs, 828 were up-regulated while 1095 were down-regulated in R-3dpi (Hm 2-2 at 3 days post-inoculation with R. solanacearum) vs. R-mock (mock-inoculated Hm 2-2); 1087 and 2187 were up- and down-regulated, respectively, in S-3dpi (BY 1-2 at 3 days post-inoculation with R. solanacearum) vs. S-mock (mock-inoculated BY 1-2). Moreover, Gene Ontology (GO) enrichment analysis revealed that the largest amount of DEGs were annotated with the Biological Process terms, followed by Cellular Component and Molecular Function terms. A total of 114, 124, 85, and 89 regulated (or altered) pathways were identified in R-3dpi vs. R-mock, S-3dpi vs. S-mock, R-mock vs. S-mock, and R-3dpi vs. S-3dpi comparisons, respectively, by Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis. These clarified the molecular function and resistance pathways of DEGs. Furthermore, quantitative RT-PCR (qRT-PCR) analysis confirmed the expression patterns of eight randomly selected DEGs, which suggested that the RNA-seq results were reliable. Subsequently, in order to further verify the reliability of the transcriptome data and the accuracy of qRT-PCR results, WRKY75, one of the eight DEGs was silenced by virus-induced gene silencing (VIGS) and the defense response of plants to R. solanacearum infection was analyzed. In conclusion, the findings of this study provide profound insight into the potential mechanism of tomato in response to R. solanacearum infection, which lays an important foundation for future studies on BW.

Genome-wide identification, characterization, evolution, and expression pattern analyses of the typical thioredoxin gene family in wheat (Triticum aestivum L.)

Typical thioredoxin (TRX) plays an important role in maintaining redox balance in plants. However, the typical TRX genes in wheat still need to be comprehensively and deeply studied. In this research, a total of 48 typical TaTRX genes belonging to eight subtypes were identified via a genome-wide search in wheat, and the gene structures, protein conserved motifs, and protein 3D structures of the same subtype were very similar. Evolutionary analysis showed that there are two pairs of tandem duplication genes and 14 clusters of segmental duplication genes in typical TaTRX family members; TaTRX15, TaTRX36, and TaTRX42 had positive selection compared with the orthologs of their ancestral species; rice and maize have 11 and 13 orthologous typical TRXs with wheat, respectively. Gene Ontology (GO) analysis indicated that typical TaTRXs were involved in maintaining redox homeostasis in wheat cells. Estimation of ROS content, determination of antioxidant enzyme activity, and gene expression analysis in a line overexpressing one typical TaTRX confirmed that TRX plays an important role in maintaining redox balance in wheat. A predictive analysis of cis-acting elements in the promoter region showed that typical TaTRXs were extensively involved in various hormone metabolism and response processes to stress. The results predicted using public databases or verified using RT-qPCR show that typical TaTRXs were able to respond to biotic and abiotic stresses, and their expression in wheat was spatiotemporal. A total of 16 wheat proteins belonging to four different families interacting with typical TaTRXs were predicted. The above comprehensive analysis of typical TaTRX genes can enrich our understanding of this gene family in wheat and provide valuable insights for further gene function research.

Genome-wide association study for grain yield and component traits in bread wheat (Triticum aestivum L.)

Genomic regions governing days to heading (DH), grain filling duration (GFD), grain number per spike (GNPS), grain weight per spike (GWPS), plant height (PH), and grain yield (GY) were investigated in a set of 280 diverse bread wheat genotypes. The genome-wide association studies (GWAS) panel was genotyped using a 35K Axiom Array and phenotyped in five environments. The GWAS analysis showed a total of 27 Bonferroni-corrected marker-trait associations (MTAs) on 15 chromosomes representing all three wheat subgenomes. The GFD showed the highest MTAs (8), followed by GWPS (7), GY (4), GNPS (3), PH (3), and DH (2). Furthermore, 20 MTAs were identified with more than 10% phenotypic variation. A total of five stable MTAs (AX-95024590, AX-94425015, AX-95210025 AX-94539354, and AX-94978133) were identified in more than one environment and associated with the expression of DH, GFD, GNPS, and GY. Similarly, two novel pleiotropic genomic regions with associated MTAs i.e. AX-94978133 (4D) and AX-94539354 (6A) harboring co-localized QTLs governing two or more traits were also identified. In silico analysis revealed that the SNPs were located on important putative candidate genes such as F-box-like domain superfamily, Lateral organ boundaries, LOB, Thioredoxin-like superfamily Glutathione S-transferase, RNA-binding domain superfamily, UDP-glycosyltransferase family, Serine/threonine-protein kinase, Expansin, Patatin, Exocyst complex component Exo70, DUF1618 domain, Protein kinase domain involved in the regulation of grain size, grain number, growth and development, grain filling duration, and abiotic stress tolerance. The identified novel MTAs will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection (MAS).

Genome-Wide Identification and Expression Analysis of the Thioredoxin (Trx) Gene Family Reveals Its Role in Leaf Rust Resistance in Wheat (Triticum aestivum L.)

Bread wheat (Triticum aestivum L.; Ta) is the staple cereal crop for the majority of the world’s population. Leaf rust disease caused by the obligate fungal pathogen, Puccinia triticina L., is a biotrophic pathogen causing significant economic yield damage. The alteration in the redox homeostasis of the cell caused by various kinds of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in response to pathogenic infections is controlled by redox regulators. Thioredoxin (Trx) is one of the redox regulators with low molecular weight and is thermostable. Through a genome-wide approach, forty-two (42) wheat Trx genes (TaTrx) were identified across the wheat chromosome groups A, B, and D genomes containing 12, 16, and 14 Trx genes, respectively. Based on in silico expression analysis, 15 TaTrx genes were selected and utilized for further experimentation. These 15 genes were clustered into six groups by phylogenetic analysis. MicroRNA (miRNA) target analysis revealed eight different miRNA-targeted TaTrx genes. Protein–protein interaction (PPI) analysis showed TaTrx proteins interact with thioredoxin reductase, peroxiredoxin, and uncharacterized proteins. Expression profiles resulting from quantitative real-time PCR (qRT-PCR) revealed four TaTrx genes (TaTrx11-5A, TaTrx13-5B, TaTrx14-5D, and TaTrx15-3B) were significantly induced in response to leaf rust infection. Localization of ROS and its content estimation and an assay of antioxidant enzymes and expression analysis suggested that Trx have been involved in ROS homeostasis at span 24HAI-72HAI during the leaf rust resistance.

The small GTP-binding protein TaRop10 interacts with TaTrxh9 and functions as a negative regulator of wheat resistance against the stripe rust

Small GTP-binding proteins, also known as ROPs (Rho of Plants), are a subfamily of the Ras superfamily of signaling G-proteins and are required for numerous signaling processes, ranging from growth and development to biotic and abiotic signaling. In this study, we cloned and characterized wheat TaRop10, a homolog of Arabidopsis ROP10 and member of the class II ROP, and uncovered a role for TaRop10 in wheat response to Puccinia striiformis f. sp. tritici (Pst). TaRop10 was downregulated by actin depolymerization and was observed to be differentially induced by abiotic stress and the perception of plant hormones. A combination of yeast two-hybrid and bimolecular fluorescence complementation assays revealed that TaRop10 interacted with a h-type thioredoxin (TaTrxh9). Knocking-down of TaRop10 and TaTrxh9 was performed using the BSMV-VIGS (barley stripe mosaic virus-based virus-induced gene silencing) technique and revealed that TaRop10 and TaTrxh9 play a role in the negative regulation of defense signaling in response to Pst infection. In total, the data presented herein further illuminate our understanding of how intact plant cells accommodate fungal infection structures, and furthermore, support the function of TaRop10 and TaTrxh9 in negative modulation of defense signaling in response to stripe rust infection.