A Phi-Class Glutathione S-Transferase Gene for Verticillium Wilt Resistance in Gossypium arboreum Identified in a Genome-Wide Association Study

Transcriptome reveals Gafmt-1 and Gadlc-1-5 play positive roles in cotton resistance to Verticillium wilt

KEY MESSAGE

Both Gafmt-1 and Gadlc-1-5 from Gossypium arboreum respond to Verticillium dahilae infection in Gossypium hirsutum and may play positive roles in Verticillium wilt resistance via the salicylic acid pathway. Verticillium wilt (VW) caused by Verticillium dahliae is one of the most destructive diseases affecting cotton production and quality worldwide. Numerous resistance genes against the disease from tetraploid cultivated cotton (2n = 4x = AADD = 52) have been cloned and functionally analyzed to attempt to develop resistant varieties. However, VW continues to pose a significant threat to global cotton production due to the lack of cost-effective resistance genes to balance resistance and yield. Resistance genes from diploid cotton species such as Gossypium arboreum (2n = 2x = AA = 26) remain largely untapped, and their functions are unknown. Here, a resistant G. hirsutum-G. arboreum introgression line, DM10781, was employed to mine new resistance genes against V. dahliae from the diploid cotton species. We performed time-course transcriptome analysis on the RNA-seq data at 0, 4, 12, 24, 48, and 96 h post-inoculation. Weighted gene co-expression network analysis showed that nine differentially expressed genes (DEGs) caused by disease resistance have been identified. Among them, seven genes were found on the introgression segments from G. arboreum and suffered from virus-induced gene silencing in DM10781. Out of them, two genes were further overexpressing in Arabidopsis. The results indicated the two genes of Gafmt-1 and Gadlc-1-5 played positive roles in both cotton and Arabidopsis. Our study demonstrates that G. arboreum has the resistance genes to VW and can be used in future disease-resistance breeding, providing insights into the resistance of Gafmt-1 and Gadlc-1-5 against VW in cotton.

Evaluation of resistance to Verticillium wilt in Gossypium hirsutum-Gossypium arboreum introgression lines and identification of putative resistance genes using RNA-seq

Verticillium wilt (VW), a fungal disease caused by Verticillium dahliae (Vd), is one of the most destructive threats to cotton production. Moreover, widely cultivated upland cotton (Gossypium hirsutum, 2n = 4x = AADD = 52) often demonstrates low resistance to Vd. In contrast, G. arboreum (2n = 2x = AA = 26) shows high resistant to VW, making it a valuable source for breeding, despite the challenges posed by hybridization incompatibility between the two species. Here, a population of introgression lines derived from G. hirsutum and G. arboreum was evaluated for resistance to VW through both glasshouse and field tests. Among these lines, DM11039 demonstrated high resistance to VW. Both DM11039 and the recipient TM-1 underwent transcriptome sequencing during Vd infection at 0, 4, 12, 24, 48, and 96 h post inoculation. The analysis identified differentially expressed genes (DEGs), which were predominantly associated with resistance mechanisms. Based on the results from transcriptome sequencing and weighted correlation network analysis, three DEGs from each parent-G. arboreum and G. hirsutum- in DM11039 were subjected to virus-induced gene silencing in cotton seedlings. The findings revealed that silencing of GaPP2A1, GaPDH-E1, or GaLRK10L-1.2, which are located within the introgression segments from G. arboreum, significantly impaired disease resistance in cotton. This suggests that these genes are potentially linked to the disease phenotype. In contrast, silencing of GHA13G1263, GhZIP1 or GHA10G2498 from G. hirsutum did not result in any changes in disease resistance in DM11039. The results indicate G. arboreum harbors resistance genes to VW. Furthermore, the introgression population presents a valuable resource for future cotton breeding.

Ceramide-1-phosphate enhances defense responses against Sclerotinia sclerotiorum in Brassica napus

Sclerotinia stem rot caused by Sclerotinia sclerotiorum is one of the most severe diseases affecting the growth and production of Brassica napus. Sphingolipid metabolism plays a crucial role in plant response to pathogens. In this study, we show that ceramide kinase (CERK) is significantly induced during S. sclerotiorum infection to produce higher levels of ceramide-1-phosphate (C1P) in B. napus. The balance between ceramide (Cer) and C1P affects plant resistance to S. sclerotiorum, with CERK mutant lines exhibiting greater susceptibility to S. sclerotiorum and CERK overexpression lines showing enhanced resistance to this pathogen. Moreover, we identified candidate C1P-binding proteins by proteomic analysis and determined that C1P binds to and promotes the activity of a Gly-Asp-Ser-Leu lipase protein involved in B. napus resistance to S. sclerotiorum infection. In conclusion, our results indicate that C1P plays a key role in S. sclerotiorum resistance through metabolic regulation and signal transduction in B. napus.

The glutathione S-transferase BnGSTU12 enhances the resistance of Brassica napus to Sclerotinia sclerotiorum through reactive oxygen species homeostasis and jasmonic acid signaling

Sclerotinia sclerotiorum is a severe disease that affects rapeseed (Brassica napus), resulting in significant yield losses. In previous study, we identified the candidate GLUTATHIONE S-TRANSFERASE (GST) gene, BnGSTU12, associated with sclerotiorum stem resistance and the expression levels of BnGSTU12 in resistant lines were higher than that in susceptible lines. We analyzed the function of the BnGSTU12 during S. sclerotiorum infection in this study. BnGSTU12 expression was induced by S. sclerotiorum, with a strong increase 24 h after onset of infection. Transgenic functional analysis indicated that overexpression of BnGSTU12 in Arabidopsis thaliana and B. napus enhanced resistance to S. sclerotiorum, whereas BnGSTU12 silencing decreased S. sclerotiorum resistance. The inoculated BnGSTU12-OE A. thaliana and B. napus plants showed higher antioxidant enzyme activity and lower H2O2 contents than the wild type. As BnGSTU12 was rapidly induced by the phytohormones salicylic acid (SA), ethylene, and methyl jasmonate (MeJA), we investigated the involvement of the JA and SA pathways in GSTU12-mediated S. sclerotiorum resistance. JA content was higher in infected BnGSTU12-OE plants than in the wild type, whereas their SA contents were comparable. In addition, the expression levels of JASMONATE RESISTANT (JAR) involved in JA-Ile biosynthesis and those of JA-responsive genes were higher, the expression of JAZ gene repressing JA signaling was less in OE plants than WT after 12 and 24 h inoculation with S. sclerotiorum. Our results show that BnGSTU12 enhances resistance to S. sclerotiorum through ROS homeostasis and JA signaling.

GhRac9 improves cotton resistance to Verticillium dahliae via regulating ROS production and lignin content

Rac/Rop proteins, a kind of unique small GTPases in plants, play crucial roles in plant growth and development and in response to abiotic and biotic stresses. However, it is poorly understood whether cotton Rac/Rop protein genes are involved in mediating cotton resistance to Verticillium dahliae. Here, we focused on the function and mechanism of cotton Rac/Rop gene GhRac9 in the defense response to Verticillium dahliae infection. The expression level of GhRac9 peaked at 24 h after V. dahliae infection and remained consistently elevated from 24 to 48 h upon SA treatment. Furthermore, silencing GhRac9 using VIGS (Virus-induced gene silence) method attenuated cotton defense response to V. dahliae by reducing ROS (Reactive Oxygen Species) burst, peroxidase activity and lignin content in cotton plants. On the contrary, heterologous overexpression of GhRac9 enhanced Arabidopsis resistance to V. dahliae and significantly increased ROS production in Arabidopsis plants. Furthemore, transient overexpressing of GhRac9 significantly enhanced ROS burst and POD activity in cotton plants. In addition, GhRac9 positively regulated the expression levels of the genes related to SA signaling pathway in cotton plants. In conclusion, GhRac9 functioned as a positive regulator in the cotton defense response to V. dahliae, which provided important insights for breeding new cotton varieties resistant to V. dahliae.

Plant extracellular vesicles contribute to the amplification of immune signals during systemic acquired resistance

KEY MESSAGE

Plant extracellular vesicles play a role in systemic acquired resistance by facilitating the transmission of immune signals between plant cells. Extracellular vesicles (EVs) play a critical role in facilitating the transfer of nucleic acids and proteins between plants and pathogens. However, the involvement of plant EVs in intercellular communication and their contribution to the regulation of physiological and pathological conditions in plants remains unclear. In this study, we isolated EVs from the apoplast of Arabidopsis plants induced by systemic acquired resistance (SAR) and conducted proteomic and physiological analyses to investigate the role of EVs in SAR. The results demonstrated that plant cells are capable of internalizing EVs, and EV secretion was enhanced in SAR-induced plants. EVs isolated from SAR-induced plants effectively inhibited the spore production of Botrytis cinerea, activated the transcription of several SAR marker genes, and improved plant resistance to Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). Several proteins associated with defense responses were enriched in EVs upon SAR induction. Among these, the receptor-like kinase H2O2-Induced Ca2+ Increase 1 (HPCA1) was identified as a crucial component in SAR. In addition, plant EVs contained numerous proteins involved in the transmission of signals related to pathogen-associated molecular patterns-triggered immunity (PTI) and effector-triggered immunity (ETI). Our findings suggest that plant EVs are functionally involved in the propagation of SAR signals and may play diverse roles in plant immune responses.

Integrated Transcriptomic and Metabolomic Analysis of G. hirsutum and G. barbadense Responses to Verticillium Wilt Infection

Verticillium wilt (VW) caused by Verticillium dahliae (Vd) is a devastating fungal cotton disease characterized by high pathogenicity, widespread distribution, and frequent variation. It leads to significant losses in both the yield and quality of cotton. Identifying key non-synonymous single nucleotide polymorphism (SNP) markers and crucial genes associated with VW resistance in Gossypium hirsutum and Gossypium barbadense, and subsequently breeding new disease-resistant varieties, are essential for VW management. Here, we sequenced the transcriptome and metabolome of roots of TM-1 (G. hirsutum) and Hai7124 (G. barbadense) after 0, 1, and 2 days of V991 inoculation. Transcriptome analysis identified a total of 72,752 genes, with 5814 differentially expressed genes (DEGs) determined through multiple group comparisons. KEGG enrichment analysis revealed that the key pathways enriched by DEGs obtained from both longitudinal and transverse comparisons contained the glutathione metabolism pathway. Metabolome analysis identified 995 metabolites, and 22 differentially accumulated metabolites (DAMs), which were correlated to pathways including glutathione metabolism, degradation of valine, leucine, and isoleucine, and biosynthesis of terpenoids, alkaloids, pyridine, and piperidine. The conjoint analysis of transcriptomic and metabolomic sequencing revealed DAMs and DEGs associated with the glutathione metabolism pathway, and the key candidate gene GH_D11G2329 (glutathione S-transferase, GSTF8) potentially associated with cotton response to VW infection was selected. These findings establish a basis for investigating the mechanisms underlying the cotton plant's resistance to VW.

Integrated Transcriptome and sRNAome Analysis Reveals the Molecular Mechanisms of Piriformospora indica-Mediated Resistance to Fusarium Wilt in Banana

Bananas (Musa spp.) are among the most important fruit and staple food crops globally, holding a significant strategic position in food security in tropical and subtropical regions. However, the industry is grappling with a significant threat from Fusarium wilt, a disease incited by Fusarium oxysporum f. sp. cubense (Foc). In this study, we explored the potential of Piriformospora indica (Pi), a mycorrhizal fungus renowned for bolstering plant resilience and nutrient assimilation, to fortify bananas against this devastating disease. Through a meticulous comparative analysis of mRNA and miRNA expression in control, Foc-inoculated, Pi-colonized, and Pi-colonized followed by Foc-inoculated plants via transcriptome and sRNAome, we uncovered a significant enrichment of differentially expressed genes (DEGs) and DE miRNAs in pathways associated with plant growth and development, glutathione metabolism, and stress response. Our findings suggest that P. indica plays a pivotal role in bolstering banana resistance to Foc. We propose that P. indica modulates the expression of key genes, such as glutathione S-transferase (GST), and transcription factors (TFs), including TCP, through miRNAs, thus augmenting the plant's defensive capabilities. This study offers novel perspectives on harnessing P. indica for the management of banana wilt disease.

Genomic insights into Verticillium: a review of progress in the genomics era

Genomics has emerged as a great tool in enhancing our understanding of the biology of Verticillium species and their interactions with the host plants. Through different genomic approaches, researchers have gained insights into genes, pathways and virulence factors that play crucial roles in both Verticillium pathogenesis and the defense responses of their host organisms. This review emphasizes the significance of genomics in uncovering the mechanisms that underlie pathogenicity, virulence, and host resistance in Verticillium fungi. Our goal is to summarize recent discoveries in Verticillium research highlighting progress made in comprehending the biology and interactions of Verticillium fungi. The integration of genomics into Verticillium studies has the potential to open avenues for developing strategies to control diseases and produce crop varieties resistant to verticillium, thereby offering sustainable solutions for enhancing agricultural productivity.

MAPK and phenylpropanoid metabolism pathways involved in regulating the resistance of upland cotton plants to Verticillium dahliae

Introduction

Verticillium dahliae causes a serious decline in cotton yield and quality, posing a serious threat to the cotton industry. However, the mechanism of resistance to V. dahliae in cotton is still unclear, which limits the breeding of resistant cultivars.

Methods

To analyze the defense mechanisms of cotton in response to V. dahliae infection, we compared the defense responses of two upland cotton cultivars from Xinjiang (JK1775, resistant; Z8,susceptible) using transcriptome sequencing at different infection stages.

Results

The results revealed a significant differential expression of genes in the two cotton cultivars post V. dahliae infection, with the number of DEGs in JK1775 being higher than that in Z8 at different infection stages of V. dahliae. Interestingly, the DEGs of both JK1775 and Z8 were enriched in the MAPK signaling pathway in the early and late stages of infection. Importantly, the upregulated DEGs in both cultivars were significantly enriched in all stages of the phenylpropanoid metabolic pathway. Some of these DEGs were involved in the regulation of lignin and coumarin biosynthesis, which may be one of the key factors contributing to the resistance of upland cotton cultivars to V. dahliae in Xinjiang. Lignin staining experiments further showed that the lignin content increased in both resistant and susceptible varieties after inoculation with V. dahliae.

Discussion

This study not only provides insights into the molecular mechanisms of resistance to Verticillium wilt in Xinjiang upland cotton but also offers important candidate gene resources for molecular breeding of resistance to Verticillium wilt in cotton.

Expression pattern of the poplar GSTU family members in response to Alternaria alternate and PdbGSTU10 confers A. alternate resistance to Populus davidiana × P. bolleana

Plant tau glutathione S-transferase (GSTU) is a kind of multiple functions enzyme, but its specific roles in poplar disease resistance remain uncertain. In this study, 27 PdbGSTU-encoding genes from Populus davidiana × P. bollena were cloned and their protein architectures and phylogenetic relationships were subsequently analyzed. Expression analysis revealed that PdbGSTUs were differentially expressed under Alternaria alternate infection. Then, the PdbGSTU10 was further induced by phytohormones and H2O2, especially salicylic acid (SA), indicating its potential role in the pathogen defense of poplar. Subsequently, gain- and loss-of-function assays showed that overexpressed PdbGSTU10 activated antioxidant enzymes and significantly decreased reactive oxygen species (ROS) content, ultimately improving the resistance to A. alternate in poplar. Conversely, silencing PdbGSTU10 had the opposite effect. Moreover, overexpressed PdbGSTU10 also increased the content of SA and induced the expression of SA signal-related genes. These results showed that PdbGSTU10 may enhance disease resistance in poplar by scavenging ROS and affecting the SA signaling pathway. Our findings contribute to the understanding of the functions of GSTU in woody plants, particularly in disease resistance.

GbPP2C80 Interacts with GbWAKL14 to Negatively Co-Regulate Resistance to Fusarium and Verticillium wilt via MPK3 and ROS Signaling in Sea Island Cotton

Fusarium wilt (FW) is widespread in global cotton production, but the mechanism underlying FW resistance in superior-fiber-quality Sea Island cotton is unclear. This study reveals that FW resistance has been the target of genetic improvement of Sea Island cotton in China since the 2010s. The key nonsynonymous single nucleotide polymorphism (SNP, T/C) of gene Gbar_D03G001670 encoding protein phosphatase 2C 80 (PP2C80) results in an amino acid shift (L/S), which is significantly associated with FW resistance of Sea Island cotton. Silencing GbPP2C80 increases FW resistance in Sea Island cotton, whereas overexpressing GbPP2C80 reduces FW resistance in Arabidopsis. GbPP2C80 and GbWAKL14 exist synergistically in Sea Island cotton accessions with haplotype forms "susceptible-susceptible" (TA) and "resistant-resistant" (CC), and interact with each other. CRISPR/Cas9-mediated knockout of GbWAKL14 enhances FW and Verticillium wilt (VW) resistance in upland cotton and overexpression of GbWAKL14 and GbPP2C80 weakens FW and VW resistance in Arabidopsis. GbPP2C80 and GbWAKL14 respond to FW and VW by modulating reactive oxygen species (ROS) content via affecting MPK3 expression. In summary, two tandem genes on chromosome D03, GbPP2C80, and GbWAKL14, functions as cooperative negative regulators in cotton wilt disease defense, providing novel genetic resources and molecular markers for the development of resistant cotton cultivars.

Terpene synthases GhTPS6 and GhTPS47 participate in resistance to Verticillium dahliae in upland cotton

Terpene synthases (TPSs) are enzymes responsible for catalyzing the production of diverse terpenes, the largest class of secondary metabolites in plants. Here, we identified 107 TPS gene loci encompassing 92 full-length TPS genes in upland cotton (Gossypium hirsutum L.). Phylogenetic analysis showed they were divided into six subfamilies. Segmental duplication and tandem duplication events contributed greatly to the expansion of TPS gene family, particularly the TPS-a and TPS-b subfamilies. Expression profile analysis screened out that GhTPSs may mediate the interaction between cotton and Verticillium dahliae. Three-dimensional structures and subcellular localizations of the two selected GhTPSs, GhTPS6 and GhTPS47, which belong to the TPS-a subfamily, demonstrated similarity in protein structures and nucleus and cytoplasm localization. Virus-induced gene silencing (VIGS) of the two GhTPSs yielded plants characterized by increased wilting and chlorosis, more severe vascular browning, and higher disease index than control plants. Additionally, knockdown of GhTPS6 and GhTPS47 led to the down-regulation of cotton terpene synthesis following V. dahliae infection, indicating that these two genes may positively regulate resistance to V. dahliae through the modulation of disease-resistant terpene biosynthesis. Overall, our study represents a comprehensive analysis of the G. hirsutum TPS gene family, revealing their potential roles in defense responses against Verticillium wilt.

Identification of PgRg1-3 Gene for Ginsenoside Rg1 Biosynthesis as Revealed by Combining Genome-Wide Association Study and Gene Co-Expression Network Analysis of Jilin Ginseng Core Collection

Ginseng, an important medicinal plant, is characterized by its main active component, ginsenosides. Among more than 40 ginsenosides, Rg1 is one of the ginsenosides used for measuring the quality of ginseng. Therefore, the identification and characterization of genes for Rg1 biosynthesis are important to elucidate the molecular basis of Rg1 biosynthesis. In this study, we utilized 39,327 SNPs and the corresponding Rg1 content from 344 core ginseng cultivars from Jilin Province. We conducted a genome-wide association study (GWAS) combining weighted gene co-expression network analysis (WGCNA), SNP-Rg1 content association analysis, and gene co-expression network analysis; three candidate Rg1 genes (PgRg1-1, PgRg1-2, and PgRg1-3) and one crucial candidate gene (PgRg1-3) were identified. Functional validation of PgRg1-3 was performed using methyl jasmonate (MeJA) regulation and RNAi, confirming that this gene regulates Rg1 biosynthesis. The spatial-temporal expression patterns of the PgRg1-3 gene and known key enzyme genes involved in ginsenoside biosynthesis differ. Furthermore, variations in their networks have a significant impact on Rg1 biosynthesis. This study established an accurate and efficient method for identifying candidate genes, cloned a novel gene controlling Rg1 biosynthesis, and identified 73 SNPs significantly associated with Rg1 content. This provides genetic resources and effective tools for further exploring the molecular mechanisms of Rg1 biosynthesis and molecular breeding.

A tau class glutathione S-transferase in tea plant, CsGSTU45, facilitates tea plant susceptibility to Colletotrichum camelliae infection mediated by jasmonate signaling pathway

Tea plant [Camellia sinensis (L.) O. Kuntze], as one of the most important commercial crops, frequently suffers from anthracnose caused by Colletotrichum camelliae. The plant-specific tau (U) class of glutathione S-transferases (GSTU) participates in ROS homeostasis. Here, we identified a plant-specific GST tau class gene from tea plant, CsGSTU45, which is induced by various stresses, including C. camelliae infection, by analyzing multiple transcriptomes. CsGSTU45 plays a negative role in disease resistance against C. camelliae by accumulating H2 O2 . JA negatively regulates the resistance of tea plants against C. camelliae, which depends on CsGSTU45. CsMYC2.2, which is the key regulator in the JA signaling pathway, directly binds to and activates the promoter of CsGSTU45. Furthermore, silencing CsMYC2.2 increased disease resistance associated with reduced transcript and protein levels of CsGSTU45, and decreased contents of H2 O2 . Therefore, CsMYC2.2 suppresses disease resistance against C. camelliae by binding to the promoter of the CsGSTU45 gene and activating CsGSTU45. CsJAZ1 interacts with CsMYC2.2. Silencing CsJAZ1 attenuates disease resistance, upregulates the expression of CsMYC2.2 elevates the level of the CsGSTU45 protein, and promotes the accumulation of H2 O2 . As a result, CsJAZ1 interacts with CsMYC2.2 and acts as its repressor to suppress the level of CsGSTU45 protein, eventually enhancing disease resistance in tea plants. Taken together, the results show that the JA signaling pathway mediated by CsJAZ1-CsMYC2.2 modulates tea plant susceptibility to C. camelliae by regulating CsGSTU45 to accumulate H2 O2 .

Genetic Mapping and Characterization of Verticillium Wilt Resistance in a Recombinant Inbred Population of Upland Cotton

Verticillium wilt (VW) is an important and widespread disease of cotton and once established is long-lived and difficult to manage. In Australia, the non-defoliating pathotype of Verticillium dahliae is the most common, and extremely virulent. Breeding cotton varieties with increased VW resistance is the most economical and effective method of controlling this disease and is greatly aided by understanding the genetics of resistance. This study aimed to investigate VW resistance in 240 F7 recombinant inbred lines (RIL) derived from a cross between MCU-5, which has good resistance, and Siokra 1-4, which is susceptible. Using a controlled environment bioassay, we found that resistance based on plant survival or shoot biomass was complex but with major contributions from chromosomes D03 and D09, with genomic prediction analysis estimating a prediction accuracy of 0.73 based on survival scores compared to 0.36 for shoot biomass. Transcriptome analysis of MCU-5 and Siokra 1-4 roots uninfected or infected with V. dahliae revealed that the two cultivars displayed very different root transcriptomes and responded differently to V. dahliae infection. Ninety-nine differentially expressed genes were located in the two mapped resistance regions and so are potential candidates for further identifying the genes responsible for VW resistance.

Glutathione Transferase Photoaffinity Labeling Displays GST Induction by Safeners and Pathogen Infection

Glutathione transferases (GSTs) represent a large and diverse enzyme family involved in the detoxification of small molecules by glutathione conjugation in crops, weeds and model plants. In this study, we introduce an easy and quick assay for photoaffinity labeling of GSTs to study GSTs globally in various plant species. The small-molecule probe contains glutathione, a photoreactive group and a minitag for coupling to reporter tags via click chemistry. Under UV irradiation, this probe quickly and robustly labels GSTs in crude protein extracts of different plant species. Purification and mass spectrometry (MS) analysis of labeled proteins from Arabidopsis identified 10 enriched GSTs from the Phi(F) and Tau(U) classes. Photoaffinity labeling of GSTs demonstrated GST induction in wheat seedlings upon treatment with safeners and in Arabidopsis leaves upon infection with avirulent bacteria. Treatment of Arabidopsis with salicylic acid (SA) analog benzothiadiazole (BTH) induces GST labeling independent of NPR1, the master regulator of SA. Six Phi- and Tau-class GSTs that are induced upon BTH treatment were identified, and their labeling was confirmed upon transient overexpression. These data demonstrate that GST photoaffinity labeling is a useful approach to studying GST induction in crude extracts of different plant species upon different types of stress.

General Regulatory Factor7 regulates innate immune signalling to enhance Verticillium wilt resistance in cotton

Sessile growing plants are always vulnerable to microbial pathogen attacks throughout their lives. To fend off pathogen invasion, plants have evolved a sophisticated innate immune system that consists of cell surface receptors and intracellular receptors. Somatic embryogenesis receptor kinases (SERKs) belong to a small group of leucine-rich repeat receptor-like kinases (LRR-RLKs) that function as co-receptors regulating diverse physiological processes. GENRAL REGULATORY FACTOR (GRF) proteins play an important role in physiological signalling transduction. However, the function of GRF proteins in plant innate immune signalling remains elusive. Here, we identified a GRF gene, GauGRF7, that is expressed both constitutively and in response to fungal pathogen infection. Intriguingly, silencing of GRF7 compromised plant innate immunity, resulting in susceptibility to Verticillium dahliae infection. Both transgenic GauGRF7 cotton and transgenic GauGRF7 Arabidopsis lines enhanced the innate immune response to V. dahliae infection, leading to high expression of two helper NLRs (hNLR) genes (ADR1 and NRG1) and pathogenesis-related genes, and increased ROS production and salicylic acid level. Moreover, GauGRF7 interacted with GhSERK1, which positively regulated GRF7-mediated innate immune response in cotton and Arabidopsis. Our findings revealed the molecular mechanism of the GRF protein in plant immune signaling and offer potential opportunities for improving plant resistance to V. dahliae infection.

A novel single nucleotide mutation of TFL1 alters the plant architecture of Gossypium arboreum through changing the pre-mRNA splicing

KEY MESSAGE

A single nucleotide mutation from G to A at the 201st position changed the 5' splice site and deleted 31 amino acids in the first exon of GaTFL1. Growth habit is an important agronomic trait that plays a decisive role in the plant architecture and crop yield. Cotton (Gossypium) tends to indeterminate growth, which is unsuitable for the once-over mechanical harvest system. Here, we identified a determinate growth mutant (dt1) in Gossypium arboreum by EMS mutagenesis, in which the main axis was terminated with the shoot apical meristem (SAM) converted into flowers. The map-based cloning of the dt1 locus showed a single nucleotide mutation from G to A at the 201st positions in TERMINAL FLOWER 1 (GaTFL1), which changed the alternative RNA 5' splice site and resulted in 31 amino acids deletion and loss of function of GaTFL1. Comparative transcriptomic RNA-Seq analysis identified many transporters responsible for the phytohormones, auxin, sugar, and flavonoids, which may function downstream of GaTFL1 to involve the plant architecture regulation. These findings indicate a novel alternative splicing mechanism involved in the post-transcriptional modification and TFL1 may function upstream of the auxin and sugar pathways through mediating their transport to determine the SAM fate and coordinate the vegetative and reproductive development from the SAM of the plant, which provides clues for the TFL1 mechanism in plant development regulation and provide research strategies for plant architecture improvement.

RVE2, a new regulatory factor in jasmonic acid pathway, orchestrates resistance to Verticillium wilt

Verticillium dahliae, one of the most destructive fungal pathogens of several crops, challenges the sustainability of cotton productivity worldwide because very few widely-cultivated Upland cotton varieties are resistant to Verticillium wilt (VW). Here, we report that REVEILLE2 (RVE2), the Myb-like transcription factor, confers the novel function in resistance to VW by regulating the jasmonic acid (JA) pathway in cotton. RVE2 expression was essentially required for the activation of JA-mediated disease-resistance response. RVE2 physically interacted with TPL/TPRs and disturbed JAZ proteins to recruit TPL and TPR1 in NINJA-dependent manner, which regulated JA response by relieving inhibited-MYC2 activity. The MYC2 then bound to RVE2 promoter for the activation of its transcription, forming feedback loop. Interestingly, a unique truncated RVE2 widely existing in D-subgenome (GhRVE2D) of natural Upland cotton represses the ability of the MYC2 to activate GhRVE2A promoter but not GausRVE2 or GbRVE2. The result could partially explain why Gossypium barbadense popularly shows higher resistance than Gossypium hirsutum. Furthermore, disturbing the JA-signalling pathway resulted into the loss of RVE2-mediated disease-resistance in various plants (Arabidopsis, tobacco and cotton). RVE2 overexpression significantly enhanced the resistance to VW. Collectively, we conclude that RVE2, a new regulatory factor, plays a pivotal role in fine-tuning JA-signalling, which would improve our understanding the mechanisms underlying the resistance to VW.

Meloidogyne enterolobii MeMSP1 effector targets the glutathione-S-transferase phi GSTF family in Arabidopsis to manipulate host metabolism and promote nematode parasitism

Meloidogyne enterolobii is an emerging root-knot nematode species that overcomes most of the nematode resistance genes in crops. Nematode effector proteins secreted in planta are key elements in the molecular dialogue of parasitism. Here, we show the MeMSP1 effector is secreted into giant cells and promotes M. enterolobii parasitism. Using co-immunoprecipitation and bimolecular fluorescent complementation assays, we identified glutathione-S-transferase phi GSTFs as host targets of the MeMSP1 effector. This protein family plays important roles in plant responses to abiotic and biotic stresses. We demonstrate that MeMSP1 interacts with all Arabidopsis GSTF. Moreover, we confirmed that the N-terminal region of AtGSTF9 is critical for its interaction, and atgstf9 mutant lines are more susceptible to root-knot nematode infection. Combined transcriptome and metabolome analyses showed that MeMSP1 affects the metabolic pathways of Arabidopsis thaliana, resulting in the accumulation of amino acids, nucleic acids, and their metabolites, and organic acids and the downregulation of flavonoids. Our study has shed light on a novel effector mechanism that targets plant metabolism, reducing the production of plant defence-related compounds while favouring the accumulation of metabolites beneficial to the nematode, and thereby promoting parasitism.

Uncovering genomic and transcriptional variations facilitates utilization of wild resources in cotton disease resistance improvement

BACKGROUND

Upland cotton wild/landraces represent a valuable resource for disease resistance alleles. Genetic differentiation between genotypes, as well as variation in Verticillium wilt (VW) resistance, has been poorly characterized for upland cotton accessions on the domestication spectrum (from wild/landraces to elite lines).

RESULTS

To illustrate the effects of modern breeding on VW resistance in upland cotton, 37 wild/landraces were resequenced and phenotyped for VW resistance. Genomic patterns of differentiation were identified between wild/landraces and improved upland cotton, and a significant decline in VW resistance was observed in association with improvement. Four genotypes representing different degrees of improvement were used in a full-length transcriptome analysis to study the genetic basis of VW resistance. ROS signaling was highly conserved at the transcriptional level, likely providing the basis for VW resistance in upland cotton. ASN biosynthesis and HSP90-mediated resistance moderated the response to VW in wild/landraces, and loss of induction activity of these genes resulted in VW susceptibility. The observed genomic differentiation contributed to the loss of induction of some important VW resistance genes such as HSP90.4 and PR16.

CONCLUSIONS

Besides providing new insights into the evolution of upland cotton VW resistance, this study also identifies important resistance pathways and genes for both fundamental research and cotton breeding.

Ca2+-responsive phospholipid-binding BONZAI genes confer a novel role for cotton resistance to Verticillium wilt

Verticillium wilt which produced by the soil-borne fungus Verticillium dahliae is an important biotic threat that limits cotton (Gossypium hirsutum) growth and agricultural productivity. It is very essential to explore new genes for the generation of V. dahliae resistance or tolerance cotton varieties. Ca²⁺ signaling as a secondary messenger is involved in pathogen stress response. Despite Ca²⁺-responsive phospholipid-binding BONZAI (BON) genes have intensively been investigated in Arabidopsis, their function has not still been characterized in cotton. Here, we showed that three copies of GhBON1, two copies of GhBON2 and GhBON3 were found from the genome sequences of upland cotton. The expression of GhBON1 was inducible to V. dahliae. Knocking down of GhBON1, GhBON2 and GhBON3 using virus induced gene silencing (VIGS) each increased up-regulation of defense responses in cotton. These GhBON1, GhBON2 and GhBON3-silenced plants enhanced resistance to V. dahliae accompanied by higher burst of hydrogen peroxide and decreased cell death and had more effect on the up-regulation of defense response genes. Further analysis revealed that GhBON1 could interacts with BAK1-interacting receptor-like kinase 1 (GhBIR1) and pathogen-associated molecular pattern (PAMP) receptor regulator BAK1 (GhBAK1) at plasma membrane. Our study further reveals that plant Ca²⁺ -responsive phospholipid-binding BONZAI genes negatively regulate Verticillium wilt with the conserved function in response to disease resistance or plant immunity.

Genome-wide association analysis reveals a novel pathway mediated by a dual-TIR domain protein for pathogen resistance in cotton

BACKGROUND

Verticillium wilt is one of the most devasting diseases for many plants, leading to global economic loss. Cotton is known to be vulnerable to its fungal pathogen, Verticillium dahliae, yet the related genetic mechanism remains unknown.

RESULTS

By genome-wide association studies of 419 accessions of the upland cotton, Gossypium hirsutum, we identify ten loci that are associated with resistance against Verticillium wilt. Among these loci, SHZDI1/SHZDP2/AYDP1 from chromosome A10 is located on a fragment introgressed from Gossypium arboreum. We characterize a large cluster of Toll/interleukin 1 (TIR) nucleotide-binding leucine-rich repeat receptors in this fragment. We then identify a dual-TIR domain gene from this cluster, GhRVD1, which triggers an effector-independent cell death and is induced by Verticillium dahliae. We confirm that GhRVD1 is one of the causal gene for SHZDI1. Allelic variation in the TIR domain attenuates GhRVD1-mediated resistance against Verticillium dahliae. Homodimerization between TIR1-TIR2 mediates rapid immune response, while disruption of its αD- and αE-helices interface eliminates the autoactivity and self-association of TIR1-TIR2. We further demonstrate that GhTIRP1 inhibits the autoactivity and self-association of TIR1-TIR2 by competing for binding to them, thereby preventing the resistance to Verticillium dahliae.

CONCLUSIONS

We propose the first working model for TIRP1 involved self-association and autoactivity of dual-TIR domain proteins that confer compromised pathogen resistance of dual-TIR domain proteins in plants. The findings reveal a novel mechanism on Verticillium dahliae resistance and provide genetic basis for breeding in future.

Cotton peroxisome-localized lysophospholipase counteracts the toxic effects of Verticillium dahliae NLP1 and confers wilt resistance

Plasma membrane represents a critical battleground between plants and attacking microbes. Necrosis-and-ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs), cytolytic toxins produced by some bacterial, fungal and oomycete species, are able to target on lipid membranes by binding eudicot plant-specific sphingolipids (glycosylinositol phosphorylceramide) and form transient small pores, causing membrane leakage and subsequent cell death. NLP-producing phytopathogens are a big threat to agriculture worldwide. However, whether there are R proteins/enzymes that counteract the toxicity of NLPs in plants remains largely unknown. Here we show that cotton produces a peroxisome-localized enzyme lysophospholipase, GhLPL2. Upon Verticillium dahliae attack, GhLPL2 accumulates on the membrane and binds to V. dahliae secreted NLP, VdNLP1, to block its contribution to virulence. A higher level of lysophospholipase in cells is required to neutralize VdNLP1 toxicity and induce immunity-related genes expression, meanwhile maintaining normal growth of cotton plants, revealing the role of GhLPL2 protein in balancing resistance to V. dahliae and growth. Intriguingly, GhLPL2 silencing cotton plants also display high resistance to V. dahliae, but show severe dwarfing phenotype and developmental defects, suggesting GhLPL2 is an essential gene in cotton. GhLPL2 silencing results in lysophosphatidylinositol over-accumulation and decreased glycometabolism, leading to a lack of carbon sources required for plants and pathogens to survive. Furthermore, lysophospholipases from several other crops also interact with VdNLP1, implying that blocking NLP virulence by lysophospholipase may be a common strategy in plants. Our work demonstrates that overexpressing lysophospholipase encoding genes have great potential for breeding crops with high resistance against NLP-producing microbial pathogens.

Efficient genotype-independent cotton genetic transformation and genome editing

Cotton (Gossypium spp.) is one of the most important fiber crops worldwide. In the last two decades, transgenesis and genome editing have played important roles in cotton improvement. However, genotype dependence is one of the key bottlenecks in generating transgenic and gene-edited cotton plants through either particle bombardment or Agrobacterium-mediated transformation. Here, we developed a shoot apical meristem (SAM) cell-mediated transformation system (SAMT) that allowed the transformation of recalcitrant cotton genotypes including widely grown upland cotton (Gossypium hirsutum), Sea island cotton (Gossypium barbadense), and Asiatic cotton (Gossypium arboreum). Through SAMT, we successfully introduced two foreign genes, GFP and RUBY, into SAM cells of some recalcitrant cotton genotypes. Within 2-3 months, transgenic adventitious shoots generated from the axillary meristem zone could be recovered and grown into whole cotton plants. The GFP fluorescent signal and betalain accumulation could be observed in various tissues in GFP- and RUBY-positive plants, as well as in their progenies, indicating that the transgenes were stably integrated into the genome and transmitted to the next generation. Furthermore, using SAMT, we successfully generated edited cotton plants with inheritable targeted mutagenesis in the GhPGF and GhRCD1 genes through CRISPR/Cas9-mediated genome editing. In summary, the established SAMT transformation system here in this study bypasses the embryogenesis process during tissue culture in a conventional transformation procedure and significantly accelerates the generation of transgenic and gene-edited plants for genetic improvement of recalcitrant cotton varieties.

Recent progression and future perspectives in cotton genomic breeding

Upland cotton is an important global cash crop for its long seed fibers and high edible oil and protein content. Progress in cotton genomics promotes the advancement of cotton genetics, evolutionary studies, functional genetics, and breeding, and has ushered cotton research and breeding into a new era. Here, we summarize high-impact genomics studies for cotton from the last 10 years. The diploid Gossypium arboreum and allotetraploid Gossypium hirsutum are the main focus of most genetic and genomic studies. We next review recent progress in cotton molecular biology and genetics, which builds on cotton genome sequencing efforts, population studies, and functional genomics, to provide insights into the mechanisms shaping abiotic and biotic stress tolerance, plant architecture, seed oil content, and fiber development. We also suggest the application of novel technologies and strategies to facilitate genome-based crop breeding. Explosive growth in the amount of novel genomic data, identified genes, gene modules, and pathways is now enabling researchers to utilize multidisciplinary genomics-enabled breeding strategies to cultivate "super cotton", synergistically improving multiple traits. These strategies must rise to meet urgent demands for a sustainable cotton industry.

Interactions between Verticillium dahliae and cotton: pathogenic mechanism and cotton resistance mechanism to Verticillium wilt

Cotton is widely grown in many countries around the world due to the huge economic value of the total natural fiber. Verticillium wilt, caused by the soil-borne pathogen Verticillium dahliae, is the most devastating disease that led to extensive yield losses and fiber quality reduction in cotton crops. Developing resistant cotton varieties through genetic engineering is an effective, economical, and durable strategy to control Verticillium wilt. However, there are few resistance gene resources in the currently planted cotton varieties, which has brought great challenges and difficulties for breeding through genetic engineering. Further revealing the molecular mechanism between V. dahliae and cotton interaction is crucial to discovering genes related to disease resistance. In this review, we elaborated on the pathogenic mechanism of V. dahliae and the resistance mechanism of cotton to Verticillium wilt. V. dahliae has evolved complex mechanisms to achieve pathogenicity in cotton, mainly including five aspects: (1) germination and growth of microsclerotia; (2) infection and successful colonization; (3) adaptation to the nutrient-deficient environment and competition of nutrients; (4) suppression and manipulation of cotton immune responses; (5) rapid reproduction and secretion of toxins. Cotton has evolved multiple physiological and biochemical responses to cope with V. dahliae infection, including modification of tissue structures, accumulation of antifungal substances, homeostasis of reactive oxygen species (ROS), induction of Ca²⁺ signaling, the mitogen-activated protein kinase (MAPK) cascades, hormone signaling, and PAMPs/effectors-triggered immune response (PTI/ETI). This review will provide an important reference for the breeding of new cotton germplasm resistant to Verticillium wilt through genetic engineering.

Multicopper oxidases GbAO and GbSKS are involved in the Verticillium dahliae resistance in Gossypium barbadense

Ascorbate oxidase (AO) and skewed5 (SKU5)-similar (SKS) proteins belong to the multicopper oxidase (MCO) family and play important roles in plants in response to environmental stress via modulation of oxidoreduction homeostasis. Currently, reports on the response of Gossypium barbadense MCO to Verticillium wilt (VW) caused by Verticillium dahliae are still limited. Herein, RNA sequencing of two G. barbadense cultivars of VW-resistant XH21 and VW-susceptible XH7 under V. dahliae treatment, combined with physiological and genetic analysis, was performed to analyze the function and mechanism of multicopper oxidases GbAO and GbSKS involved in V. dahliae resistance. The identified differentially expressed genes are mainly involved in the regulation of oxidoreduction reaction, and extracellular components and signaling. Interestingly, ascorbate oxidase family members were discovered as the most significantly upregulated genes after V. dahliae treatment, including GbAO3A/D, GbSKS3A/D, and GbSKS16A/D. H₂O₂ and Asc contents, especially reductive Asc in both XH21 and XH7, were shown to be increased. Silenced expression of respective GbAO3A/D, GbSKS3A/D, and GbSKS16A/D in virus-induced gene silencing (VIGS) cotton plants significantly decreased the resistance to V. dahliae, coupled with the reduced contents of pectin and lignin. Our results indicate that AO might be involved in cotton VW resistance via the regulation of cell wall components.

Reactive oxygen species-related genes participate in resistance to cucumber green mottle mosaic virus infection regulated by boron in Nicotiana benthamiana and watermelon

Cucumber green mottle mosaic virus (CGMMV) infection causes acidification and rot of watermelon flesh, resulting in serious economic losses. It is widely reported the interaction relationship between boron and reactive oxygen species (ROS) in regulating normal growth and disease resistance in plants. Our previous results demonstrated that exogenous boron could improve watermelon resistance to CGMMV infection. However, the roles of ROS-related genes regulated by boron in resistance to CGMMV infection are unclear. Here, we demonstrated that CGMMV symptoms were alleviated, and viral accumulations were decreased by boron application in Nicotiana benthamiana, indicating that boron contributed to inhibiting CGMMV infection. Meanwhile, we found that a number of differentially expressed genes (DEGs) associated with inositol biosynthesis, ethylene synthesis, Ca²⁺ signaling transduction and ROS scavenging system were up-regulated, while many DEGs involved in ABA catabolism, GA signal transduction and ascorbic acid metabolism were down-regulated by boron application under CGMMV infection. Additionally, we individually silenced nine ROS-related genes to explore their anti-CGMMV roles using a tobacco rattle virus (TRV) vector. The results showed that NbCat1, NbGME1, NbGGP and NbPrx Q were required for CGMMV infection, while NbGST and NbIPS played roles in resistance to CGMMV infection. The similar results were obtained in watermelon by silencing of ClCat, ClPrx or ClGST expression using a pV190 vector. This study proposed a new strategy for improving plant resistance to CGMMV infection by boron-regulated ROS pathway and provided several target genes for watermelon disease resistance breeding.

Cytological, genetic and transcriptomic characterization of a cucumber albino mutant

Photosynthesis, a fundamental process for plant growth and development, is dependent on chloroplast formation and chlorophyll synthesis. Severe disruption of chloroplast structure results in albinism of higher plants. In the present study, we report a cucumber albino alc mutant that presented white cotyledons under normal light conditions and was unable to produce first true leaf. Meanwhile, alc mutant could grow creamy green cotyledons under dim light conditions but died after exposure to normal light irradiation. No chlorophyll and carotenoid were detected in the alc mutant grown under normal light conditions. Using transmission electron microscopy, impaired chloroplasts were observed in this mutant. The genetic analysis indicated that the albino phenotype was recessively controlled by a single locus. Comparative transcriptomic analysis between the alc mutant and wild type revealed that genes involved in chlorophyll metabolism and the methylerythritol 4-phosphate pathway were affected in the alc mutant. In addition, three genes involved in chloroplast development, including two FtsH genes and one PPR gene, were found to have negligible expression in this mutant. The quality of RNA sequencing results was further confirmed by real-time quantitative PCR analysis. We also examined 12 homologous genes from alc mutant in other plant species, but no genetic variation in the coding sequences of these genes was found between alc mutant and wild type. Taken together, we characterized a cucumber albino mutant with albinism phenotype caused by chloroplast development deficiency and this mutant can pave way for future studies on plastid development.

Status and prospects of genome-wide association studies in cotton

Over the last two decades, the use of high-density SNP arrays and DNA sequencing have allowed scientists to uncover the majority of the genotypic space for various crops, including cotton. Genome-wide association study (GWAS) links the dots between a phenotype and its underlying genetics across the genomes of populations. It was first developed and applied in the field of human disease genetics. Many areas of crop research have incorporated GWAS in plants and considerable literature has been published in the recent decade. Here we will provide a comprehensive review of GWAS studies in cotton crop, which includes case studies on biotic resistance, abiotic tolerance, fiber yield and quality traits, current status, prospects, bottlenecks of GWAS and finally, thought-provoking question. This review will serve as a catalog of GWAS in cotton and suggest new frontiers of the cotton crop to be studied with this important tool.

Defense Mechanisms of Cotton Fusarium and Verticillium Wilt and Comparison of Pathogenic Response in Cotton and Humans

Cotton is an important economic crop. Fusarium and Verticillium are the primary pathogenic fungi that threaten both the quality and sustainable production of cotton. As an opportunistic pathogen, Fusarium causes various human diseases, including fungal keratitis, which is the most common. Therefore, there is an urgent need to study and clarify the resistance mechanisms of cotton and humans toward Fusarium in order to mitigate, or eliminate, its harm. Herein, we first discuss the resistance and susceptibility mechanisms of cotton to Fusarium and Verticillium wilt and classify associated genes based on their functions. We then outline the characteristics and pathogenicity of Fusarium and describe the multiple roles of human neutrophils in limiting hyphal growth. Finally, we comprehensively compare the similarities and differences between animal and plant resistance to Fusarium and put forward new insights into novel strategies for cotton disease resistance breeding and treatment of Fusarium infection in humans.

WGCNA Identifies a Comprehensive and Dynamic Gene Co-Expression Network That Associates with Smut Resistance in Sugarcane

Sugarcane smut is a major fungal disease caused by Sporisorium scitamineum, which seriously reduces the yield and quality of sugarcane. In this study, 36 transcriptome data were collected from two sugarcane genotypes, YT93-159 (resistant) and ROC22 (susceptible) upon S. scitamineum infection. Data analysis revealed 20,273 (12,659 up-regulated and 7614 down-regulated) and 11,897 (7806 up-regulated and 4091 down-regulated) differentially expressed genes (DEGs) in YT93-159 and ROC22, respectively. A co-expression network was then constructed by weighted gene co-expression network analysis (WGCNA), which identified 5010 DEGs in 15 co-expressed gene modules. Four of the 15 modules, namely, Skyblue, Salmon, Darkorange, and Grey60, were significantly associated with smut resistance. The GO and KEGG enrichment analyses indicated that the DEGs involving in these four modules could be enriched in stress-related metabolic pathways, such as MAPK and hormone signal transduction, plant-pathogen interaction, amino acid metabolism, glutathione metabolism, and flavonoid, and phenylpropanoid biosynthesis. In total, 38 hub genes, including six from the Skyblue module, four from the Salmon module, 12 from the Darkorange module, and 16 from the Grey60 module, were screened as candidate hub genes by calculating gene connectivity in the corresponding network. Only 30 hub genes were amplifiable with RT-qPCR, of which 27 were up-regulated upon S. scitamineum infection. The results were consistent with the trend of gene expression in RNA-Seq, suggesting their positive roles in smut resistance. Interestingly, the expression levels of AOX, Cyb5, and LAC were higher in ROC22 than in YT93-159, indicating these three genes may act as negative regulators in response to S. scitamineum infection. This study revealed the transcriptome dynamics in sugarcane challenged by S. scitamineum infection and provided gene targets for smut resistance breeding in sugarcane.

The Past, Present, and Future of Host Plant Resistance in Cotton: An Australian Perspective

Cotton is a key global fiber crop. However, yield potential is limited by the presence of endemic and introduced pests and diseases. The introduction of host plant resistance (HPR), defined as the purposeful use of resistant crop cultivars to reduce the impact of pests and diseases, has been a key breeding target for the Commonwealth Scientific and Industrial Research Organisation (CSIRO) cotton breeding program. The program has seen success in releasing cultivars resistant to Bacterial blight, Verticillium wilt, Fusarium wilt, and Cotton bunchy top. However, emerging biotic threats such as Black root rot and secondary pests, are becoming more frequent in Australian cotton production systems. The uptake of tools and breeding methods, such as genomic selection, high throughput phenomics, gene editing, and landscape genomics, paired with the continued utilization of sources of resistance from Gossypium germplasm, will be critical for the future of cotton breeding. This review celebrates the success of HPR breeding activities in the CSIRO cotton breeding program and maps a pathway for the future in developing resistant cultivars.

Identification of positive and negative regulators of antiviral RNA interference in Arabidopsis thaliana

Virus-host coevolution often drives virus immune escape. However, it remains unknown whether natural variations of plant virus resistance are enriched in genes of RNA interference (RNAi) pathway known to confer essential antiviral defense in plants. Here, we report two genome-wide association study screens to interrogate natural variation among wild-collected Arabidopsis thaliana accessions in quantitative resistance to the endemic cucumber mosaic virus (CMV). We demonstrate that the highest-ranked gene significantly associated with resistance from both screens acts to regulate antiviral RNAi in ecotype Columbia-0. One gene, corresponding to Reduced Dormancy 5 (RDO5), enhances resistance by promoting amplification of the virus-derived small interfering RNAs (vsiRNAs). Interestingly, the second gene, designated Antiviral RNAi Regulator 1 (VIR1), dampens antiviral RNAi so its genetic inactivation by CRISPR/Cas9 editing enhances both vsiRNA production and CMV resistance. Our findings identify positive and negative regulators of the antiviral RNAi defense that may play important roles in virus-host coevolution.

VIGS Goes Viral: How VIGS Transforms Our Understanding of Plant Science

Virus-induced gene silencing (VIGS) has developed into an indispensable approach to gene function analysis in a wide array of species, many of which are not amenable to stable genetic transformation. VIGS utilizes the posttranscriptional gene silencing (PTGS) machinery of plants to restrain viral infections systemically and is used to downregulate the plant's endogenous genes. Here, we review the molecular mechanisms of DNA- and RNA-virus-based VIGS, its inherent connection to PTGS, and what is known about the systemic spread of silencing. Recently, VIGS-based technologies have been expanded to enable not only gene silencing but also overexpression [virus-induced overexpression (VOX)], genome editing [virus-induced genome editing (VIGE)], and host-induced gene silencing (HIGS). These techniques expand the genetic toolbox for nonmodel organisms even more. Further, we illustrate the versatility of VIGS and the methods derived from it in elucidating molecular mechanisms, using tomato fruit ripening and programmed cell death as examples. Finally, we discuss challenges of and future perspectives on the use of VIGS to advance gene function analysis in nonmodel plants in the postgenomic era.

Solanaceous plants switch to cytokinin-mediated immunity against Ralstonia solanacearum under high temperature and high humidity

Plant diseases generally tend to be more serious under conditions of high temperature and high humidity (HTHH) than under ambient temperature, but plant immunity against pathogen attacks under HTHH remains elusive. Herein, we used pepper as an example to study how Solanaceae cope with Ralstonia solanacearum infection (RSI) under HTHH by performing RNA-seq combined with the reverse genetic method. The result showed that immunities mediated by salicylic acid (SA) and jasmonic acid (JA) in pepper roots were activated by RSI under ambient temperature. However, upon RSI under HTHH, JA signalling was blocked and SA signalling was activated early but its duration was greatly shortened in pepper roots, instead, expression of CaIPT5 and Glutathione S-transferase encoding genes, as well as endogenous content of trans-Zeatin, were enhanced. In addition, by silencing in pepper plants and overexpression in Nicotiana benthamiana, CaIPT5 was found to act positively in the immune response to RSI under HTHH in a way related to CaPRP1 and CaMgst3. Furthermore, the susceptibility of pepper, tomato and tobacco to RSI under HTHH was significantly reduced by exogenously applied tZ, but not by either SA or MeJA. All these data collectively suggest that pepper employs cytokinin-mediated immunity to cope with RSI under HTHH.

CaAIL1 Acts Positively in Pepper Immunity against Ralstonia solanacearum by Repressing Negative Regulators

APETALA2 (AP2) subfamily transcription factors participate in plant growth and development, but their roles in plant immunity remain unclear. Here, we discovered that the AP2 transcription factor CaAIL1 functions in immunity against Ralstonia solanacearum infection (RSI) in pepper (Capsicum annuum). CaAIL1 expression was upregulated by RSI, and loss- and gain-of-function assays using virus-induced gene silencing and transient overexpression, respectively, revealed that CaAIL1 plays a positive role in immunity to RSI in pepper. Chromatin immunoprecipitation sequencing (ChIP-seq) uncovered a subset of transcription-factor-encoding genes, including CaRAP2-7, CaGATA17, CaGtf3a and CaTCF25, that were directly targeted by CaAIL1 via their cis-elements, such as GT or AGGCA motifs. ChIP-qPCR and electrophoretic mobility shift assays confirmed these findings. These genes, encoding transcription factors with negative roles in immunity, were repressed by CaAIL1 during pepper response to RSI, whereas genes encoding positive immune regulators such as CaEAS were derepressed by CaAIL1. Importantly, we showed that the atypical EAR motif (LXXLXXLXX) in CaAIL1 is indispensable for its function in immunity. These findings indicate that CaAIL1 enhances the immunity of pepper against RSI by repressing a subset of negative immune regulators during the RSI response through its binding to several cis-elements in their promoters.

BIN2 negatively regulates plant defence against Verticillium dahliae in Arabidopsis and cotton

Verticillium wilt is caused by the soil-borne vascular pathogen Verticillium dahliae, and affects a wide range of economically important crops, including upland cotton (Gossypium hirsutum). Previous studies showed that expression levels of BIN2 were significantly down-regulated during infestation with V. dahliae. However, the underlying molecular mechanism of BIN2 in plant regulation against V. dahliae remains enigmatic. Here, we characterized a protein kinase GhBIN2 from Gossypium hirsutum, and identified GhBIN2 as a negative regulator of resistance to V. dahliae. The Verticillium wilt resistance of Arabidopsis and cotton were significantly enhanced when BIN2 was knocked down. Constitutive expression of BIN2 attenuated plant resistance to V. dahliae. We found that BIN2 regulated plant endogenous JA content and influenced the expression of JA-responsive marker genes. Further analysis revealed that BIN2 interacted with and phosphorylated JAZ family proteins, key repressors of the JA signalling pathway in both Arabidopsis and cotton. Spectrometric analysis and site-directed mutagenesis showed that BIN2 phosphorylated AtJAZ1 at T196, resulting in the degradation of JAZ proteins. Collectively, these results show that BIN2 interacts with JAZ proteins and plays a negative role in plant resistance to V. dahliae. Thus, BIN2 may be a potential target gene for genetic engineering against Verticillium wilt in crops.

The GhSWEET42 Glucose Transporter Participates in Verticillium dahliae Infection in Cotton

The SWEET (sugars will eventually be exported transporter) proteins, a family of sugar transporters, mediate sugar diffusion across cell membranes. Pathogenic fungi can acquire sugars from plant cells to satisfy their nutritional demands for growth and infection by exploiting plant SWEET sugar transporters. However, the mechanism underlying the sugar allocation in cotton plants infected by Verticillium dahliae, the causative agent of Verticillium wilt, remains unclear. In this study, observations of the colonization of cotton roots by V. dahliae revealed that a large number of conidia had germinated at 48-hour post-inoculation (hpi) and massive hyphae had appeared at 96 hpi. The glucose content in the infected roots was significantly increased at 48 hpi. On the basis of an evolutionary analysis, an association analysis, and qRT-PCR assays, GhSWEET42 was found to be closely associated with V. dahliae infection in cotton. Furthermore, GhSWEET42 was shown to encode a glucose transporter localized to the plasma membrane. The overexpression of GhSWEET42 in Arabidopsis thaliana plants led to increased glucose content, and compromised their resistance to V. dahliae. In contrast, knockdown of GhSWEET42 expression in cotton plants by virus-induced gene silencing (VIGS) led to a decrease in glucose content, and enhanced their resistance to V. dahliae. Together, these results suggest that GhSWEET42 plays a key role in V. dahliae infection in cotton through glucose translocation, and that manipulation of GhSWEET42 expression to control the glucose level at the infected site is a useful method for inhibiting V. dahliae infection.

Orchestration of plant development and defense by indirect crosstalk of salicylic acid and brassinosteorid signaling via transcription factor GhTINY2

Salicylic acid (SA) and brassinosteroids (BRs) are well known to regulate diverse processes of plant development and stress responses, but the mechanisms by which these phytohormones mediate the growth and defense trade-off are largely unclear. In addition, little is known about the roles of DEHYDRATION RESPONSIVE ELEMENT BINDING transcription factors, especially in biotic stress and plant growth. Here, we identified a cotton (Gossypium hirsutum) APETALA2/ETHYLENE RESPONSIVE FACTOR gene GhTINY2 that is strongly induced by Verticillium dahliae. Overexpression of GhTINY2 in cotton and Arabidopsis enhanced tolerance to V. dahliae, while knockdown of expression increased the susceptibility of cotton to the pathogen. GhTINY2 was found to promote SA accumulation and SA signaling transduction by directly activating expression of WRKY51. Moreover, GhTINY2-overexpressing cotton and Arabidopsis showed retardation of growth, increased sensitivity to inhibitors of BR biosynthesis, down-regulation of several BR-induced genes, and up-regulation of BR-repressed genes, while GhTINY2-RNAi cotton showed the opposite effects. We further determined that GhTINY2 negatively regulates BR signaling by interacting with BRASSINAZOLE-RESISTANT 1 (BZR1) and restraining its transcriptional activation of the expression of INDOLE-3-ACETIC ACID INDUCIBLE 19 (IAA19). These findings indicate that GhTINY2 fine-tunes the trade-off between immunity and growth via indirect crosstalk between WRKY51-mediated SA biosynthesis and BZR1-IAA19-regulated BR signaling.

Genomic insight into the divergence and adaptive potential of a forgotten landrace G. hirsutum L. purpurascens

Wild progenitors are an excellent source for strengthening the genetic basis and accumulation of desirable variation lost because of directional selection and adaptation in modern cultivars. Here, we re-evaluate a landrace of Gossypium hirsutum, formerly known as Gossypium purpurascens. Our study seeks to understand the genomic structure, variation, and breeding potential of this landrace, providing potential insights into the biogeographic history and genomic changes likely associated with domestication. A core set of accessions, including current varieties, obsolete accessions, G. purpurascens, and other geographical landraces, are subjected to genotyping along with multilocation phenotyping. Population fixation statistics suggests a marked differentiation between G. purpurascens and three other groups, emphasizing the divergent genomic behavior of G. purpurascens. Phylogenetic analysis establishes the primitive nature of G. purpurascens, identifying it as a vital source of functional variation, the inclusion of which in the upland cotton (cultivated G. hirsutum) gene pool may broaden the genetic basis of modern cultivars. Genome-wide association results indicate multiple loci associated with domestication regions corresponding to flowering and fiber quality. Moreover, the conserved nature of G. purpurascens can also provide insights into the evolutionary process of G. hirsutum.

Physiochemical and molecular features of the necrotic lesion in the Heterobasidion-Norway spruce pathosystem

In the forest of Northern Hemisphere, the fungi Heterobasidion annosum (Fr.) Bref. s.l. causes severe root and stem rot diseases, dramatically reducing the wood quality of conifer trees. The hallmark of the host response during the infection process is the formation of necrotic lesions and reaction zones. To characterize physiochemical and molecular features of the necrotic lesion, we conducted artificial inoculations on Norway spruce plants at different developmental stages: seedlings, young and mature trees. The results were further compared against data available on the formation of reaction zones. Strong necrosis browning or enlarged necrotic lesions were observed in infected tissues. This was accompanied by elevated pH. However, the increased pH, around 6.0 in necrotic lesions, was not as high as that documented in reaction zones, above 7.0 as marked by the intensity of the blue colour in response to 2,6-dichlorophenol indophenol dye. Peroxidase activity increased in infected plants and RNA-seq analysis of necrotic lesions showed marked upregulation of defence-related genes. Our findings highlight similarities and differences between the reaction zone and necrotic lesion formation in response of conifer trees to biotic stress.

A Single-Nucleotide Mutation in a GLUTAMATE RECEPTOR-LIKE Gene Confers Resistance to Fusarium Wilt in Gossypium hirsutum

Fusarium wilt (FW) disease of cotton, caused by the fungus Fusarium oxysporum f. sp. vasinfectum (Fov), causes severe losses in cotton production worldwide. Though significant advancements have been made in development of FW-resistant Upland cotton (Gossypium hirsutum) in resistance screening programs, the precise resistance genes and the corresponding molecular mechanisms for resistance to Fov remain unclear. Herein it is reported that Fov7, a gene unlike canonical plant disease-resistance (R) genes, putatively encoding a GLUTAMATE RECEPTOR-LIKE (GLR) protein, confers resistance to Fov race 7 in Upland cotton. A single nucleotide polymorphism (SNP) (C/A) in GhGLR4.8, resulting in an amino acid change (L/I), is associated with Fov resistance. A PCR-based DNA marker (GhGLR4.8SNP(A/C) ) is developed and shown to cosegregate with the Fov resistance. CRISPR/Cas9-mediated knockout of Fov7 results in cotton lines extremely susceptible to Fov race 7 with a loss of the ability to induce calcium influx in response to total secreted proteins (SEPs) of Fov. Furthermore, coinfiltration of SEPs with GhGLR4.8A results in a hypersensitive response. This first report of a GLR-encoding gene that functions as an R gene provides a new insight into plant-pathogen interactions and a new handle to develop cotton cultivars with resistance to Fov race 7.

Detection of candidate genes and development of KASP markers for Verticillium wilt resistance by combining genome-wide association study, QTL-seq and transcriptome sequencing in cotton

Combining GWAS, QTL-seq and transcriptome sequencing detected basal defense-related genes showing gDNA sequence variation and expression difference in diverse cotton lines, which might be the molecular mechanisms of VW resistance in G. hirsutum. Verticillium wilt (VW), which is caused by the soil-borne fungus Verticillium dahliae, is a major disease in cotton (Gossypim hirsutum) worldwide. To facilitate the understanding of the genetic basis for VW resistance in cotton, a genome-wide association study (GWAS), QTL-seq and transcriptome sequencing were performed. The GWAS of VW resistance in a panel of 120 core elite cotton accessions using the Cotton 63K Illumina Infinium SNP array identified 5 QTL from 18 significant SNPs meeting the 5% false discovery rate threshold on 5 chromosomes. All QTL identified through GWAS were found to be overlapped with previously reported QTL. By combining GWAS, QTL-seq and transcriptome sequencing, we identified eight candidate genes showing both gDNA sequence variation and expression difference between resistant and susceptible lines, most related to transcription factors (TFs), flavonoid biosynthesis and those involving in the plant basal defense and broad-spectrum disease resistance. Ten KASP markers were successfully validated in diverse cotton lines and could be deployed in marker-assisted breeding to enhance VW resistance. These results supported our inference that the gDNA sequence variation or expression difference of those genes involving in the basal defense in diverse cotton lines might be the molecular mechanisms of VW resistance in G. hirsutum.

Transformation and evaluation of Broad-Spectrum insect and weedicide resistant genes in Gossypium arboreum (Desi Cotton)

Gossypium arboreum (Desi Cotton) holds a special place in cotton industry because of its inherent ability to withstand drought, salinity, and remarkable resistance to sucking pests and cotton leaf curl virus. However, it suffers yield losses due to weeds and bollworm infestation. Genetic modification of G. arboreum variety FBD-1 was attempted in the current study to combat insect and weedicide resistance by incorporating cry1Ac, cry2A and cp4-EPSPS genes under control of 35S promoter in two different cassettes using kanamycin and GUS as markers through Agrobacterium-mediated shoot apex cut method of cotton transformation. The efficiency of transformation was found to be 1.57%. Amplification of 1700 bp for cry1Ac, 167 bp for cry2A and 111 bp for cp4-EPSPS confirmed the presence of transgenes in cotton plants. The maximum mRNA expression of cry1Ac and cp4-EPSPS was observed in transgenic cotton line L3 while minimum in transgenic cotton line L1. The maximum protein concentrations of Cry1Ac, Cry2A and Cp4-EPSPS of 3.534 µg g^-1, 2.534 µg g^-1 and 3.58 µg-g^-1 respectively were observed for transgenic cotton line L3 as compared to control cotton line. On leaf-feed-based insect bioassay, almost 99% mortality was observed for Helicoverpa armigera on the transgenic cotton plant (L3). It completely survived the 1900 ml hectare^-1 glyphosate spray assay as compared to non-transgenic cotton plants. The necrotic spots appeared on the third day, leading to the complete death of control plants on the fifth day of assay. The successful multiple gene-stacking in G. arboreum FBD-1 variety could be further used for qualitative improvement of cotton fiber through plant breeding techniques.

Regulatory Network of Cotton Genes in Response to Salt, Drought and Wilt Diseases (Verticillium and Fusarium): Progress and Perspective

In environmental conditions, crop plants are extremely affected by multiple abiotic stresses including salinity, drought, heat, and cold, as well as several biotic stresses such as pests and pathogens. However, salinity, drought, and wilt diseases (e.g., Fusarium and Verticillium) are considered the most destructive environmental stresses to cotton plants. These cause severe growth interruption and yield loss of cotton. Since cotton crops are central contributors to total worldwide fiber production, and also important for oilseed crops, it is essential to improve stress tolerant cultivars to secure future sustainable crop production under adverse environments. Plants have evolved complex mechanisms to respond and acclimate to adverse stress conditions at both physiological and molecular levels. Recent progresses in molecular genetics have delivered new insights into the regulatory network system of plant genes, which generally includes defense of cell membranes and proteins, signaling cascades and transcriptional control, and ion uptake and transport and their relevant biochemical pathways and signal factors. In this review, we mainly summarize recent progress concerning several resistance-related genes of cotton plants in response to abiotic (salt and drought) and biotic (Fusarium and Verticillium wilt) stresses and classify them according to their molecular functions to better understand the genetic network. Moreover, this review proposes that studies of stress related genes will advance the security of cotton yield and production under a changing climate and that these genes should be incorporated in the development of cotton tolerant to salt, drought, and fungal wilt diseases (Verticillium and Fusarium).

Calcium-Dependent Protein Kinase GhCDPK28 Was Dentified and Involved in Verticillium Wilt Resistance in Cotton

Verticillium dahliae is a soil-borne fungus that causes vascular wilt through the roots of plants. Verticillium wilt caused by V. dahliae is one of the main diseases in cotton producing areas of the world, resulting in huge economic losses. Breeding resistant varieties is the most economical and effective method to control Verticillium wilt. Calcium-dependent protein kinases (CDPKs) play a pivotal role in plant innate immunity, including regulation of oxidative burst, gene expression as well as hormone signal transduction. However, the function of cotton CDPKs in response to V. dahliae stress remains unexplored. In this study, 96, 44 and 57 CDPKs were identified from Gossypium hirsutum, Gossypium raimondii and Gossypium arboretum, respectively. Phylogenetic analysis showed that these CDPKs could be divided into four branches. All GhCDPKs of the same clade are generally similar in gene structure and conserved domain arrangement. Cis-acting elements related to hormones, stress response, cell cycle and development were predicted in the promoter region. The expression of GhCDPKs could be regulated by various stresses. Gh_D11G188500.1 and Gh_A11G186100.1 was up-regulated under Vd0738 and Vd991 stress. Further phosphoproteomics analysis showed that Gh_A11G186100.1 (named as GhCDPK28-6) was phosphorylated under the stress of V. dahliae. Knockdown of GhCDPK28-6 expression, the content of reactive oxygen species was increased, a series of defense responses were enhanced, and the sensitivity of cotton to V. dahliae was reduced. Moreover, overexpression of GhCDPK28-6 in Arabidopsis thaliana weakened the resistance of plants to this pathogen. Subcellular localization revealed that GhCDPK28-6 was localized in the cell membrane. We also found that GhPBL9 and GhRPL12C may interact with GhCDPK28-6. These results indicate that GhCDPK28-6 is a potential molecular target for improving resistance to Verticillium wilt in cotton. This lays a foundation for breeding disease-resistant varieties.

Rapid Mining of Candidate Genes for Verticillium Wilt Resistance in Cotton Based on BSA-Seq Analysis

Cotton is a globally important cash crop. Verticillium wilt (VW) is commonly known as "cancer" of cotton and causes serious loss of yield and fiber quality in cotton production around the world. Here, we performed a BSA-seq analysis using an F_2:3 segregation population to identify the candidate loci involved in VW resistance. Two QTLs (qvw-D05-1 and qvw-D05-2) related to VW resistance in cotton were identified using two resistant/susceptible bulks from the F₂ segregation population constructed by crossing the resistant cultivar ZZM2 with the susceptible cultivar J11. A total of 30stop-lost SNPs and 42 stop-gained SNPs, which included 17 genes, were screened in the qvw-D05-2 region by SnpEff analysis. Further analysis of the transcriptome data and qRT-PCR revealed that the expression level of Ghir_D05G037630 (designated as GhDRP) varied significantly at certain time points after infection with V. dahliae. The virus-induced gene silencing of GhDRP resulted in higher susceptibility of the plants to V. dahliae than the control, suggesting that GhDRP is involved in the resistance to V. dahlia infection. This study provides a method for rapid mining of quantitative trait loci and screening of candidate genes, as well as enriches the genomic information and gene resources for the molecular breeding of disease resistance in cotton.